diff options
Diffstat (limited to 'sci-chemistry')
581 files changed, 28809 insertions, 0 deletions
diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.1.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.1.ebuild new file mode 100644 index 000000000000..4c953dd73e3c --- /dev/null +++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +if [[ $PV = *9999* ]]; then + scm_eclass=git-2 + EGIT_REPO_URI="https://github.com/orbeckst/${PN}.git" + EGIT_BRANCH="develop" + SRC_URI="" + KEYWORDS="" +else + scm_eclass=vcs-snapshot + SRC_URI="https://github.com/orbeckst/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +inherit eutils distutils-r1 ${scm_eclass} + +DESCRIPTION="Python framework for Gromacs" +HOMEPAGE="https://orbeckst.github.com/GromacsWrapper/" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +IUSE="" + +DEPEND=" + >=dev-python/matplotlib-0.91.3[${PYTHON_USEDEP}] + >=dev-python/RecSQL-0.3[${PYTHON_USEDEP}] + >=sci-libs/scipy-0.9[${PYTHON_USEDEP}] + " +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/0001-Drop-chmod-hack.patch" +) diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.2.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.2.ebuild new file mode 100644 index 000000000000..dc2488dd3b95 --- /dev/null +++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.3.2.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +if [[ $PV = *9999* ]]; then + scm_eclass=git-2 + EGIT_REPO_URI="https://github.com/orbeckst/${PN}.git" + EGIT_BRANCH="develop" + SRC_URI="" + KEYWORDS="" +else + scm_eclass=vcs-snapshot + SRC_URI="https://github.com/orbeckst/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +inherit eutils distutils-r1 ${scm_eclass} + +DESCRIPTION="Python framework for Gromacs" +HOMEPAGE="https://orbeckst.github.com/GromacsWrapper/" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +IUSE="" + +DEPEND=" + >=dev-python/matplotlib-0.91.3[${PYTHON_USEDEP}] + >=dev-python/RecSQL-0.3[${PYTHON_USEDEP}] + >=sci-libs/scipy-0.9[${PYTHON_USEDEP}] + " +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/0001-Drop-chmod-hack.patch" +) diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.5.1.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.5.1.ebuild new file mode 100644 index 000000000000..3e946ea31dd4 --- /dev/null +++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.5.1.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +if [[ $PV = *9999* ]]; then + scm_eclass=git-2 + EGIT_REPO_URI="https://github.com/orbeckst/${PN}.git" + EGIT_BRANCH="develop" + SRC_URI="" + KEYWORDS="" +else + scm_eclass=vcs-snapshot + SRC_URI="https://github.com/orbeckst/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +inherit eutils distutils-r1 ${scm_eclass} + +DESCRIPTION="Python framework for Gromacs" +HOMEPAGE="https://orbeckst.github.com/GromacsWrapper/" + +LICENSE="GPL-3 LGPL-3" +SLOT="0" +IUSE="" + +DEPEND=" + >=dev-python/matplotlib-0.91.3[${PYTHON_USEDEP}] + >=dev-python/RecSQL-0.3[${PYTHON_USEDEP}] + >=sci-libs/scipy-0.9[${PYTHON_USEDEP}] + " +RDEPEND="${DEPEND}" diff --git a/sci-chemistry/GromacsWrapper/Manifest b/sci-chemistry/GromacsWrapper/Manifest new file mode 100644 index 000000000000..6c87a8b274c7 --- /dev/null +++ b/sci-chemistry/GromacsWrapper/Manifest @@ -0,0 +1,10 @@ +AUX 0001-Drop-chmod-hack.patch 863 SHA256 1a54e89fd14ab57db0a928dc7ac3e9cd505bb4659e7c6ec849e213aca9e089a2 SHA512 d37a73ca6ecd54c149699177cd10af9782a7ee48c77911a027705728f76a1631f71b37d0263285373877c2e5db8b00dcaafd3e1d6a8dd7d62b1253a905fc5d58 WHIRLPOOL e387b678ed67b3fdba2f1dbe0b9160db3909c331f09faec3824e69147da567acad6719fc3d2dcad616071be83be7f865a7bc524839244a0c4153049d072315d5 +DIST GromacsWrapper-0.3.1.tar.gz 1575486 SHA256 ddd2668060668528878370961a9a33257cf3643fd0d9e9191b1d26d4f78e803b SHA512 655dae431bf575963af58a5f75abe6703fe1ecdddba5839b671d9237ddee0e33ab19b528e89bcba4db9063fe30622d44e8f47c7b6452b4d1eed8c7400873a012 WHIRLPOOL 3b848aff931190eabd49426d61186a3c1eef9779a9fabf95b4d21d47793e5543adbcba5ac2b39c8a9af7c2479930a8ea65bb336e2155dfca98378df56ba4cb3e +DIST GromacsWrapper-0.3.2.tar.gz 1592147 SHA256 2fe0173275ca125a4260aa05f82746338f237766fe8aa998e85a5b40cf83e42c SHA512 a9e0abb5e7ad0c6831e23b6a8c09c6e4cc74b33d66cd17df8e00b876dc275dda11c3d3723565d8d58c45bdf6b2b00323bf85e24e2d5324a8d8b597cc3e5d78a4 WHIRLPOOL 852d73d01e1060369521ec5ff5197c86daa30ae98f285fe5e3d392a315cff10c68e2ba54ec9a2659260cf6830cf17cb1e094eecbd63652e9c3f13fff8707a824 +DIST GromacsWrapper-0.5.1.tar.gz 1247839 SHA256 cca0713a50bdceaae554b4a41f2c0b6d1c66074e9eaca17ecd87ce074cc56f7d SHA512 43b6b47e24cbb118492495370b165eb4b0e7672ba4e1c868d3039a0ad0b9828058f30ab7344118c7b0e7dd166ac325ea2b3483bd28b8f65dd972a101a5b9facd WHIRLPOOL f705d86725d95a226e74e589cf9ccc98a9e366c3aaea4818788e6ea1a359d048000718607274aa783c779c91c88bd882e65e1840a6b3c156fa374655de47b40a +EBUILD GromacsWrapper-0.3.1.ebuild 848 SHA256 4ece5ca4fcbca77b3e0c047189dc638e41f4dfefb4eb34a41649d010d0545eb4 SHA512 0bf92353d341f72ab5dee745cae125329032fb9109524d9a388853b8a6c8ff425da8d7a806f98a9d5a5ce6d29646c5755d39e4ab18815429b58b987eb06e5ce0 WHIRLPOOL 2f7a7b4fee83505e3a37800c1e44433853d81a0979275db9c9210a2b5220e4202c010b8c3b22ff56d7b2f7b08b3e6d434ba1bc55ada649d7e9124e0051a96bee +EBUILD GromacsWrapper-0.3.2.ebuild 844 SHA256 57abe96d5ce3e017a66a4f6b3024f0df2a8d4e9e9b2ff326ecb7c0d69c7037b5 SHA512 84d8ca613fd783ea77f916ae44390bed18d36a445ef06abfdfc7c9f413eb05a00a6b4c35706d78eef0cae209343e6c7246270dfd2d3d682f028b56ef00fbd057 WHIRLPOOL f6c04b452ff9c8737a5a2f12993fa9044851aad7174f9b6b7b50c3f2765a668ea76e41774886cd81d478a919fdca02755a69ea049d9fb8305c11f09e919aad7b +EBUILD GromacsWrapper-0.5.1.ebuild 789 SHA256 4420a357f5e134005b8096abe131b253ce5a160d8ae3bafc8c28fda9be5268d1 SHA512 47a145cee1780f80a90a289d29d795141ff1a7d98a443b3fedf44bd173358e1a86b04ec2c72118faa9f715484973c15877e1bc92696ab65f84ecf1dd3f3f98ca WHIRLPOOL b669714f853e6b289afacd4af13a3e548d66299b5e00ef6edddcdfcfbfa252f93481f2f9c5a60ab69bbc7220611da0575d21f310ba8cc7988d5e51f4b9119dd8 +MISC ChangeLog 2991 SHA256 eea78355770b60b36887dd626c3d2a996b6b36ef0b454d26b977c3ae5a60c426 SHA512 a8ae761bc986c1a83d2cf5e888bc22cca7a7c1bddd50a883b1830350affe311f97d628a449559fb3d2add99c5ab7116c090d912a91175868cc5481bcab3a3d1f WHIRLPOOL 8c7595083cd0150b80bfc4cf27b5180fb2cb46d9b806e37d816a65c76c4e0b582ec396c9165a2d109c72b664374c63a445b46ad71d43d154e0b88379f36b81b3 +MISC ChangeLog-2015 888 SHA256 6fe1011aa45e46b92ec378aca1d0cf87c4d2a91a8b74791af91b12a82c5877cf SHA512 36d954e3c5c1fed8193e7fa4e752fa750ec64d080b303babd3aeb505212e1fec783dd47f6a936a1aadfcf3c90eb695eaf21db957ea7dd6d2a4953daf9b5ef83a WHIRLPOOL 415fd208950d1c4c6e039429583bc59e2b5407284d89fe8a92cd45fdfe93d829c4b8562d912e37eff7c58eafcb5c4ba16212d8e218a679e5f2bf5870aa8a76bf +MISC metadata.xml 478 SHA256 0b8bba3244d50e99b18269f7fb068c9c52d5f5fe1ec54188e7642af4abd2b9e7 SHA512 2214eed914af825f9ab83c1de633c00cf2d3f39ad9f88dde4b21264856e3f7ba960fcacf512d0308f6d351857c76a8ad5aa494988c3c03bfd172a233a7f3207a WHIRLPOOL 97cab39f1d4ea05e638eeac095eb877ab8d99d5c7eaf345c571a90e22a8c23d4588b6eba271bfb5b36a16e4a1954134addb14cbdbf2b04d40fac98513bc13ec9 diff --git a/sci-chemistry/GromacsWrapper/files/0001-Drop-chmod-hack.patch b/sci-chemistry/GromacsWrapper/files/0001-Drop-chmod-hack.patch new file mode 100644 index 000000000000..8645df77b86e --- /dev/null +++ b/sci-chemistry/GromacsWrapper/files/0001-Drop-chmod-hack.patch @@ -0,0 +1,28 @@ +From 49b8d9662365e0e9b0725682b8a8479de402b272 Mon Sep 17 00:00:00 2001 +From: Alexey Shvetsov <alexxy@gentoo.org> +Date: Sat, 23 Mar 2013 16:40:04 +0400 +Subject: [PATCH] Drop chmod hack. + +It doesnt work if wrapper installed system-wide + +Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org> +--- + gromacs/config.py | 2 -- + 1 file changed, 2 deletions(-) + +diff --git a/gromacs/config.py b/gromacs/config.py +index cece6fc..2e686e7 100644 +--- a/gromacs/config.py ++++ b/gromacs/config.py +@@ -619,8 +619,6 @@ del g + # Must extract because it is part of a zipped python egg; + # see http://peak.telecommunity.com/DevCenter/PythonEggs#accessing-package-resources + GridMAT_MD = resource_filename(__name__,'external/GridMAT-MD_v1.0.2/GridMAT-MD.pl') +-os.chmod(GridMAT_MD, 0755) +- + + #: 3rd party bundled analysis scripts and tools; this is a list of triplets of + #: +-- +1.8.1.5 + diff --git a/sci-chemistry/GromacsWrapper/metadata.xml b/sci-chemistry/GromacsWrapper/metadata.xml new file mode 100644 index 000000000000..16752065b886 --- /dev/null +++ b/sci-chemistry/GromacsWrapper/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="github">orbeckst/GromacsWrapper</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/ParmEd/Manifest b/sci-chemistry/ParmEd/Manifest new file mode 100644 index 000000000000..2db256147555 --- /dev/null +++ b/sci-chemistry/ParmEd/Manifest @@ -0,0 +1,3 @@ +DIST ParmEd-2.7.3.tar.gz 34494858 SHA256 56b3097625be3a5037a5b3d7c4d9467a97f0dd44fea79cf2873f0e56d3409975 SHA512 a3444f915e188bcc924f28b6b4235246e2c063ae98881c48f6e13ebc685d085d6a1bcb61b29509a343cbe58369bc6233acc20ee620c6f1d42da2033772a12e07 WHIRLPOOL 909e2c1681fa3d37c0f43e3584df27bc5af351cfdd8c3726da02a29507fe31d1551cb95cb15e8beb88c52ccf0debe3cb0e2006401e8445a829ef618e8ccddb01 +EBUILD ParmEd-2.7.3.ebuild 834 SHA256 ce859d2788bc2fde0bd445970228c699e2c29390de2eeb6b94ef676aa2b33cf3 SHA512 af1046b0ea4ad34a6ec3871da13fb42b1290654d26278c77dc4a2d27bde941f4782acc0da7bf6c3b9fcb0599596938e1bce60572a7768bdef2cf516f888c6df3 WHIRLPOOL 6ef56f6d4cffb92d6375a421c375e96fc63d1aa1f075cc2919ae31649faed8e68189b9f35b120db661d87efb505e33c1e6e323042d580a1894037eb2bea61d1c +MISC metadata.xml 468 SHA256 2f5f6e9647b71679aa1f504339002a2910dbec29e8ce1cc6ded959c263274e8f SHA512 47e3516aabe02112a52e851ac9294a0096001373d546462f9185754356c72dd37a0a8efa3b40311e43e27e2953ea5879c1141488649f3faef0aa43a692205499 WHIRLPOOL a057ef0ca6ec44ec1c1fd274c7061bec15f441872ae26f399fc092bd4bbf2c5837b356b2b926f620eaaf7e15e300a2ac623fa33ad6ff2e5009b0e872fc1c865f diff --git a/sci-chemistry/ParmEd/ParmEd-2.7.3.ebuild b/sci-chemistry/ParmEd/ParmEd-2.7.3.ebuild new file mode 100644 index 000000000000..88e65d86e229 --- /dev/null +++ b/sci-chemistry/ParmEd/ParmEd-2.7.3.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} ) + +if [[ $PV = *9999* ]]; then + scm_eclass=git-2 + EGIT_REPO_URI="https://github.com/${PN}/${PN}.git" + SRC_URI="" + KEYWORDS="" +else + scm_eclass=vcs-snapshot + SRC_URI="https://github.com/${PN}/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +inherit eutils distutils-r1 ${scm_eclass} + +DESCRIPTION="Parameter/topology editor and molecular simulator" +HOMEPAGE="https://parmed.github.io/ParmEd/html/index.html" + +LICENSE="LGPL-2" +SLOT="0" +IUSE="" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] +" + +RDEPEND="${DEPEND}" + +src_prepare() { + sed \ + -e "/delfile/d" \ + -e "/deldir/d" \ + -i setup.py || die + distutils-r1_src_prepare +} diff --git a/sci-chemistry/ParmEd/metadata.xml b/sci-chemistry/ParmEd/metadata.xml new file mode 100644 index 000000000000..6272f2698a54 --- /dev/null +++ b/sci-chemistry/ParmEd/metadata.xml @@ -0,0 +1,15 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="github">ParmEd/ParmEd</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/PyMca/Manifest b/sci-chemistry/PyMca/Manifest new file mode 100644 index 000000000000..db219019680b --- /dev/null +++ b/sci-chemistry/PyMca/Manifest @@ -0,0 +1,6 @@ +AUX PyMca-4.6.2-gentoo.patch 538 SHA256 cd9170ba6219c4fb78aed0bbb972da452255a95b361117dc9942e8dce86b381f SHA512 cdc3cbe8264310748ef065cf07b1d1d8c9b39f560a6317924a34c795c4a62fceba7de0847c9a325133fe87acdbedf4ec7b75583402cb1a6aac0b4ff6437337e4 WHIRLPOOL 096b537ee484e447017c3cb846d0eb5875225558c10efed3a9236aa78d55cec8e18f595aba27eb9dfb1fa025792b108340d278e80f7f90c2eef75f5cd78a36cf +DIST pymca4.6.2-src.tgz 15979581 SHA256 c50d3a54cad633bac3ec361d1b3b63a78292f1ad4ed976e5206665edd76bc32d SHA512 e33188b446c399e50cf65ebca4bfeef34e1b7d99c331f670dc41ca204284fbba996a1c83bd12a2410a9972927aa9c92b42b5374c58c924b3a8583d4f37be6528 WHIRLPOOL 47f0491aa0e470661bea1aa247d1db730f1db7266f1d2be2272d08f203faa2a084bcb40d579861365ace26d2f94abe03485183eed03139ad7b697cf57bfa5324 +EBUILD PyMca-4.6.2-r1.ebuild 955 SHA256 e5f9bc774c1a9257b4a63c2df8f88fd91885bad97c0eda4d38be508619d2f3a0 SHA512 3f4c7c35cd9efadb5fac06bc0ef000d8687b77630d3d7165df4c1dfcb8e60d2ed1ce17332646041a7668bb699c23cd7555bd0e7a638e84dac60ddef2316aea8d WHIRLPOOL ccf020cede7f4769e75d0806ac9dea67e4252be13e875e5d5459d0f355e3ef86c11c23de56aad903d0bf36e860cf51936d56350bba2aa525206271b763759f74 +MISC ChangeLog 2719 SHA256 3ec0ac52be69ecd61c301767cc28044aaadad7428a07c92867e650e72c3d5a43 SHA512 dc6114341951756fab7ea5ffad6946806e6dc66f916deef04aa983eb675d4f78ceffe4f8b6cc6db7dcf06f0f8da6cae0cb2793d088d51b329e236a2aa4a955ab WHIRLPOOL d5e806ac7fbc4be68f668b07d9b5eaa4eb3ad7f6844c3fdc8620c48d2efce0b4aa95935789315b1e589d7eabfd7c21cad4f342848966638b54b1d355fcf886a9 +MISC ChangeLog-2015 1258 SHA256 73b1bc98a54fa96f00c678d3c7bce9052acc38eeb27bf045ddca2bdadb614307 SHA512 310a562adb6407a849c303020f680dc86c403fb9e7197afdab5a15dcdbd0fc76194baf51bf60002862679d76b568981438931f5f14b8d31572713b59bdc2aa69 WHIRLPOOL 8aa527f339006ee7aaf0161129811b9d4cdc8c3577fb2a6c5c73a759ed229de7173644984dfb87bd336767f1bc33abab800d3e94bef4b1dca279b9dbadab7379 +MISC metadata.xml 858 SHA256 a82d6768ea0415df92baa043ae0486040f70d99dd305879db54da5ccd84ec4ab SHA512 bc8e357b6c327c215134e6535de7d6349a8498efa9e5a0a156e7f760f8c9376e8c7c8dbdd83ae2ed0861def6b0cbd6f072be67199dce6eb2de5391c7b743a651 WHIRLPOOL 41b7345552bb2214d583f1f12fb7f136562e605e9f94a3e71dfadea7a2b0713cef3572c0a08dbf218011c713b4e1d93c7c1f44d499e9491cad8c6e1cd95998ca diff --git a/sci-chemistry/PyMca/PyMca-4.6.2-r1.ebuild b/sci-chemistry/PyMca/PyMca-4.6.2-r1.ebuild new file mode 100644 index 000000000000..1f2caf4c70f0 --- /dev/null +++ b/sci-chemistry/PyMca/PyMca-4.6.2-r1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +MY_PV="${PV/_}" + +DESCRIPTION="X-ray Fluorescence Toolkit" +HOMEPAGE="http://pymca.sourceforge.net/" +SRC_URI="mirror://sourceforge/project/pymca/pymca/${PN}${PV/_p1}/pymca${MY_PV}-src.tgz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="X hdf5 matplotlib" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pyopengl[${PYTHON_USEDEP}] + dev-python/sip[${PYTHON_USEDEP}] + virtual/opengl + X? ( + dev-python/PyQt4[${PYTHON_USEDEP}] + dev-python/pyqwt[${PYTHON_USEDEP}] + ) + hdf5? ( dev-python/h5py[${PYTHON_USEDEP}] ) + matplotlib? ( dev-python/matplotlib[${PYTHON_USEDEP}] )" +RDEPEND="${DEPEND}" + +#S="${WORKDIR}/${PN}${MY_PV}" + +python_prepare_all() { + local PATCHES=( "${FILESDIR}"/${P}-gentoo.patch ) + export SPECFILE_USE_GNU_SOURCE=1 + distutils-r1_python_prepare_all +} diff --git a/sci-chemistry/PyMca/files/PyMca-4.6.2-gentoo.patch b/sci-chemistry/PyMca/files/PyMca-4.6.2-gentoo.patch new file mode 100644 index 000000000000..81dfaf038fa6 --- /dev/null +++ b/sci-chemistry/PyMca/files/PyMca-4.6.2-gentoo.patch @@ -0,0 +1,16 @@ + setup.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/setup.py b/setup.py +index 0a77cdf..e7ba643 100644 +--- a/setup.py ++++ b/setup.py +@@ -55,7 +55,7 @@ packages = ['PyMca','PyMca.PyMcaPlugins', 'PyMca.tests'] + py_modules = [] + + # Specify all the required PyMca data +-data_files = [(PYMCA_DATA_DIR, ['LICENSE.GPL', ++data_files = [(PYMCA_DATA_DIR, [ + 'PyMca/PyMcaData/Scofield1973.dict', + 'changelog.txt', + 'PyMca/PyMcaData/McaTheory.cfg', diff --git a/sci-chemistry/PyMca/metadata.xml b/sci-chemistry/PyMca/metadata.xml new file mode 100644 index 000000000000..4067b2f8b26a --- /dev/null +++ b/sci-chemistry/PyMca/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +The PyMca Toolkit is a collection of Python tools for visualization and +analysis of energy-dispersive X-ray fluorescence data. It builds its graphic +interface and plotting routines on top of the C++ libraries Qt and Qwt +through their respective Python bindings PyQt and PyQwt. Nevertheless, +the data analysis routines can be used independently of any graphical +interface. +</longdescription> + <use> + <flag name="matplotlib">Support for plotting through matplotlib</flag> + </use> + <upstream> + <remote-id type="sourceforge">pymca</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest new file mode 100644 index 000000000000..244816343796 --- /dev/null +++ b/sci-chemistry/apbs/Manifest @@ -0,0 +1,8 @@ +AUX apbs-1.4.1-manip.patch 1522 SHA256 155c6fcd777c1c00e313bbdae60b6ccf373af0d50b05398d928bb7662378801c SHA512 b2517b86b688091a9ae6a78132e8cd5a451eff6150211459dae6919bf2ee61edcf2cf1b95d8b2922050a3a7a3aaaa9ce8e2be6766116a1e66d413339b291326b WHIRLPOOL a215daf24985d7847210b4286a662b461d5c4b714a5585eb21b781911f95853c41c1f40109e53d6f8008c0c5c291c0d8b4f06044bf767d6049bff3e6167162c2 +AUX apbs-1.4.1-multilib.patch 3301 SHA256 21c1934eb5694737d6049eb8da868ee81f15ff86dacc09f89f0024c263929ddc SHA512 cdd72fd23a57ee8413f72bf674ae246543b1c9f326727ff07c3b8848d59f98ab7d2daf28677460cb4726f919832079c1d280bcdc86a8bef5c0875583c789b7c0 WHIRLPOOL 07ae32ecd14c21d3cce59bb904533faa1b9de532d6411176d5ee2d52ed91ef6da88b52cec0ef7b989dab253300a9d89182ddc25323347a48eb8d3355c16cb3a4 +AUX apbs-1.4.1-python.patch 4109 SHA256 793257f3581c768951c27742ecf299f462fbc7fc78635e2d7c8dd0ade69c9738 SHA512 369c0fa08187ba80d8ce72542fc2942f28426beed39619dd6a90a9ef8dfecb47ea6dc7aa20994629a69d63b55d72d1f837c442744bf5499a942bf312f6723092 WHIRLPOOL 39d2445e7d3ed1974dffeaad4c0772238cf6e508f4e002636c833921f124fe7d7d9732d23a7ffc5341815152d4ddc6cd0565bebc46988caf7f742bb2f3031033 +DIST apbs-1.4.1.zip 37999283 SHA256 1156c44fb65bb7c884801f3111ca1cdb1dfba6f5308226587db112aac4969027 SHA512 3a127af3940054e5a43b3c0c620507f4f9baa69049e5a0933d8e8825458ad2faba840392752de49fe68d91e2054fb1394cf87bb5bb1c0b48305368e2f404cf6a WHIRLPOOL 6729571f13c953ec0bcf90da73ef0c39cf769f1498a767d3280de3ffbeea18eda718373efca0468436c4b18357fe450865f661daba79eeb66778c572c43ff39a +EBUILD apbs-1.4.1-r2.ebuild 3117 SHA256 5507aca1b88d0adda0c2be27909003fc883389fba4432904c675e15950e5ecc5 SHA512 e8f20517537119640c8f12accdcc37a2f25b30d3b25923f54a5bff3c88b679219f029b49ae96ac66acf04599877f1b33289e1ce15462a0e7a6a4cd5f979ac3fc WHIRLPOOL 545345956524d58837eb9ce695f9345e8982ad5b701c7f096b925d6d6eef8a705e80b1ac68b90346949163f1601290118cfae7f3cd062d17713366fa00102c41 +MISC ChangeLog 3214 SHA256 e0b2adfcaa34ee20dc0b58b5e974de0468af66a44ba6151667d57c092abd7da2 SHA512 0c1c9785f9491c10d5c9f39dfecf103df55a4f739dcf6f3b7b21485dd2f2cc40f40f522fe6ea658d7cc40f4467c694b756f08450f5dbd6922d083e5eda9fbe27 WHIRLPOOL 78c8915a4b56c1cd3ad33478695505a7869416942c91bb6d58a4d96ab01ec27247271810cc39fdab370daedcf01450e3337043f2690a86bf14b12fb6195ba305 +MISC ChangeLog-2015 14824 SHA256 b1a615bb8bed5a1d101dd74d47a193a02c99841cee1f9a9aa7610d524c478be8 SHA512 d07bc5197b2e015b705fb1e98c1520152563e9e27581344a544fc12fa227811a30da6bfd94cece054347057726821f1173d5530eb4278f8aff1ed50e2781a721 WHIRLPOOL 83cc9763efb8062d8badc10756f9c413f2146065bf0565488b56f6c189c523b604efe5a0e6eb8a7808ab2b04e3bb2343414fda00bdd1228de110179fde8ebf6f +MISC metadata.xml 1048 SHA256 60359c99f46f5d15b36dc2c43d20e6ae42189ff34256ad15012eb1fe6ccbfab0 SHA512 7d68049cb9b044676430fe879890cc4cd869b99f85696f579d9cbf3b156081301792fd7f03205a9b9d429d71c9a35b4815f4236573f68d3ef6b4718e6e1f0bb3 WHIRLPOOL e317d7b4cc4b18c66f1943a87a69e173abd9fd151f5610881fbb8a7955e993954209f504cafce053c2e95eda94ecd394c742483b6b55e0f3b3e553f55d1a79b0 diff --git a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild new file mode 100644 index 000000000000..aecbcd3ce745 --- /dev/null +++ b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild @@ -0,0 +1,127 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +DISTUTILS_SINGLE_IMPL=true + +inherit cmake-utils distutils-r1 flag-o-matic multilib toolchain-funcs + +GITHUB_REV="74fcb8676de69ed04ddab8976a8b05a6caaf4d65" + +DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems" +HOMEPAGE="http://www.poissonboltzmann.org/apbs/" +#SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz" +SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${GITHUB_REV}.zip -> ${P}.zip" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="debug doc examples fast +fetk iapbs mpi openmp python tools" + +REQUIRED_USE=" + iapbs? ( fetk ) + mpi? ( !python ) + python? ( tools fetk iapbs ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + dev-cpp/eigen:3 + dev-libs/maloc[mpi=] + virtual/blas + sys-libs/readline + fetk? ( + sci-libs/fetk + sci-libs/amd + sci-libs/umfpack + sci-libs/superlu + ) + mpi? ( virtual/mpi ) + python? ( ${PYTHON_DEPS} ) +" +DEPEND="${DEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen ) +" + +S="${WORKDIR}"/${PN}-pdb2pqr-${GITHUB_REV}/${PN} + +PATCHES=( + "${FILESDIR}"/${P}-multilib.patch + "${FILESDIR}"/${P}-manip.patch + "${FILESDIR}"/${P}-python.patch +) + +src_prepare() { + cmake-utils_src_prepare + append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) + + sed \ + -e "s:-lblas:$($(tc-getPKG_CONFIG) --libs blas):g" \ + -e "/TOOLS_PATH/d" \ + -i CMakeLists.txt || die + use doc && MAKEOPTS+=" -j1" + if use python; then + unset PATCHES || die + cd tools/python && distutils-r1_src_prepare + fi +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_SKIP_RPATH=ON + -DTOOLS_PATH="${ED}"/usr + -DSYS_LIBPATHS="${EPREFIX}"/usr/$(get_libdir) + -DLIBRARY_INSTALL_PATH=$(get_libdir) + -DFETK_PATH="${EPREFIX}"/usr/ + -DBUILD_SHARED_LIBS=ON + -DENABLE_QUIT=OFF + $(cmake-utils_use_build doc DOC) + $(cmake-utils_use_build tools TOOLS) + -DENABLE_BEM=OFF +# ENABLE_BEM: Boundary element method using TABIPB + $(cmake-utils_use_enable debug DEBUG) + $(cmake-utils_use_enable debug VERBOSE_DEBUG) + $(cmake-utils_use_enable fast FAST) + $(cmake-utils_use_enable fetk FETK) + $(cmake-utils_use_enable mpi MPI) + $(cmake-utils_use_enable python PYTHON) +# ENABLE_TINKER: Enable TINKER support + $(cmake-utils_use_enable iapbs iAPBS) +# MAX_MEMORY: Set the maximum memory (in MB) to be used for a job + ) + cmake-utils_src_configure + if use python; then + cd tools/python && distutils-r1_src_configure + fi +} + +src_compile(){ + cmake-utils_src_compile + if use python; then + append-ldflags -L"${S}"/lib + cd tools/python && distutils-r1_src_compile + fi +} + +src_test() { + python_export_best + cd tests || die + LD_LIBRARY_PATH="${S}"/lib "${PYTHON}" apbs_tester.py -l log || die + grep -q 'FAILED' log && die "Tests failed" +} + +src_install() { + dodir /usr/bin + cmake-utils_src_install + local i + for i in "${ED}"/usr/bin/*; do + if [[ ! "${i}" =~ .*apbs$ ]]; then + mv "${i}" "${i}-apbs" || die + fi + done + if use python; then + cd tools/python && distutils-r1_src_install + rm -rf "${ED}"/usr/share/apbs/tools/python || die + fi +} diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch new file mode 100644 index 000000000000..378223397594 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch @@ -0,0 +1,50 @@ + apbs/CMakeLists.txt | 2 +- + apbs/tools/CMakeLists.txt | 4 ---- + apbs/tools/mesh/CMakeLists.txt | 4 ++-- + 4 files changed, 5 insertions(+), 9 deletions(-) + +diff --git a/apbs/CMakeLists.txt b/apbs/CMakeLists.txt +index 8917fc4..5152008 100644 +--- a/apbs/CMakeLists.txt ++++ b/apbs/CMakeLists.txt +@@ -293,7 +293,7 @@ option(ENABLE_FETK "Enable the finite element solver" OFF) + + if(ENABLE_FETK) + message(STATUS "Checking for fetk components") +- set(FETK_ENALBED 1) ++ set(FETK_ENABLED 1) + + list(APPEND APBS_LIBS "-lstdc++") + list(APPEND APBS_LIBS "-L${FETK_PATH}/lib") +diff --git a/apbs/tools/manip/CMakeLists.txt b/apbs/tools/manip/CMakeLists.txt +index 937dac7..5768cc5 100644 +--- a/apbs/tools/manip/CMakeLists.txt ++++ b/apbs/tools/manip/CMakeLists.txt +@@ -4,9 +4,9 @@ set(LIBS "") + list(APPEND LIBS "apbs_generic") + list(APPEND LIBS "apbs_mg") + list(APPEND LIBS "apbs_pmgc") +-if(FETK_ENALBED) ++if(FETK_ENABLED) + list(APPEND LIBS "apbs_fem") +-endif(FETK_ENALBED) ++endif(FETK_ENABLED) + + message(STATUS "libraries: ${LIBS}") + +diff --git a/apbs/tools/mesh/CMakeLists.txt b/apbs/tools/mesh/CMakeLists.txt +index 1406377..6e6dfb9 100644 +--- a/apbs/tools/mesh/CMakeLists.txt ++++ b/apbs/tools/mesh/CMakeLists.txt +@@ -4,9 +4,9 @@ set(LIBS "") + list(APPEND LIBS "apbs_generic") + list(APPEND LIBS "apbs_mg") + list(APPEND LIBS "apbs_pmgc") +-if(FETK_ENALBED) ++if(FETK_ENABLED) + list(APPEND LIBS "apbs_fem") +-endif(FETK_ENALBED) ++endif(FETK_ENABLED) + + message(STATUS "libraries: ${LIBS}") + diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch b/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch new file mode 100644 index 000000000000..a4e2d1761cf4 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch @@ -0,0 +1,92 @@ + CMakeLists.txt | 18 +++++++++--------- + src/CMakeLists.txt | 1 - + src/fem/CMakeLists.txt | 2 +- + src/pmgc/CMakeLists.txt | 2 +- + 4 files changed, 11 insertions(+), 12 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 75ddbdd..c46f5e7 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -61,7 +61,7 @@ set(LIBRARY_OUTPUT_PATH ${APBS_ROOT}/lib) + set(TOOLS_PATH ${APBS_ROOT}/tools) + set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs) + +-set(LIBRARY_INSTALL_PATH lib) ++set(LIBRARY_INSTALL_PATH ${CMAKE_INSTALL_LIBDIR}) + set(HEADER_INSTALL_PATH include/apbs) + set(EXECUTABLE_INSTALL_PATH bin) + set(SHARE_INSTALL_PATH share/apbs) +@@ -93,8 +93,6 @@ set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}") + list(APPEND CMAKE_INCLUDE_PATH /usr/include) + list(APPEND CMAKE_INCLUDE_PATH /usr/local/include) + +-set(APBS_LIBS "-L${APBS_ROOT}/lib -lapbs_geoflow") +- + ################################################################################ + # Enable ansi pedantic compiling # + ################################################################################ +@@ -193,9 +191,11 @@ if(ENABLE_BEM) + else() + set(TABI_LIBRARY_BASENAME ${CMAKE_STATIC_LIBRARY_PREFIX}${TABI}${CMAKE_STATIC_LIBRARY_SUFFIX}) + endif() +- ++ ++ file(GLOB MODS ${LIBRARY_OUTPUT_PATH}/*.mod) ++ + install( +- FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${LIBRARY_OUTPUT_PATH}/*.mod ++ FILES ${LIBRARY_OUTPUT_PATH}/${TABI_LIBRARY_BASENAME} ${MODS} + DESTINATION ${LIBRARY_INSTALL_PATH} + ) + set(TABI_LIBRARY ${APBS_ROOT}/${LIBRARY_INSTALL_PATH}/${TABI_LIBRARY_BASENAME}) +@@ -210,7 +210,7 @@ if(ENABLE_BEM) + endif() + get_filename_component(LIBGFORTRANPATH ${LIBGFORTRANPATH} PATH) + find_path(LIBGFORTRAN_PATH ${LIBGFORTRAN_NAME} PATH ${LIBGFORTRANPATH}) +- list(APPEND APBS_LIBS "-L${APBS_ROOT}/${LIBRARY_INSTALL_PATH} -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" ) ++ list(APPEND APBS_LIBS "-L${APBS_ROOT}/lib -L${LIBGFORTRAN_PATH} -lgfortran -ltabipb" ) + endif() # ENABLE_BEM + + find_file( # this should be find path... +@@ -228,7 +228,7 @@ endif() + + + find_library(MALOC_LIBRARY "maloc" +- PATHS ${FETK_PATH}/lib ${CONTRIB_PATH} ++ PATHS ${FETK_PATH}/${CMAKE_INSTALL_LIBDIR} ${CONTRIB_PATH} + DOC "The fetk/maloc library" + ) + if(MALOC_LIBRARY) +@@ -296,9 +296,9 @@ if(ENABLE_FETK) + set(FETK_ENALBED 1) + + list(APPEND APBS_LIBS "-lstdc++") +- list(APPEND APBS_LIBS "-L${FETK_PATH}/lib") ++ list(APPEND APBS_LIBS "-L${FETK_PATH}/${CMAKE_INSTALL_LIBDIR}") + list(APPEND APBS_LIBS -lamd -lpunc -lmc -lgamer -lsuperlu -lumfpack +--lblas -lvf2c -ltetgen -ltriangle -lg2c -lreadline ) ++-lblas -lvf2c -ltetgen -ltriangle -lreadline ) + + SET(HAVE_MC_H YES) + endif() +diff --git a/src/fem/CMakeLists.txt b/src/fem/CMakeLists.txt +index 5a950c2..dc37f48 100644 +--- a/src/fem/CMakeLists.txt ++++ b/src/fem/CMakeLists.txt +@@ -12,4 +12,4 @@ add_items( + vpee.h + ) + +-add_sublibrary(fem) ++add_sublibrary(fem apbs_geoflow) +diff --git a/src/pmgc/CMakeLists.txt b/src/pmgc/CMakeLists.txt +index 85b0c1e..97c95f0 100644 +--- a/src/pmgc/CMakeLists.txt ++++ b/src/pmgc/CMakeLists.txt +@@ -42,4 +42,4 @@ add_items( + mgfasd.h + ) + +-add_sublibrary(pmgc) ++add_sublibrary(pmgc apbs_geoflow) diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-python.patch b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch new file mode 100644 index 000000000000..db9f86ba120a --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch @@ -0,0 +1,122 @@ + apbs/contrib/iapbs/src/apbs_driver.c | 6 +++--- + apbs/src/CMakeLists.txt | 1 + + apbs/tools/CMakeLists.txt | 2 +- + apbs/tools/python/CMakeLists.txt | 1 + + apbs/tools/python/apbslib.c | 4 ++-- + apbs/tools/python/apbslib.i | 4 ++-- + apbs/tools/python/setup.py | 16 ++++++++++++++++ + 7 files changed, 26 insertions(+), 8 deletions(-) + +diff --git a/apbs/contrib/iapbs/src/apbs_driver.c b/apbs/contrib/iapbs/src/apbs_driver.c +index c9e443b..e1ad67f 100644 +--- a/apbs/contrib/iapbs/src/apbs_driver.c ++++ b/apbs/contrib/iapbs/src/apbs_driver.c +@@ -595,7 +595,7 @@ int apbsdrv_( + printPBEPARM(pbeparm); + + /* Refine mesh */ +- if (!preRefineFE(i, nosh, feparm, fetk)) { ++ if (!preRefineFE(i, feparm, fetk)) { + Vnm_tprint( 2, "Error pre-refining mesh!\n"); + VJMPERR1(0); + } +@@ -609,7 +609,7 @@ int apbsdrv_( + Vnm_tprint(1, " Beginning solve-estimate-refine cycle:\n"); + for (isolve=0; isolve<feparm->maxsolve; isolve++) { + Vnm_tprint(1, " Solve #%d...\n", isolve); +- if (!solveFE(i, nosh, pbeparm, feparm, fetk)) { ++ if (!solveFE(i, pbeparm, feparm, fetk)) { + Vnm_tprint(2, "ERROR SOLVING EQUATION!\n"); + VJMPERR1(0); + } +@@ -622,7 +622,7 @@ int apbsdrv_( + /* We're not going to refine if we've hit the max number + * of solves */ + if (isolve < (feparm->maxsolve)-1) { +- if (!postRefineFE(i, nosh, feparm, fetk)) break; ++ if (!postRefineFE(i, feparm, fetk)) break; + } + bytesTotal = Vmem_bytesTotal(); + highWater = Vmem_highWaterTotal(); +diff --git a/apbs/src/CMakeLists.txt b/apbs/src/CMakeLists.txt +index 44d20fa..2577343 100644 +--- a/apbs/src/CMakeLists.txt ++++ b/apbs/src/CMakeLists.txt +@@ -68,6 +68,7 @@ configure_file( + + if(ENABLE_iAPBS) + ADD_LIBRARY(apbs_routines routines.c routines.h) ++ target_link_libraries(apbs_routines apbs_mg apbs_fem) + INSTALL(TARGETS apbs_routines DESTINATION ${LIBRARY_INSTALL_PATH}) + INSTALL(FILES apbscfg.h DESTINATION ${HEADER_INSTALL_PATH}) + endif() +diff --git a/apbs/tools/CMakeLists.txt b/apbs/tools/CMakeLists.txt +index 1982a3c..4acbe68 100644 +--- a/apbs/tools/CMakeLists.txt ++++ b/apbs/tools/CMakeLists.txt +@@ -4,5 +4,5 @@ add_subdirectory(mesh) + add_subdirectory(manip) + + if(ENABLE_PYTHON) +- add_subdirectory(manip) ++ add_subdirectory(python) + endif(ENABLE_PYTHON) +diff --git a/apbs/tools/python/CMakeLists.txt b/apbs/tools/python/CMakeLists.txt +new file mode 100644 +index 0000000..8b13789 +--- /dev/null ++++ b/apbs/tools/python/CMakeLists.txt +@@ -0,0 +1 @@ ++ +diff --git a/apbs/tools/python/apbslib.c b/apbs/tools/python/apbslib.c +index fef5cc8..feaaa2c 100644 +--- a/apbs/tools/python/apbslib.c ++++ b/apbs/tools/python/apbslib.c +@@ -2504,8 +2504,8 @@ static swig_module_info swig_module = {swig_types, 24, 0, 0, 0, 0}; + #include "maloc/maloc.h" + #include "apbscfg.h" + #include "routines.h" +-#include "apbs/valist.h" +-#include "apbs/vatom.h" ++#include "generic/valist.h" ++#include "generic/vatom.h" + + + #include <limits.h> +diff --git a/apbs/tools/python/apbslib.i b/apbs/tools/python/apbslib.i +index 17fe521..44d05ea 100644 +--- a/apbs/tools/python/apbslib.i ++++ b/apbs/tools/python/apbslib.i +@@ -15,8 +15,8 @@ Header files: + #include "maloc/maloc.h" + #include "apbscfg.h" + #include "routines.h" +-#include "apbs/valist.h" +-#include "apbs/vatom.h" ++#include "generic/valist.h" ++#include "generic/vatom.h" + %} + + /* +diff --git a/apbs/tools/python/setup.py b/apbs/tools/python/setup.py +new file mode 100644 +index 0000000..4a20198 +--- /dev/null ++++ b/apbs/tools/python/setup.py +@@ -0,0 +1,16 @@ ++from distutils.core import setup, Extension ++setup(name='apbs', ++ version='1.4.1', ++ package_dir={'apbs': '', 'vgrid': 'vgrid'}, ++ packages=['apbs', 'vgrid'], ++ py_modules=['apbslib', 'main', 'noinput'], ++ ext_modules=[ ++ Extension( ++ '_apbslib', ++ ['apbslib.i'], ++ swig_opts=['-module', 'apbslib', '-I../include'], ++ include_dirs=["../../src"], ++ libraries=["apbs_generic", "apbs_routines"] ++ ) ++ ], ++ ) diff --git a/sci-chemistry/apbs/metadata.xml b/sci-chemistry/apbs/metadata.xml new file mode 100644 index 000000000000..a33a5468d19c --- /dev/null +++ b/sci-chemistry/apbs/metadata.xml @@ -0,0 +1,25 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="fetk">Include support for FeTK</flag> + <flag name="fast">APBS fast mode (experimental)</flag> + <flag name="iapbs">C/C++/Fortran interface</flag> + <flag name="tools">Install optional tools</flag> + </use> + <longdescription> +APBS is a software package for modeling biomolecular solvation through solution +of the Poisson-Boltzmann equation (PBE), one of the most popular continuum +models for describing electrostatic interactions between molecular solutes in +salty, aqueous media. Continuum electrostatics plays an important role in +several areas of biomolecular simulation + </longdescription> + <upstream> + <remote-id type="github">Electrostatics/apbs-pdb2pqr</remote-id> + <remote-id type="sourceforge">apbs</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/aqua/Manifest b/sci-chemistry/aqua/Manifest new file mode 100644 index 000000000000..0a70a95426cb --- /dev/null +++ b/sci-chemistry/aqua/Manifest @@ -0,0 +1,7 @@ +AUX aqua-3.2-flags.patch 4211 SHA256 dab0b840c6425d0295727224e5ef7ba9f48a4c013d45d24a141c46684e0d8eee SHA512 059cea5403fb4cb01b0fcd4d2a2fe4b4aea725e9362a6188ccd3756ced35e324cda5efb21d3ad2a95a842e9d83f8e728a16b36e4b6a479ae32da8816d7eafdfc WHIRLPOOL b1c2f4eff77458cb662b3aadc1c3f065cb2a7fb6c01bb3a2f41ce8a66b9d4c5153aff228b0e29a707d9a75cdef3f253572ba8479b0d3c26ddc812f72c6247b03 +DIST aqua-3.2-nmr_manual.tar.gz 632031 SHA256 89bbc2501831e547fec2fe755bbc0081f672e5e2c7adb83618699e6825f73996 SHA512 9b125b03507afebf15301c893efffae9be4e9695b9c577e5c2a80e83b620d04b4c27e867adf06336afa1556eddc96aa97de936028e503b1e85e156542664da0f WHIRLPOOL 181d320edd32faaac71a48163975ab6899221d7c85744eedfb8954d3360c974a0c8223b8b0f00375e2369fa7350df2e16a1062698be01c625ef00308a8ee0887 +DIST aqua3.2.tar.gz 688408 SHA256 895291b1771f4db5b4a010ce797400a8c4d84095bf34d660dd3405223419242f SHA512 1939f662a68122da613368aa106d7a31525903014420035eba9d10c3bd99b04d654d156328d308673003854233a02c1da48c036f3187fa1f0f303cc5928edd6a WHIRLPOOL 458fc0e574273fd9d2647ef8b2788c98669c9f96133f7132eddc9cbfb981e42894f5e4fd0e8d67f52ddb4c6424399b21973d4d87a175b440d81b7b955fe3fe41 +EBUILD aqua-3.2-r3.ebuild 2071 SHA256 2358cf9bc664f64e3e832c99c0f8aba97141a1ece67263abd97c58ec09be9b28 SHA512 4135a83c758759697fba718388473dfbc6893844db980b19174fe167a9e029aa273a04b04376404cf6a88378dda3e2ac7c2f8f3f526b75765f7f2abd054b802c WHIRLPOOL 238820a9d5a409006a6629c66fb3e7089cc630a1cf43c6e7ed76951fe955b5c96e657186aa92668b0b7b652e290bf5fef1867635f25dcb600c413991ba4478a8 +MISC ChangeLog 2589 SHA256 6a4cefc3a06bf04f71dee23fc72f450f8ff1723b214a7d92745fdf8a7e2cd20e SHA512 975a6f59950625b119248a1f0704ad3d2fb060ea776ac731481cb919b6198fdeadef8840008d4f1c1b5105292f9b708720a4519aa7a95701a244bb1f3581da74 WHIRLPOOL 1d228388d85f96d4bf7fb0416e03f12129d02457f2e52a2933dc96f37143995c219001f491ae85711474bbd22c7c767125728ba710b0a1eed25a5744d609cdec +MISC ChangeLog-2015 1234 SHA256 2e29785d9cd11da6615c45c9a7c47c077c19cefa07b670f0a0167712efdc6b59 SHA512 36243b25e872810d330f05bc488572a1fe334f7b20c0e3b7cd61404647d10f55076b5a55d39dfe353cf65053ae2feefe6b9f8137dc04475b42c0bb5a4c73ac0f WHIRLPOOL c87e94c566d0b2247afb1f7a0a24dee565c5908a67e3fc4726383a0db9baa32655af58e57665f25b1950c31ba77eefc70e7ba901a45792d6943c08b524d69bc2 +MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d diff --git a/sci-chemistry/aqua/aqua-3.2-r3.ebuild b/sci-chemistry/aqua/aqua-3.2-r3.ebuild new file mode 100644 index 000000000000..74e4e60416f7 --- /dev/null +++ b/sci-chemistry/aqua/aqua-3.2-r3.ebuild @@ -0,0 +1,95 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit fortran-2 toolchain-funcs + +DESCRIPTION="Program suite in this distribution calculates restraint violations" +HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html" +SRC_URI=" + ${PN}${PV}.tar.gz + doc? ( ${P}-nmr_manual.tar.gz )" + +SLOT="0" +LICENSE="procheck" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples" + +RDEPEND="sci-chemistry/procheck" +DEPEND="app-shells/tcsh" + +RESTRICT="fetch" + +S="${WORKDIR}"/${PN}${PV} + +PATCHES=( + "${FILESDIR}"/${P}-flags.patch +) + +pkg_nofetch() { + elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html" + elog "And follow the instruction for downloading ${PN}${PV}.tar.gz -> ${DISTDIR}/${PN}${PV}.tar.gz." + if use doc; then + elog "nmr_manual.tar.gz -> ${DISTDIR}/${P}-nmr_manual.tar.gz" + fi +} + +src_prepare() { + sed \ + -e 's:nawk:gawk:g' \ + -e "s:/bin/gawk:${EPREFIX}/usr/bin/gawk:g" \ + -e "s:/usr/local/bin/perl:${EPREFIX}/usr/bin/perl:g" \ + -i $(find . -type f) || die + default +} + +src_compile() { + cd src || die + emake \ + MYROOT="${WORKDIR}" \ + CC="$(tc-getCC)" \ + FC="$(tc-getFC)" \ + CFLAGS="${CFLAGS} -I../sub/lib" \ + FFLAGS="${FFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + exth + emake \ + MYROOT="${WORKDIR}" \ + CC="$(tc-getCC)" \ + FC="$(tc-getFC)" \ + CFLAGS="${CFLAGS} -I../sub/lib" \ + FFLAGS="${FFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_install() { + rm -f scripts/conv* || die + dobin bin/* scripts/* + dosym AquaWhat /usr/bin/qwhat + dosym AquaHow /usr/bin/qhow + dosym AquaPseudo /usr/bin/qpseudo + dosym AquaDist /usr/bin/qdist + dosym AquaCalc /usr/bin/qcalc + dosym AquaAssign /usr/bin/qassign + dosym AquaRedun /usr/bin/qredun + dosym AquaCompl /usr/bin/qcompl + + dodoc HISTORY HOW_TO_USE NEW README doc/* + dohtml html/* + + insinto /usr/share/${PN} + doins data/* + if use examples; then + doins -r exmpls + fi + + if use doc; then + dohtml -r manual + fi + + cat >> "${T}"/34aqua <<- EOF + AQUADATADIR="${EPREFIX}/usr/share/${PN}" + EOF + doenvd "${T}"/34aqua +} diff --git a/sci-chemistry/aqua/files/aqua-3.2-flags.patch b/sci-chemistry/aqua/files/aqua-3.2-flags.patch new file mode 100644 index 000000000000..a60841b8ce08 --- /dev/null +++ b/sci-chemistry/aqua/files/aqua-3.2-flags.patch @@ -0,0 +1,84 @@ +diff --git a/src/makefile b/src/makefile +index 3113471..dd7a320 100644 +--- a/src/makefile ++++ b/src/makefile +@@ -176,47 +176,46 @@ nrutil.h: + # Executable files + + $(BIN)/AquaWhat: AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaWhat AquaWhat.o $(OBJECTS) $(R_OBJECTS) $(RNG_OBJECTS) + + $(BIN)/AquaHow: AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaHow AquaHow.o $(OBJECTS) $(R_OBJECTS) AquaFuncts_dr.o $(RNG_OBJECTS) + + $(BIN)/AquaPseudo: AquaPseudo.o $(OBJECTS) $(R_OBJECTS) +- $(CC) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaPseudo AquaPseudo.o $(OBJECTS) $(R_OBJECTS) + + $(BIN)/AquaDist: AquaDist.o $(OBJECTS) +- $(CC) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) $(LDFLAGS) -lm ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaDist AquaDist.o $(OBJECTS) -lm + + $(BIN)/AquaCalc: AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) $(LDFLAGS) -lm ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaCalc AquaCalc.o $(OBJECTS) $(RNG_OBJECTS) -lm + + $(BIN)/AquaAssign: AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaAssign AquaAssign.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) + + $(BIN)/AquaCompl: AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) -lm ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaCompl AquaCompl.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) -lm + + $(BIN)/AquaRedun: AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) +- $(CC) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaRedun AquaRedun.o AquaCommon.o $(OBJECTS) $(R_OBJECTS) nrutil.o AquaFuncts_dr.o $(RNG_OBJECTS) + + $(BIN)/testnew: testnew.o $(OBJECTS) +- $(CC) -o $(BIN)/testnew testnew.o $(OBJECTS) $(LDFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/testnew testnew.o $(OBJECTS) + + $(BIN)/getproj: getproj.c +- $(CC) -o $(BIN)/getproj -O getproj.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(BIN)/getproj getproj.c + + $(BIN)/AquaPlot: AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o +- $(CC) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/AquaPlot AquaPlot.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o + + $(BIN)/Qext: Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o +- $(CC) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o $(LDFLAGS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/Qext Qext.o $(LIB)/MenuFuncts.o $(LIB)/Functs.o + + $(BIN)/StarTest: StarTest.o +- $(CC) -o $(BIN)/StarTest StarTest.o $(LDFLAGS) $(STARFLAGS) $(STARLIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $(BIN)/StarTest StarTest.o $(STARFLAGS) $(STARLIBS) + + exth: exth.f +- f77 -o exth -O2 exth.f +- strip exth ++ $(FC) $(FFLAGS) $(LDFLAGS) -o exth -O2 exth.f + + + # Object files +@@ -269,7 +268,7 @@ AquaCommon.o: AquaCommon.c AquaCommon.h nrutil.h \ + $(CC) -c AquaCommon.c $(CFLAGS) + + nrutil.o: nrutil.c nrutil.h +- $(CC) -c nrutil.c -DANSI ++ $(CC) $(CFLAGS) -c nrutil.c -DANSI + + AquaFuncts.o: AquaFuncts.c AquaFuncts.h AquaFuncts_cv.h AquaFuncts_io.h\ + AquaStrucset.h AquaFiles.h\ +@@ -319,7 +318,7 @@ $(LIB)/MenuFuncts.o: $(LIB)/MenuFuncts.c $(LIB)/MenuTypes.h $(LIB)/MenuFuncts.h\ + cd $(LIB); $(CC) -c MenuFuncts.c $(CFLAGS) + + cv_subs.o: cv_subs.f +- f77 -c cv_subs.f $(FFLAGS) ++ $(FC) -c cv_subs.f $(FFLAGS) + + Qext.o: Qext.c Qext.h\ + $(LIB)/MenuFuncts.h $(LIB)/Functs.h $(G_HEADERS) diff --git a/sci-chemistry/aqua/metadata.xml b/sci-chemistry/aqua/metadata.xml new file mode 100644 index 000000000000..da36ecbfcd6a --- /dev/null +++ b/sci-chemistry/aqua/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/aria/Manifest b/sci-chemistry/aria/Manifest new file mode 100644 index 000000000000..79b9b94a8bd1 --- /dev/null +++ b/sci-chemistry/aria/Manifest @@ -0,0 +1,5 @@ +DIST aria2.3.2_08.26.2013.tar.gz 1878602 SHA256 b9b892de2070a77812733faf4b6a1dbec4bba6dec80e5630088cab8b11cbfaf0 SHA512 a6d8c45218f5d494174587a5f8f1feec940ac8cc4cd7b707dac65b2378219ecf27967e70807e6cb7ae22a7d4aec7239af763f077ad7183c078b1991cac71bc3e WHIRLPOOL 59c0b79fab40201d903c484bf63e8339c235207306efc848965d260c02b00c9a408297df0f211cf45f30d13ec35175bf7d566bb5c6d59b944eb22d9aacf0384d +EBUILD aria-2.3.2_p20130826.ebuild 1918 SHA256 11bf3ea780ec7d1d36cbddf069a529b9686bf5ac4d5fee62fdfa08e1e33d0dfa SHA512 97f30da0e83cee0e9ed20c0d81b020fa55d3b62c60f25014b4b83888e3004f01b94216ba13257b8fe2fb92156391f3c08845d6f1cf5684739a1fc6d412ecd712 WHIRLPOOL 3488b567dac571b2af63b7e16dc885a90e465fc970f8795dfc7146cde59a8a30146f76b8e7430a6d5552af03c82b77de8f9877c05f4669cd0f029bae65adaa41 +MISC ChangeLog 2835 SHA256 c6b6bcb19baf6a9585efd50ae0334fd10b7f0659ce81eafe031ea90fae924a62 SHA512 fa68904e18078d6a686304309a2518a1ad99481bc6522c6e65c0f3dcf8e4aabd161ed604d47863e00601a14ad6114aaf46e7eaec9b4131ec0b53806bb989fe08 WHIRLPOOL 6cf1ed79e98234ad17fa7a45cca57509053a87056c4ce873cc863e6745296bc55ddbc5b2a459ce8747c5ebdcddb375206875bc9ef17f855e8ab86df822188fef +MISC ChangeLog-2015 3528 SHA256 4c5587b2f95197300a51bbabf99a75b5de5d3a55b957b46ac4789070691e2062 SHA512 ff6a65fba911bb08ff0d86bb464402b424fe670ec55e462f31c14bca5561c9a934c153654034eb1c9885dd7221c8b5b819e3730c6e920b1e4ff09e0ca6a9cbae WHIRLPOOL 98241b5b155e081994c9200062c319757185ebf2e895e711bbc9766df1164cbf15cbc8f0f66f3fc358405e47fde2b29605b3239c045a7e0779f51303534d86ad +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild b/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild new file mode 100644 index 000000000000..84f75d11ed6e --- /dev/null +++ b/sci-chemistry/aria/aria-2.3.2_p20130826.ebuild @@ -0,0 +1,88 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="tk" + +inherit eutils python-single-r1 versionator + +MY_P="${PN}$(get_version_component_range 1-2 ${PV})" +DATE="08.26.2013" + +DESCRIPTION="Automated NOE assignment and NMR structure calculation" +HOMEPAGE="http://aria.pasteur.fr/" +SRC_URI="http://aria.pasteur.fr/archives/${MY_P}.2_${DATE}.tar.gz" + +SLOT="0" +LICENSE="cns" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-tcltk/tix + dev-lang/tk:0= + >=dev-python/numpy-1.1[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP},tk] + >=sci-chemistry/cns-1.2.1-r7[aria,openmp] + >=sci-chemistry/ccpn-2.2[${PYTHON_USEDEP}] + sci-chemistry/clashlist + sci-chemistry/procheck + sci-libs/clashscore-db" +DEPEND="${RDEPEND}" + +RESTRICT="fetch" + +S="${WORKDIR}/${MY_P}" + +pkg_nofetch(){ + einfo "Go to http://aria.pasteur.fr/archives/aria2.3.2.tar.gz/view, download ${A}" + einfo "and place it in ${DISTDIR}" +} + +pkg_setup() { + python-single-r1_pkg_setup +} + +src_test(){ + export CCPNMR_TOP_DIR=$(python_get_sitedir) + export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python + ${PYTHON} check.py || die +} + +src_install(){ + python_moduleinto ${PN} + python_domodule src aria2.py + python_moduleinto ${PN}/cns + python_domodule cns/{protocols,toppar,src/helplib} + + if use examples; then + insinto /usr/share/${P}/ + doins -r examples + fi + + # ENV + cat >> "${T}"/20aria <<- EOF + ARIA2="$(python_get_sitedir)/${PN}" + EOF + + doenvd "${T}"/20aria + + # Launch Wrapper + cat >> "${T}"/aria <<- EOF + #!/bin/sh + export CCPNMR_TOP_DIR="$(python_get_sitedir)" + export PYTHONPATH="$(python_get_sitedir)/ccpn/python" + exec "${PYTHON}" -O "\${ARIA2}"/aria2.py \$@ + EOF + + dobin "${T}"/aria + dosym aria /usr/bin/aria2 + + dodoc README + python_optimize "${D}/$(python_get_sitedir)" +} diff --git a/sci-chemistry/aria/metadata.xml b/sci-chemistry/aria/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/aria/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/autodock/Manifest b/sci-chemistry/autodock/Manifest new file mode 100644 index 000000000000..1d8ebab45df7 --- /dev/null +++ b/sci-chemistry/autodock/Manifest @@ -0,0 +1,6 @@ +AUX autodock-4.2.6-buildsystem.patch 1500 SHA256 4ff8d1c05f2dcb61edc36b82a13e3542f27b06b8d53e6939866b481da1f38155 SHA512 08a7643e2973f2ebdd01c54acb1e3e0802ea3d7a33cbed4c03f58d29c7e13a246418feb4a61088dae18c3ab78db6fd5b3c11f9974dec59fe46dbf7cfbbe98c3a WHIRLPOOL bfb4ff1ce12a2fe3f841043a4413f9bb42f828e665a67914dd75e4f7b2be0cea8e98649f9596c494d8cd45baa7177b03ef0540acc4068ee0085741750c4260c2 +DIST autodocksuite-4.2.6-src.tar.gz 35438010 SHA256 4b24ce4baf216a5e1a6a79bb664eeed684aed17cede64ff0061aa1bcc17874c4 SHA512 75b8878f948c4f6bc28adb442997192dad0c36bbede2fd698623903cb27b06b4df3ba038bfc70fc13b4bdee864fd2344f0f7208be2020da4e01a00b842b46bbb WHIRLPOOL 18230783d13c2d82ad6427711a48dec0c6695301a52dcf419cf4feefb0b5f41bac5de53824313e75d9040ac8623915ba266e764e92ecad9869d845053ec60b93 +EBUILD autodock-4.2.6.ebuild 2178 SHA256 33b86ac589ad95502ff32dcba4bf67397ed81fbab8c6d9ab7a1decc5f857e7c6 SHA512 f8b186454cec3e7deb6078cfa659d15eeebdc7e4bcb36d03327603ecda063b8a383a032001b8db9ad849dddb2c5992ec57c4f0bb6d8031a89cdad44fb3d82acb WHIRLPOOL de4f8b0ef5da206b52a69e03db0909693ca524700aaf7a1beced43e6ebbe556252e16a7464c0d1b97e4af95299e1780a068e040803c022190ba29ecad4533a96 +MISC ChangeLog 2506 SHA256 f2fbd31d2ccda5afbbf4b84bef834b8cfe32808361e569cd9fc9e431fcfae230 SHA512 e48184516de00a54b87402a3d164ffc0630b9c732ce75e527435180fbfcebb8c9f2c2749770fed1baee43cd0d615ad40ff5efde7e2934fbb56089a3f01cec745 WHIRLPOOL d7431d9d8ef285e01914015bd4cf2c83a51aaf7c43c4781e6a882075d6d8f54c6c1d83753bcf8120ff0490be41aeced741cecee2023e6d1dc99f9393e9ada4c5 +MISC ChangeLog-2015 1951 SHA256 a50f671c0007f340554e37ec4cedadf54088746b7e061a4105a89311470c8b32 SHA512 8127922c5acd3b9a24e4ad496bded17b0f1d7575ffad2cc308182730e5a0b69db9f4838f22345ac9807666ce43935dcbd3d8a3020a8a178ce92ce5c339090ecd WHIRLPOOL 9e0822256de0dbf4fd418d22f8b485da54268c242e6796afc13368b5758483596079588d33e83defebbe942de5f5ff9211c8405c996eca753f287fb5daa7d7db +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/autodock/autodock-4.2.6.ebuild b/sci-chemistry/autodock/autodock-4.2.6.ebuild new file mode 100644 index 000000000000..862cda1437b9 --- /dev/null +++ b/sci-chemistry/autodock/autodock-4.2.6.ebuild @@ -0,0 +1,101 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools eutils python-any-r1 versionator + +MY_PN="autodocksuite" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="A suite of automated docking tools" +HOMEPAGE="http://autodock.scripps.edu/" +SRC_URI="http://autodock.scripps.edu/downloads/autodock-registration/tars/dist$(delete_all_version_separators)/${MY_P}-src.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="examples openmp test" + +RDEPEND="" +DEPEND="test? ( ${PYTHON_DEPS} )" + +S="${WORKDIR}/src" + +PATCHES=( + "${FILESDIR}"/${P}-buildsystem.patch +) + +src_prepare() { + local i + + epatch "${PATCHES[@]}" + + sed \ + -e "s/\tcsh/\tsh/" \ + -i auto{dock,grid}/Makefile.am || die + for i in autodock autogrid; do + pushd $i &>/dev/null + eautoreconf + popd &>/dev/null + done +} + +src_configure() { + local i + for i in autodock autogrid; do + pushd $i &>/dev/null + econf $(use_enable openmp) + popd &>/dev/null + done +} + +src_compile() { + emake -C autodock + emake -C autogrid +} + +src_test() { + elog "Testing autodock" + cd "${S}/autodock/Tests" || die + cp ../*.dat . || die + ${EPYTHON} test_autodock4.py || die "AutoDock tests failed." + einfo "Testing autogrid" + cd "${S}/autogrid/Tests" || die + ${EPYTHON} test_autogrid4.py || die "AutoGrid tests failed." +} + +src_install() { + if use openmp; then + newbin autodock/autodock4.omp ${PN}4 + dobin autogrid/autogrid4 + else + dobin autodock/autodock4 autogrid/autogrid4 + fi + + insinto /usr/share/${PN} + doins -r \ + autodock/{AD4_parameters.dat,AD4_PARM99.dat} \ + $(usex examples "autodoc/EXAMPLES" "") + + DOCS=( + RELEASENOTES + autodock/{AUTHORS,README} + autodock/USERGUIDES/AutoDock4.{0,1,2}_UserGuide.doc + autodock/USERGUIDES/AutoDock4.2_UserGuide.pdf + ) + einstalldocs +} + +pkg_postinst() { + elog "The AutoDock development team requests all users to fill out the" + elog "registration form at:" + echo + elog "\thttp://autodock.scripps.edu/downloads/autodock-registration" + echo + elog "The number of unique users of AutoDock is used by Prof. Arthur J." + elog "Olson and the Scripps Research Institude to support grant" + elog "applications." +} diff --git a/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch b/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch new file mode 100644 index 000000000000..ae44ffeb3159 --- /dev/null +++ b/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch @@ -0,0 +1,44 @@ + src/autodock/Makefile.am | 6 +++--- + src/autogrid/Makefile.am | 4 ++-- + 2 files changed, 5 insertions(+), 5 deletions(-) + +diff --git a/src/autodock/Makefile.am b/src/autodock/Makefile.am +index 799a3c4..911897b 100644 +--- a/src/autodock/Makefile.am ++++ b/src/autodock/Makefile.am +@@ -459,7 +459,8 @@ endif + + BUILT_SOURCES = $(autodock4_SOURCES) default_parameters.h + +-AM_CXXFLAGS = -O3 # Agressive optimization ++AM_CXXFLAGS = ++#AM_CXXFLAGS = -O3 # Agressive optimization + #AM_CXXFLAGS = -g # debug + + # if gnu c++ compiler +@@ -488,8 +489,7 @@ endif + AM_CPPFLAGS = -DNOSQRT \ + -DUSE_DOUBLE \ + -DUSE_8A_NBCUTOFF \ +- -DUSE_INT_AS_FOURBYTELONG \ +- -O3 ++ -DUSE_INT_AS_FOURBYTELONG + # AM_LDFLAGS = -g # -g is MP debug + + +diff --git a/src/autogrid/Makefile.am b/src/autogrid/Makefile.am +index b531099..b78b380 100644 +--- a/src/autogrid/Makefile.am ++++ b/src/autogrid/Makefile.am +@@ -94,9 +94,9 @@ autogrid4_SOURCES = main.cpp \ + BUILT_SOURCES = default_parameters.h + + +-AM_CFLAGS = -Wall -O3 # All warnings, Agressive optimization ++AM_CFLAGS = -Wall # All warnings, Agressive optimization + +-AM_CPPFLAGS = -Wall -O3 -I $(srcdir) -I$(srcdir)/../autodock # All warnings, Agressive optimization ++AM_CPPFLAGS = -Wall -I $(srcdir) -I$(srcdir)/../autodock # All warnings, Agressive optimization + AM_CPPFLAGS += -Wno-write-strings # increase compatibility with pre 4.x compilers for string handling + # M Pique - add USE_8A_NBCUTOFF + AM_CPPFLAGS += -DUSE_8A_NBCUTOFF diff --git a/sci-chemistry/autodock/metadata.xml b/sci-chemistry/autodock/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/autodock/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest new file mode 100644 index 000000000000..5dbd7c90c62e --- /dev/null +++ b/sci-chemistry/autodock_vina/Manifest @@ -0,0 +1,7 @@ +AUX 1.1.2-gentoo.patch 2448 SHA256 41a0f4091be44dc2a59a7f32fedc18fb6e8266740284c756f5b79f39a5080d57 SHA512 d8165d88f3e91064c74f1506a7f58473a74f6ebf993165827694d78170b29227dc378c61a7f096a3c49708b713583aca3d5714827d1fe43a5bb37f3d648d2613 WHIRLPOOL b169152e3e00b479a1cc7ef3dd6bcfa00dd2f9eb2b3f2ec0b584e2d894c515507ae1036fc3c009d2bd6f180afc086f3ffccd9570ffa34383f5846d3fa60a27d4 +AUX autodock_vina-1.1.2-boost-filesystem.patch 2936 SHA256 b7e6304fcee336bccd4f0244a24745f34f3bc7582f9f887fa885af99aa4f0947 SHA512 4226fb0d7196362a02afa4e0b0616146ef816a439dd63e1bffbfef183975fe7e6260318f919e9d9835d2d47973542b5340e93ad35b070467e42c0990f9a635f7 WHIRLPOOL 845159f7ea1caad30926b812867fe9e93377d27d83a486b504bf6d9876e2f13ca48855f803108c41b63da4070ec7ff23a65c64995ced0be8db1aa005c20cfe37 +DIST autodock_vina_1_1_2.tgz 67366 SHA256 b86412d316960b1e4e319401719daf57ff009229d91654d623c3cf09339f6776 SHA512 f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9 WHIRLPOOL b68f3bb81fe957fddb6674f71e0c63d1425eb5b4de0615258545ba8e241b347380c8745ee47bd2ee2257f29916191773440e3dd4e9ce857b83a947074eae8d45 +EBUILD autodock_vina-1.1.2.ebuild 932 SHA256 1b93b28ae1a083e18488a051203a3b5b6bf19e2f4ffad2e5e7350b1fa4f45164 SHA512 39f8acb795d17786a5112a4e70bf67c6ab594d25ab5eb4b739e2b0c70a9e0548265bcd5f36b6d4915b82b43a0f463187f8d9dc5aaa62f925c5172950a6bc26ee WHIRLPOOL a248e2bbd762f2af05afbc06f87af44280b725c66a584dd133f2e0d41aff764a6148a13d5441d3a3e078235c42df77a4079e4c28b083959794ddd6cb02835dd9 +MISC ChangeLog 2908 SHA256 1709392f8c6af9c9a333c7f41b8704a24b8faa024a576465512ce04ad527f9e7 SHA512 6adfb55110faf393f71a490f34d7c0c37494ede8192bfa05e683533f955cc82ae4c82ec2b65ad375d9d24219c4befac9fb86547e14187500f1f84cda46c35b8c WHIRLPOOL 42220c8bf5a5ab34c7bd8083c55741d2e85a1be69acf362fbbb5ca2dfc39f93e7cdb7c28bf7bf2c1b413cb5ef8134f2df26ce708d8f574f2d355b60825e43aeb +MISC ChangeLog-2015 1914 SHA256 129b9a4a71807910a677edfa70f2bf88f46bd895a185febca45289ec0e9f71e7 SHA512 662b2f5038db3fe01bea84ad8a1ed40c95fbb5e4c28533ef8d665e06efd64f4fe40f0f5d7dc11497799aa72aae5557255b6913b122fbc3c78ab8e5875474de3c WHIRLPOOL 4a26d113831b76b817cf0dd195fbd388e3edf51e177e5e735e7158a7924d0089bf1e1815883a9ddb5c03d81412fe2898cde5e7528456339b6029f4ab3448cc33 +MISC metadata.xml 1234 SHA256 9c8715e6ffac3433885b0c5a5b778d19134e45b20bcf41ac4bbfeb0d6ad54cfa SHA512 b9b8753dacfaf0e511a90ad6fd1612fa3f11ac238654ccb6ad3a052026e366fc141776c6578923a024c77b8f2d6e37a9949822daa8d458902d383c1434eb6da9 WHIRLPOOL d808fedd3597aa5f4a71adbcfcde1d29d37f04442d9d7cbf5976c4e9023cbcae12d47c706a0dca1fe815bba4f7137ce0e4929b02400e778971c98b01a5da2bf4 diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild new file mode 100644 index 000000000000..bbff27f85e2f --- /dev/null +++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic versionator + +MY_P="${PN}_$(replace_all_version_separators _)" + +DESCRIPTION="Program for drug discovery, molecular docking and virtual screening" +HOMEPAGE="http://vina.scripps.edu/" +SRC_URI="http://vina.scripps.edu/download/${MY_P}.tgz" + +SLOT="0" +KEYWORDS="amd64 x86" +LICENSE="Apache-2.0" +IUSE="debug" + +RDEPEND="dev-libs/boost[threads]" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${MY_P}/build/linux/release + +src_prepare() { + cd "${WORKDIR}"/${MY_P} || die + epatch \ + "${FILESDIR}"/${PV}-gentoo.patch \ + "${FILESDIR}"/${P}-boost-filesystem.patch +} + +src_compile() { + local c_options + + use debug || c_options="-DNDEBUG" + + append-cxxflags -DBOOST_FILESYSTEM_VERSION=3 + + emake \ + BASE="${EPREFIX}"/usr/ \ + GPP="$(tc-getCXX)" \ + C_OPTIONS="${c_options}" +} + +src_install() { + dobin vina{,_split} +} diff --git a/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch b/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch new file mode 100644 index 000000000000..61ae8bec36f5 --- /dev/null +++ b/sci-chemistry/autodock_vina/files/1.1.2-gentoo.patch @@ -0,0 +1,72 @@ + build/linux/debug/Makefile | 2 +- + build/linux/release/Makefile | 2 +- + build/makefile_common | 14 +++++++------- + 3 files changed, 9 insertions(+), 9 deletions(-) + +diff --git a/build/linux/debug/Makefile b/build/linux/debug/Makefile +index 6a41cfc..8097fb9 100644 +--- a/build/linux/debug/Makefile ++++ b/build/linux/debug/Makefile +@@ -1,7 +1,7 @@ + BASE=/usr/local + BOOST_VERSION=1_41 + BOOST_INCLUDE = $(BASE)/include +-C_PLATFORM=-static -pthread ++C_PLATFORM=-pthread + GPP=/usr/local/bin/g++ + C_OPTIONS= -g + BOOST_LIB_VERSION= +diff --git a/build/linux/release/Makefile b/build/linux/release/Makefile +index 1de1063..ded8133 100644 +--- a/build/linux/release/Makefile ++++ b/build/linux/release/Makefile +@@ -1,7 +1,7 @@ + BASE=/usr/local + BOOST_VERSION=1_41 + BOOST_INCLUDE = $(BASE)/include +-C_PLATFORM=-static -pthread ++C_PLATFORM=-pthread + GPP=/usr/local/bin/g++ + C_OPTIONS= -O3 -DNDEBUG + BOOST_LIB_VERSION= +diff --git a/build/makefile_common b/build/makefile_common +index a940329..96336e8 100644 +--- a/build/makefile_common ++++ b/build/makefile_common +@@ -2,29 +2,29 @@ LIBOBJ = cache.o coords.o current_weights.o everything.o grid.o szv_grid.o manif + MAINOBJ = main.o + SPLITOBJ = split.o + +-INCFLAGS = -I $(BOOST_INCLUDE) ++INCFLAGS = -I$(BOOST_INCLUDE) + + # -pedantic fails on Mac with Boost 1.41 (syntax problems in their headers) + #CC = ${GPP} ${C_PLATFORM} -ansi -pedantic -Wno-long-long ${C_OPTIONS} $(INCFLAGS) + CC = ${GPP} ${C_PLATFORM} -ansi -Wno-long-long ${C_OPTIONS} $(INCFLAGS) + +-LDFLAGS = -L$(BASE)/lib -L. ++LDFLAGS += -L. + +-LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread ++LIBS = -lboost_system -lboost_thread -lboost_serialization -lboost_filesystem -lboost_program_options -lpthread + + .SUFFIXES: .cpp .o + + %.o : ../../../src/lib/%.cpp +- $(CC) $(CFLAGS) -o $@ -c $< ++ $(CC) $(CXXFLAGS) -o $@ -c $< + + %.o : ../../../src/design/%.cpp +- $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< ++ $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< + + %.o : ../../../src/main/%.cpp +- $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< ++ $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< + + %.o : ../../../src/split/%.cpp +- $(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< ++ $(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< + + all: vina vina_split + diff --git a/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-boost-filesystem.patch b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-boost-filesystem.patch new file mode 100644 index 000000000000..298aaa9ab993 --- /dev/null +++ b/sci-chemistry/autodock_vina/files/autodock_vina-1.1.2-boost-filesystem.patch @@ -0,0 +1,79 @@ + src/main/main.cpp | 10 +++++++++- + src/split/split.cpp | 11 ++++++++++- + 2 files changed, 19 insertions(+), 2 deletions(-) + +diff --git a/src/main/main.cpp b/src/main/main.cpp +index f49c8f5..b566aa2 100644 +--- a/src/main/main.cpp ++++ b/src/main/main.cpp +@@ -47,7 +47,7 @@ + using boost::filesystem::path;
+
+ path make_path(const std::string& str) {
+- return path(str, boost::filesystem::native);
++ return path(str);
+ }
+
+ void doing(int verbosity, const std::string& str, tee& log) {
+@@ -661,7 +661,11 @@ Thank you!\n"; + cpu, seed, verbosity, max_modes_sz, energy_range, log);
+ }
+ catch(file_error& e) {
++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
++ std::cerr << "\n\nError: could not open \"" << e.name.string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++#else
+ std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++#endif
+ return 1;
+ }
+ catch(boost::filesystem::filesystem_error& e) {
+@@ -673,7 +677,11 @@ Thank you!\n"; + return 1;
+ }
+ catch(parse_error& e) {
++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
++ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.string() << "\": " << e.reason << '\n';
++#else
+ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n';
++#endif
+ return 1;
+ }
+ catch(std::bad_alloc&) {
+diff --git a/src/split/split.cpp b/src/split/split.cpp +index 54c614b..bc5530e 100644 +--- a/src/split/split.cpp ++++ b/src/split/split.cpp +@@ -38,7 +38,7 @@ + using boost::filesystem::path;
+
+ path make_path(const std::string& str) {
+- return path(str, boost::filesystem::native);
++ return path(str);
+ }
+
+ std::string default_prefix(const std::string& input_name, const std::string& add) {
+@@ -208,7 +208,12 @@ Thank you!\n"; + write_multimodel_pdbqt(tmp, ligand_prefix, flex_prefix);
+ }
+ catch(file_error& e) {
++
++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
++ std::cerr << "\n\nError: could not open \"" << e.name.string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++#else
+ std::cerr << "\n\nError: could not open \"" << e.name.native_file_string() << "\" for " << (e.in ? "reading" : "writing") << ".\n";
++#endif
+ return 1;
+ }
+ catch(boost::filesystem::filesystem_error& e) {
+@@ -220,7 +225,11 @@ Thank you!\n"; + return 1;
+ }
+ catch(parse_error& e) {
++#if defined(BOOST_FILESYSTEM_VERSION) && BOOST_FILESYSTEM_VERSION >= 3
++ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.string() << "\": " << e.reason << '\n';
++#else
+ std::cerr << "\n\nParse error on line " << e.line << " in file \"" << e.file.native_file_string() << "\": " << e.reason << '\n';
++#endif
+ return 1;
+ }
+ catch(std::bad_alloc&) {
diff --git a/sci-chemistry/autodock_vina/metadata.xml b/sci-chemistry/autodock_vina/metadata.xml new file mode 100644 index 000000000000..e255923b229e --- /dev/null +++ b/sci-chemistry/autodock_vina/metadata.xml @@ -0,0 +1,29 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +AutoDock Vina is a new open-source program for drug discovery, molecular +docking and virtual screening, offering multi-core capability, high +performance and enhanced accuracy and ease of use. [1] +AutoDock Vina has been designed and implemented by Dr. Oleg Trott +in the Molecular Graphics Lab at The Scripps Research Institute. +If you used AutoDock Vina in your work, please cite: +O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy +of docking with a new scoring function, efficient optimization and +multithreading +Journal of Computational Chemistry 31 (2010) 455-461 +</longdescription> + <!-- +<use> + <flag name='flag'>Description of how USE='flag' affects this package</flag> + <flag name='userland_GNU'>Description of how USERLAND='GNU' affects this + package</flag> + <flag name='aspell'>Uses <pkg>app-text/aspell</pkg> for spell checking. + Requires an installed dictionary from <cat>app-dicts</cat></flag> +</use> +--> +</pkgmetadata> diff --git a/sci-chemistry/avogadro/Manifest b/sci-chemistry/avogadro/Manifest new file mode 100644 index 000000000000..e517a85fbcf7 --- /dev/null +++ b/sci-chemistry/avogadro/Manifest @@ -0,0 +1,18 @@ +AUX 1.0.1-gl2ps.patch 1511 SHA256 0aae5556233c8e413739fdd890b5d8453d9a1e39dd3251a5a7a7705227a13e7b SHA512 b4a8d0138bffa7c018e2125e16a47cefefba01f19ce3d460488f36e44f55b212cea9c9875429e7c0c596388366adea045b50ace579b6352d2b7e0b073420c67f WHIRLPOOL 015420a79e56b5f3da238d73d12e28573636161e4edcdc94db80149aa84621de05b84f08332d701b5ed89dadb414a30e33badc686788698dd539603d2eeb5a05 +AUX avogadro-1.1.0-textrel.patch 1535 SHA256 55a58d29f47d441a5877e32acf9f9a8ad1e408a75a6629ccdc23ebec8f4d40f8 SHA512 5872a773668cb38b27ab0dbaf14d947eff4cb3d4ae99410c8968cafe576a9df5d3b0937d028b9ffd076c212c5f9b8e213cda74a63afff6caa713346ee338be77 WHIRLPOOL f5478f34db2d20ae08c26b3db4c9334c7794c5948652c0199e78ea760054932297c00b5ff4c001ed3eed98e050c6970766d8c117748d5dc6a43ed0cc15ab5651 +AUX avogadro-1.1.0-xlibs.patch 680 SHA256 13f01a86b51ab48dab22ea8e547946eaa48b5c4a650ad95fcafc8f9fc21e21dc SHA512 df2727e4aea1549daada56778d7710656f3f6ff9fa31c441c06e82241c8e5b0733c39d575c98f2d1b57b9be0a52d445412ecd6cca7a1f319c6982035e789f21d WHIRLPOOL 2cadc10899f317ce1f90da250486b839604ce6664da568178243538966023591753ec0354f515c22548426f3263540117efd36d401b0f454ae704c48fd37a3ec +AUX avogadro-1.1.1-boost-join-moc.patch 2051 SHA256 133c121ff6ec2a1e0a76727d61edfcac4f76207a0d605b2d745ce114498ae976 SHA512 d4e4ef54d94cccb0f34c4960d302772f9da47e27cb79e1ee0a4e928ef248ac629fd59f1564bedf7c82a2a7ca8b25456878c22569dbcda26478a6c06e5815a084 WHIRLPOOL d5a32e4a7bc51b112fe5c01bb001da752319747d7adc7faf1f7da811acb781e1314ebdd8737fb11cd397ce25412c7e4bd0858926d1be29758d5d3add21d5eb08 +AUX avogadro-1.1.1-eigen3.patch 2230 SHA256 4ff7d5f079376d8e125b6f32a27d6eb1a356eafe5c50c66f0d8b8da75b58bf36 SHA512 df6a53cacebee613739d230fc0c7dc21cb67d553950af82cf83d04750f1d9fa98a3bb052c15fffebacf41d2e53dcd3503bffff2aa8dfbfcb47e2d1ebccd77614 WHIRLPOOL 0675c74c759cf67b703add1b9483895ecba83d40bf943e011b0e6edc2eafe2c0f91d78472e6f554bd340236330c3cf1f3fbd0da65fe2158cca7feed727127463 +AUX avogadro-1.1.1-mkspecs-dir.patch 580 SHA256 ffa4e6b05884feabe688dd856efab0f00c9df8358bd17846e74291606b40465a SHA512 6c5b67d9f9e1e9fa3c11ae235f467525129fa9d81f34211ed8b97c199690e12cd1457df3aac861615d94efb452af306df6b53218309ff87f6ca1f68edffbf6b2 WHIRLPOOL e2f2c3521519cfcfe390fe8f1758576741f62ebca7f4ac3dae9e72390b25ef4595f270ae37c4fdc0217ff5265259f2dfaf529ec48e7422debf0bb65b15e8e40e +AUX avogadro-1.1.1-no-strip.patch 745 SHA256 90cbae3e12a7f64e7f2ec61086b66e229e75bb1aafc5a3d987acf392b7ddc971 SHA512 921b1333bf37135d5890222193ebdb5b351739d16bf1434c59509e8aab0135ea5cde6812b63d4159fafac29d4eb6297320d03513e474466a7fb857ed16301d6e WHIRLPOOL ea1a6006fbb911974d30c65c72def85ce3265818186aa88a21eb7df511f16939a7bb381bc0390e996f138636db9d6350972896c60b45a687c1467e12f8ab7c9f +AUX avogadro-1.1.1-openbabel.patch 655 SHA256 9208ddd27d182a799b54480520df6050433aecb7c8e74a4aa5d8492c1a592bd7 SHA512 23f477c9deb4befb87a92eb1edaabdd8e52a25f24a36ec9dbf345b0686442cec229a16fbb118e3336cf28592d8af4fc51d0a3e5e9d7a7d7c11a65080c08a074d WHIRLPOOL 74cdb0c4530c7376456217a91b0fa1e73e7199ca5fdab273d8e208910f79a53ccf1997ef6329c3add54bedf01eb05f699ba80c0abe92b2682e4b82952b285517 +AUX avogadro-1.1.1-pkgconfig_eigen.patch 387 SHA256 57fa3b1bbc22b17feffcaa4f763ef50aa4c125ab6a85aafde21898331020ab94 SHA512 4e1e838f7cd88ef3ef49c26565aecf16a3cfb5c735d67c2525e877aa64671ac787733b0eee7f02ef79c6ada05d7dd7fc3c4a470e6d4549fcd0fea7d49e780e99 WHIRLPOOL 3e01193837f5542c722d92820916a323ce7caf4d254c179c095d1fd007add898a668d0fb94ea064f19d3b5b0329f4f93c6efee02faafb070018c85e280198b43 +DIST avogadro-1.0.3.tar.bz2 4971989 SHA256 efb6fda223da3c027436f0c218a47ce804f7469c58b41134230e9ebad1c98468 SHA512 49e7b8ca43f0f52a65efc7bf9dc45670ae5a5de5d1aa6bf7b58b8368e816be30fe6529c45fa658d7337d4a69327bb0aa8799d8d4b4805860aace28011cc74210 WHIRLPOOL c835ac24b317a1fa310bf3ea75bae4002d01f364d4754e6a7d841594dcce321435c827d60e125d9410f05670a94c887cc250bf49759d02cde34a5839d2324c92 +DIST avogadro-1.1.0.tar.bz2 10741835 SHA256 6b4eaf57ae52bf43df9b103c77e6abae71e067053d5c99f82acbce9855ecceb0 SHA512 d621dd3ea9e9223d3a29c6b0c0eec89a935837d0c587fcaaa549f91274a76f78a8c60c2a68a67d2f3aa2e107826befb6658be601c46c5bc0760c95bf7284540a WHIRLPOOL c81e866e60b3383a58de515317c754e3982e716c27974ce43ca0c1209d24544949361a7f2f93a4a940d73fd7a18b184f68c7a1856fea89ae5eba75db74b1012d +DIST avogadro-1.1.1.tar.bz2 11118046 SHA256 fe6f7bdea17a27a20be25b70d975145999aae9d90ef320217af2bc4d6e7a0a14 SHA512 37e2fc9400f8727b7e69d84c13989aaba6fc88287e106a6ed137e4d0fd8ea181dc4ab49b08148d2077754f014748c8ed6f46881f31a1455029f876b599754827 WHIRLPOOL 6bea2c25675ba29729785b561cbaed33929aeb4638180454b1aed8913160cd6d0315bb09e6ee4033a8d27ce84fd7a4573851fd02c76b64b6aa86e615a19b8c38 +EBUILD avogadro-1.0.3-r2.ebuild 1298 SHA256 af4e3cd17a733b067b991a7457bf974631fb5d3a06d5f18c0bd1a2ff66d2e60e SHA512 54b364267975e585b7fdc510688d92f3aa7e5cf477a0288f6ccfe7d468c496d785b1c9f3d37e7b0ce7df8729565614b63fa3544507c50359d5e67189a4ab6e45 WHIRLPOOL d0053824b722643b3975bbf2c44bd1fda162ae5dbb3cf857aad8f56a1e733e9edb09528d6ee9711d8d6c7479b0bfea6dfc69cd4921ec0b179cc01e3caddd6ffb +EBUILD avogadro-1.1.0.ebuild 1482 SHA256 b924e0bb506bdebbf5d86e8d61e52f137dd2ba19832f6a3d47ba1aae77e74fe0 SHA512 d3f0095e7b1644cb963ad4223a43fcc0201f5c14247b0e0b04c570f47ce2c33f52bb46373d347dedeee662cdfd4924dce27d809bdc9826e785e34e5f73f935d9 WHIRLPOOL d1a94503cc711087d424968b6e0c1103022a7f9021d8ac6559db256d6d45df102f2b6b2429756119cd2082f53ff3ece22f7db179ce77e4263da86a5eaedda57e +EBUILD avogadro-1.1.1.ebuild 1976 SHA256 5abae5f879b0b0fa30baba648102d3a69e618b989cc151cf483453a3226e9171 SHA512 c6a83d047ab126e32ce74adc07f6702da476c19c96483b30753a634a66521f712ca302c71f1ff7bc72e92da0874e419f5a7edaf1a926631baa0e05634bccd909 WHIRLPOOL 7412f68617c56e86ce7e6c242053b38c0bb9e00339368e2c87ed28ede74e8b7d084d8158562b3c1fe830b822b4d0b8fcf4ab06065c4df334d2ccd385a3e6a6a0 +MISC ChangeLog 3988 SHA256 0c2f9a9d7e8b549f4e4e97756463e58d52520625e3a3292ad67e860d1e2ed4f6 SHA512 a518a58d309a39f60762e2fff76a48c891a4785103fb7727939244996c03492ffa92b0a2610320fad08ddff5f92155509b6da1f69c4fc1a60e1fb99193bdce19 WHIRLPOOL 8e3c8306dde4a18b585bfd84a5870290401269bab4519cd20a83ad005b2656472c86c22a967fa4f6d4960059a1fb6b4ee2b8f263f2d690ec4db934a6369dff3d +MISC ChangeLog-2015 8157 SHA256 b764019c5586469b24e84bbef958e4df39ef4019ddb1be25f95bfce96c549c83 SHA512 fc061195a7e791a171759d27ac25fc7cd2cc2c0347a7d353af49c449c1131c50cc7ba0b325d752785c563eb0d5c20a5a3933f37438bc3552f2fb41ffc355edec WHIRLPOOL 10b2d933a605479bc4389e93eeba6351d48cc7695675e298cb0aeeca62d41ba22aa952bb26a01aaf4e5a28adb6f78c12124d66dfb58c4aff76a8ac0be7331fcc +MISC metadata.xml 718 SHA256 3f6c835242302a435220bf9ef9fbe4033578b9ff4040d59e49b14bb8705c8a38 SHA512 c462030593317c5ad343161cc387df47249a728e96eacf736569f9fb8762c22343f4b8b9ba07ee1c728f296951940f690b5c8676908bc50e71d517c542ac15c1 WHIRLPOOL 05477e56231f70a777009a2a4bdc024be4ceec0691de1b36eadf746dadc26755c52215b743c16071ffb0614336443b114c1972c58246568eb41460f635607981 diff --git a/sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild b/sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild new file mode 100644 index 000000000000..ce624e4ae71f --- /dev/null +++ b/sci-chemistry/avogadro/avogadro-1.0.3-r2.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils eutils python-single-r1 + +DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL" +HOMEPAGE="http://avogadro.openmolecules.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~arm ~x86" +IUSE="+glsl python cpu_flags_x86_sse2" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + >=sci-chemistry/openbabel-2.2.3 + >=dev-qt/qtgui-4.5.3:4 + >=dev-qt/qtopengl-4.5.3:4 + x11-libs/gl2ps + glsl? ( >=media-libs/glew-1.5.0:0= ) + python? ( + >=dev-libs/boost-1.35.0-r5[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/sip[${PYTHON_USEDEP}] + ${PYTHON_DEPS} + )" +DEPEND="${RDEPEND} + dev-cpp/eigen:2" + +PATCHES=( + "${FILESDIR}"/1.0.1-gl2ps.patch +) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_configure() { + local mycmakeargs=( + -DENABLE_THREADGL=OFF + -DENABLE_RPATH=OFF + -DENABLE_UPDATE_CHECKER=OFF + -DQT_MKSPECS_DIR="${EPREFIX}/usr/share/qt4/mkspecs" + -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs + $(cmake-utils_use_enable glsl) + $(cmake-utils_use_with cpu_flags_x86_sse2 SSE2) + $(cmake-utils_use_enable python) + ) + + cmake-utils_src_configure +} diff --git a/sci-chemistry/avogadro/avogadro-1.1.0.ebuild b/sci-chemistry/avogadro/avogadro-1.1.0.ebuild new file mode 100644 index 000000000000..ff3a9036301b --- /dev/null +++ b/sci-chemistry/avogadro/avogadro-1.1.0.ebuild @@ -0,0 +1,62 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils eutils python-single-r1 + +DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL" +HOMEPAGE="http://avogadro.openmolecules.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~arm ~x86" +IUSE="+glsl python cpu_flags_x86_sse2 test" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + >=sci-chemistry/openbabel-2.3.0 + >=dev-qt/qtgui-4.5.3:4 + >=dev-qt/qtopengl-4.5.3:4 + x11-libs/gl2ps + glsl? ( >=media-libs/glew-1.5.0:0= ) + python? ( + >=dev-libs/boost-1.35.0-r5[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/sip[${PYTHON_USEDEP}] + ${PYTHON_DEPS} + )" +DEPEND="${RDEPEND} + dev-cpp/eigen:2" + +# https://sourceforge.net/p/avogadro/bugs/653/ +RESTRICT="test" + +PATCHES=( + "${FILESDIR}"/${P}-textrel.patch + "${FILESDIR}"/${P}-xlibs.patch + "${FILESDIR}"/${PN}-1.1.1-openbabel.patch +) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_configure() { + local mycmakeargs=( + -DENABLE_THREADGL=OFF + -DENABLE_RPATH=OFF + -DENABLE_UPDATE_CHECKER=OFF + -DQT_MKSPECS_DIR="${EPREFIX}/usr/share/qt4/mkspecs" + -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs + $(cmake-utils_use_enable glsl) + $(cmake-utils_use_enable test TESTS) + $(cmake-utils_use_with cpu_flags_x86_sse2 SSE2) + $(cmake-utils_use_enable python) + ) + + cmake-utils_src_configure +} diff --git a/sci-chemistry/avogadro/avogadro-1.1.1.ebuild b/sci-chemistry/avogadro/avogadro-1.1.1.ebuild new file mode 100644 index 000000000000..5e9225721e1d --- /dev/null +++ b/sci-chemistry/avogadro/avogadro-1.1.1.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils flag-o-matic python-single-r1 + +DESCRIPTION="Advanced molecular editor that uses Qt4 and OpenGL" +HOMEPAGE="http://avogadro.openmolecules.net/" +SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~arm ~x86" +IUSE="+glsl python cpu_flags_x86_sse2 test" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + >=sci-chemistry/openbabel-2.3.0 + >=dev-qt/qtgui-4.8.5:4 + >=dev-qt/qtopengl-4.8.5:4 + x11-libs/gl2ps + glsl? ( >=media-libs/glew-1.5.0:0= ) + python? ( + >=dev-libs/boost-1.35.0-r5[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/sip[${PYTHON_USEDEP}] + ${PYTHON_DEPS} + )" +DEPEND="${RDEPEND} + virtual/pkgconfig + dev-cpp/eigen" + +# https://sourceforge.net/p/avogadro/bugs/653/ +RESTRICT="test" + +PATCHES=( + #"${FILESDIR}"/${PN}-1.1.0-textrel.patch + "${FILESDIR}"/${PN}-1.1.0-xlibs.patch + "${FILESDIR}"/${P}-eigen3.patch + "${FILESDIR}"/${P}-mkspecs-dir.patch + "${FILESDIR}"/${P}-no-strip.patch + "${FILESDIR}"/${P}-pkgconfig_eigen.patch + "${FILESDIR}"/${P}-openbabel.patch + "${FILESDIR}"/${P}-boost-join-moc.patch +) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_prepare() { + sed \ + -e 's:_BSD_SOURCE:_DEFAULT_SOURCE:g' \ + -i CMakeLists.txt || die + # warning: "Eigen2 support is deprecated in Eigen 3.2.x and it will be removed in Eigen 3.3." + append-cppflags -DEIGEN_NO_EIGEN2_DEPRECATED_WARNING + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DENABLE_THREADEDGL=OFF + -DENABLE_RPATH=OFF + -DENABLE_UPDATE_CHECKER=OFF + -DQT_MKSPECS_DIR="${EPREFIX}/usr/share/qt4/mkspecs" + -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs + -DENABLE_glsl="$(usex glsl)" + -DENABLE_TESTS="$(usex test)" + -DWITH_SSE2="$(usex cpu_flags_x86_sse2)" + -DENABLE_python="$(usex python)" + ) + + cmake-utils_src_configure +} diff --git a/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch b/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch new file mode 100644 index 000000000000..d8a0c0f758e1 --- /dev/null +++ b/sci-chemistry/avogadro/files/1.0.1-gl2ps.patch @@ -0,0 +1,39 @@ +diff --git a/avogadro/src/CMakeLists.txt b/avogadro/src/CMakeLists.txt +index 75b6dfb..d87ac2c 100644 +--- a/avogadro/src/CMakeLists.txt ++++ b/avogadro/src/CMakeLists.txt +@@ -45,7 +45,7 @@ endif(ENABLE_UPDATE_CHECKER) + FILE(GLOB projectDelegates_SRCS "projectdelegates/*.cpp") + set(avogadro_SRCS ${avogadro_SRCS} ${projectDelegates_SRCS}) + # Add GL2PS to the executable +-set(avogadro_SRCS ${avogadro_SRCS} "../gl2ps/gl2ps.c") ++#set(avogadro_SRCS ${avogadro_SRCS} "../gl2ps/gl2ps.c") + + if( WIN32 ) + set(avogadro_SRCS ${avogadro_SRCS} windows/avogadro.rc) +diff --git a/avogadro/src/mainwindow.cpp b/avogadro/src/mainwindow.cpp +index 66785fd..2933953 100644 +--- a/avogadro/src/mainwindow.cpp ++++ b/avogadro/src/mainwindow.cpp +@@ -51,7 +51,7 @@ + //#endif + + // Include the GL2PS header +-#include "../gl2ps/gl2ps.h" ++#include <gl2ps.h> + + #include <avogadro/pluginmanager.h> + +diff --git a/libavogadro/src/CMakeLists.txt b/libavogadro/src/CMakeLists.txt +index cce8ece..cc084fb 100644 +--- a/libavogadro/src/CMakeLists.txt ++++ b/libavogadro/src/CMakeLists.txt +@@ -152,7 +152,7 @@ endforeach(headerFile ${libavogadro_HDRS}) + add_library(avogadro SHARED ${libavogadro_SRCS} ${libavogadro_QM} ${pythontool_RC_SRCS}) + set_target_properties(avogadro + PROPERTIES VERSION ${Avogadro_VERSION_FULL} SOVERSION 1 ) +-target_link_libraries(avogadro ${AVO_LINK_LIBRARIES}) ++target_link_libraries(avogadro ${AVO_LINK_LIBRARIES} gl2ps) + + install(TARGETS avogadro DESTINATION ${LIB_INSTALL_DIR}) + install(FILES ${libavogadro_HDRS} diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch b/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch new file mode 100644 index 000000000000..6d4536ef7c9b --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.0-textrel.patch @@ -0,0 +1,29 @@ + libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt | 2 +- + libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt b/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt +index fb88316..2ddcfdf 100644 +--- a/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt ++++ b/libavogadro/src/extensions/crystallography/spglib/CMakeLists.txt +@@ -20,6 +20,6 @@ add_library(spglib STATIC ${spglib_SRCS}) + set_target_properties(spglib PROPERTIES COMPILE_FLAGS "-w") + + # Set -fPIC on x86_64 +-if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64") ++if("${CMAKE_SYSTEM_PROCESSOR}" MATCHES "^(i.86|x86|x86_64|ppc|ppc64)$") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC" ) + endif() +diff --git a/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt b/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt +index 0cd0c3e..9e89daf 100644 +--- a/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt ++++ b/libavogadro/src/extensions/swcntbuilder/tubegen/CMakeLists.txt +@@ -19,7 +19,7 @@ add_library(tubegen STATIC ${tubegen_SRCS}) + set_target_properties(tubegen PROPERTIES COMPILE_FLAGS "-w") + + # Set -fPIC on x86_64 +-if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64") ++if("${CMAKE_SYSTEM_PROCESSOR}" MATCHES "^(i.86|x86|x86_64|ppc|ppc64)$") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC" ) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC" ) + endif() diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch b/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch new file mode 100644 index 000000000000..74a5889ec8ae --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch @@ -0,0 +1,16 @@ + * Info: Using [gentoo] (https://bugs.gentoo.org/xmlrpc.cgi) + * Info: Getting attachment 403034 + * Info: Viewing attachment: "X11.patch" +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 60ec98f..03443a7 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -225,6 +225,7 @@ set(I18N_LANGUAGE "" CACHE STRING "Build i18n only for selected language") + + find_package(Qt4 4.6.0 REQUIRED) # find and setup Qt4 for this project + find_package(OpenGL REQUIRED) # find and setup OpenGL ++find_package(X11 REQUIRED) + find_package(Linguist) # find and setup Linguist + if(NOT Linguist_FOUND) + message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations") + diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-boost-join-moc.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-boost-join-moc.patch new file mode 100644 index 000000000000..a464fdac42ca --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-boost-join-moc.patch @@ -0,0 +1,78 @@ +Add include guards to all boost includes, as qt's moc trips +over nested BOOST_JOIN macros: +* usr/include/boost/type_traits/detail/has_binary_operator.hp:50: Parse error at "BOOST_JOIN" +* libavogadro/src/CMakeFiles/avogadro.dir/build.make:217: recipe for target 'libavogadro/src/moc_pythonengine_p.cxx' failed +See also: https://bugs.gentoo.org/show_bug.cgi?id=578896 + +--- avogadro-1.1.1/libavogadro/src/pythonengine_p.h ++++ avogadro-1.1.1/libavogadro/src/pythonengine_p.h +@@ -27,7 +27,9 @@ + + #include <avogadro/global.h> + #include <avogadro/engine.h> ++#ifndef Q_MOC_RUN + #include <boost/python.hpp> ++#endif + + namespace Avogadro { + +--- avogadro-1.1.1/libavogadro/src/pythonextension_p.h ++++ avogadro-1.1.1/libavogadro/src/pythonextension_p.h +@@ -29,7 +29,9 @@ + #include <avogadro/extension.h> + #include <avogadro/primitive.h> + #include <avogadro/glwidget.h> ++#ifndef Q_MOC_RUN + #include <boost/python.hpp> ++#endif + + #include <QWidget> + #include <QList> +--- avogadro-1.1.1/libavogadro/src/pythoninterpreter.h ++++ avogadro-1.1.1/libavogadro/src/pythoninterpreter.h +@@ -26,7 +26,9 @@ + #define PYTHONINTERPRETER_H + + #include <avogadro/global.h> ++#ifndef Q_MOC_RUN + #include <boost/python.hpp> ++#endif + #include <avogadro/primitive.h> + #include <QString> + +--- avogadro-1.1.1/libavogadro/src/pythonscript.h ++++ avogadro-1.1.1/libavogadro/src/pythonscript.h +@@ -27,7 +27,9 @@ + #define PYTHONSCRIPT_H + + #include <avogadro/global.h> ++#ifndef Q_MOC_RUN + #include <boost/python.hpp> ++#endif + + #include "pythonerror.h" + +--- avogadro-1.1.1/libavogadro/src/pythonthread_p.h ++++ avogadro-1.1.1/libavogadro/src/pythonthread_p.h +@@ -26,7 +26,9 @@ + #define PYTHONTHREAD_H + + #include <avogadro/global.h> ++#ifndef Q_MOC_RUN + #include <boost/python.hpp> ++#endif + + namespace Avogadro { + +--- avogadro-1.1.1/libavogadro/src/pythontool_p.h ++++ avogadro-1.1.1/libavogadro/src/pythontool_p.h +@@ -27,7 +27,9 @@ + + #include <avogadro/global.h> + #include <avogadro/tool.h> ++#ifndef Q_MOC_RUN + #include <boost/python.hpp> ++#endif + + #include <QObject> + #include <QAction> diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch new file mode 100644 index 000000000000..dc07d6974e12 --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-eigen3.patch @@ -0,0 +1,51 @@ +--- avogadro-1.1.1/CMakeLists.txt.omv~ 2014-01-30 13:58:22.999443609 +0100 ++++ avogadro-1.1.1/CMakeLists.txt 2014-01-30 13:59:31.086106925 +0100 +@@ -230,13 +230,15 @@ if(NOT Linguist_FOUND) + message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations") + endif() + +-find_package(Eigen3) # find and setup Eigen3 if available ++find_package(Eigen3 REQUIRED) # find and setup Eigen3 if available + if(NOT EIGEN3_FOUND) + message(STATUS "Cannot find Eigen3, trying Eigen2") +- find_package(Eigen2 REQUIRED) # Some version is required ++ find_package(Eigen2) # Some version is required + else() + # Use Stage10 Eigen3 support + set (EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API TRUE) ++ add_definitions (-DEIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API) ++ set (EIGEN2_INCLUDE_DIR ${EIGEN3_INCLUDE_DIR}) + endif() + + find_package(ZLIB REQUIRED) +--- avogadro-1.1.1/libavogadro/src/extensions/qtaim/CMakeLists.txt.omv~ 2014-01-30 14:12:33.859401753 +0100 ++++ avogadro-1.1.1/libavogadro/src/extensions/qtaim/CMakeLists.txt 2014-01-30 14:15:07.652727522 +0100 +@@ -4,6 +4,8 @@ set(LINK_LIBS avogadro) + set(PLUGIN_LABEL extensions) + set(PLUGIN_TARGET extensions) + ++add_definitions(-DEIGEN2_SUPPORT_STAGE20_RESOLVE_API_CONFLICTS -std=gnu++11) ++ + set(qtaimextension_SRCS + qtaimextension.cpp + # qtaimdialog.cpp +--- avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt.omv~ 2014-01-30 13:59:05.889441500 +0100 ++++ avogadro-1.1.1/libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt 2014-01-30 13:59:08.832774688 +0100 +@@ -1,5 +1,5 @@ + find_package(Qt4 4.6 REQUIRED) +-find_package(Eigen2 REQUIRED) ++find_package(Eigen3 REQUIRED) + + include_directories(${QT_INCLUDE_DIR} ${EIGEN2_INCLUDE_DIR}) + +--- avogadro-1.1.1/cmake/modules/AvogadroUse.cmake.orig 2014-10-13 20:13:59.909828034 +0100 ++++ avogadro-1.1.1/cmake/modules/AvogadroUse.cmake 2014-10-13 20:15:09.492822908 +0100 +@@ -12,7 +12,7 @@ + + # Add the Avogadro modules directory to the CMake module path + set(CMAKE_MODULE_PATH ${Avogadro_PLUGIN_DIR}/cmake ${CMAKE_MODULE_PATH}) +-find_package(Eigen2 REQUIRED) ++find_package(Eigen3 REQUIRED) + include_directories(${EIGEN2_INCLUDE_DIR}) + if(Avogadro_ENABLE_GLSL) + find_package(GLEW) diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch new file mode 100644 index 000000000000..45c616422efe --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-mkspecs-dir.patch @@ -0,0 +1,12 @@ +diff -up avogadro-1.1.1/CMakeLists.txt.mkspecs-dir avogadro-1.1.1/CMakeLists.txt +--- avogadro-1.1.1/CMakeLists.txt.mkspecs-dir 2014-01-24 23:43:01.618510517 -0600 ++++ avogadro-1.1.1/CMakeLists.txt 2014-01-24 23:44:03.236844746 -0600 +@@ -547,7 +547,7 @@ if(QT_MKSPECS_DIR AND INSTALL_QMAKE_PRF) + # ) + install(FILES + "${CMAKE_CURRENT_BINARY_DIR}/avogadro.prf" +- DESTINATION "${CMAKE_INSTALL_PREFIX}/${QT_MKSPECS_RELATIVE}/features" ++ DESTINATION "${QT_MKSPECS_DIR}/features" + ) + # endif ("${QT_MKSPECS_DIR}" MATCHES ^$"${CMAKE_INSTALL_PREFIX}/") + else() diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch new file mode 100644 index 000000000000..490dd58907df --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-no-strip.patch @@ -0,0 +1,12 @@ +diff -up avogadro-1.1.1/CMakeLists.txt.no-strip avogadro-1.1.1/CMakeLists.txt +--- avogadro-1.1.1/CMakeLists.txt.no-strip 2014-01-24 23:14:44.473840038 -0600 ++++ avogadro-1.1.1/CMakeLists.txt 2014-01-24 23:15:46.869166459 -0600 +@@ -114,7 +114,7 @@ if (CMAKE_COMPILER_IS_GNUCXX) + endif() + # Set up additional build flags for particular build types. These will be added to CMAKE_CXX_FLAGS, + # they will not replace them. +- set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s") ++ set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG -DQT_NO_DEBUG_OUTPUT") + set(CMAKE_CXX_FLAGS_RELWITHDEBINFO + "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} ${CMAKE_CXX_FLAGS_WARN}") + set(CMAKE_CXX_FLAGS_DEBUG "-g3 -fno-inline ${CMAKE_CXX_FLAGS_WARN}") diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-openbabel.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-openbabel.patch new file mode 100644 index 000000000000..4bdc6b2e780e --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-openbabel.patch @@ -0,0 +1,16 @@ + libavogadro/src/python/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/libavogadro/src/python/CMakeLists.txt b/libavogadro/src/python/CMakeLists.txt +index efb518a..1a3d91a 100644 +--- a/libavogadro/src/python/CMakeLists.txt ++++ b/libavogadro/src/python/CMakeLists.txt +@@ -21,7 +21,7 @@ if (WIN32) + target_link_libraries(python-module avogadro ${PYTHON_LIBRARIES}) + else() + target_link_libraries(python-module stdc++ avogadro +- ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${Boost_LIBRARIES}) ++ ${QT_LIBRARIES} ${PYTHON_LIBRARIES} ${Boost_LIBRARIES} ${OPENBABEL2_LIBRARIES}) + endif() + + # Let's try to use this instead: diff --git a/sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch b/sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch new file mode 100644 index 000000000000..93dbe2ff4ecc --- /dev/null +++ b/sci-chemistry/avogadro/files/avogadro-1.1.1-pkgconfig_eigen.patch @@ -0,0 +1,8 @@ +diff -up avogadro-1.1.1/avogadro.pc.in.eigen avogadro-1.1.1/avogadro.pc.in +--- avogadro-1.1.1/avogadro.pc.in.eigen 2013-12-06 09:50:04.000000000 -0600 ++++ avogadro-1.1.1/avogadro.pc.in 2014-01-25 00:37:45.732007852 -0600 +@@ -9,3 +9,4 @@ Description: Avogadro libraries + Version: @Avogadro_VERSION_FULL@ + Libs: -L${libdir} -lavogadro + Cflags: -I${pkgincludedir} ++Requires.private: eigen3 diff --git a/sci-chemistry/avogadro/metadata.xml b/sci-chemistry/avogadro/metadata.xml new file mode 100644 index 000000000000..152f2bd72abd --- /dev/null +++ b/sci-chemistry/avogadro/metadata.xml @@ -0,0 +1,20 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> + Avogadro is an advanced molecular editor designed for cross-platform use in + computational chemistry, molecular modeling, bioinformatics, materials + science, and related areas. It offers flexible rendering and a powerful + plugin architecture. + </longdescription> + <use> + <flag name="glsl">Enable glsl features via GLEW.</flag> + </use> + <upstream> + <remote-id type="sourceforge">avogadro</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/avogadro2/Manifest b/sci-chemistry/avogadro2/Manifest new file mode 100644 index 000000000000..6efded77282d --- /dev/null +++ b/sci-chemistry/avogadro2/Manifest @@ -0,0 +1,4 @@ +DIST avogadro2-0.9.0.tar.gz 1096442 SHA256 3af7faf0cc534953f40f4d77d9a5b6bdf1699d8c8bce9fb72834aaef10deddd1 SHA512 bc780b1f45822ffc6cef82cf5fbe04cfbab035e553037959965eb0cad2c3f87e53bc71a574c7154cae5909377c74d14708550070c1794bdd5d83d738846b03ba WHIRLPOOL a7633bec714f1decc339d8a9a131f047b733fc2e30d80f2ed9ff904b89e03091bed4c242452e222e441ecbea02fe95c06a6ef9faed354a565b1a89d9d00bc049 +EBUILD avogadro2-0.9.0.ebuild 1031 SHA256 023a3dad1c42e5296d171999076238a74716f090bdc776c401b5e687597d3216 SHA512 3290929eca3db226824837533d8e0da2e13bc9aa8b7c4ae449aed7ebca743b2b669cb1cc3151a9df47ee30b932b149bd6b55ff4bf2e7e2d5934f1a10dca9a922 WHIRLPOOL d7f804fafd34ca3ea5922cf2228cca80917f24790b7478566fd648dc1dd979631bddc057a5e2b74ee41011d9bc9d8a32e45dec822651541442d68ca11ead0e43 +MISC ChangeLog 1026 SHA256 3c8db792334cd406419dae2b685545166fd78615c4c9887bb8a43a1181a7a0fb SHA512 ab891ae86f9cf5f1e204a77d473aab10b367aca6429feda8a36d7c36fbc941197b208fc1a531f00e3272b79b6f4cae9024008525116c0909ab813f4a3ed2fa07 WHIRLPOOL 7987e0897e91a7b224d7e2a9611f2e76bf0a7618d64c6658c93fb4529e303bd36a70680ffd5302ea2491ba810f31d6673676e3d1f28cc8debfa7f5ea23eeac2e +MISC metadata.xml 513 SHA256 9e6f9634c6d9822d535f6954d69103d926a962de400af784325f630baa67ac2b SHA512 4209c0681f7055b240f1054a10d58d5c22dca467903096ab1f5eb1b8cf276990f694b2033b4e9b4e4838cce65dd7c7660633079764248f394e32ece0048f09a0 WHIRLPOOL de9405700e679a5d7a9aba646e93fd4173c200fe8339eb881ad8ad351904c16c2c32814436aa6e4ee820d7c599f3cd61500777c096de861aa90f2d0fbbdf0f16 diff --git a/sci-chemistry/avogadro2/avogadro2-0.9.0.ebuild b/sci-chemistry/avogadro2/avogadro2-0.9.0.ebuild new file mode 100644 index 000000000000..201fc77dace6 --- /dev/null +++ b/sci-chemistry/avogadro2/avogadro2-0.9.0.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils + +MY_PN=avogadroapp +MY_P=${MY_PN}-${PV} + +DESCRIPTION="Advanced molecule editor and visualizer 2" +HOMEPAGE="http://www.openchemistry.org/" +SRC_URI="https://github.com/OpenChemistry/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="BSD GPL-2+" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc rpc test vtk" + +RDEPEND=" + dev-qt/qtcore:5 + dev-qt/qtgui:5 + dev-qt/qtopengl:5 + dev-qt/qtwidgets:5 + ~sci-libs/avogadrolibs-${PV}[qt5,opengl] + sci-libs/hdf5:= + rpc? ( sci-chemistry/molequeue ) +" +DEPEND="${DEPEND} + dev-cpp/eigen:3 + test? ( dev-qt/qttest:5 ) +" + +RESTRICT=test + +S="${WORKDIR}"/${MY_P} + +src_prepare() { + cmake-utils_src_prepare + sed '/COPYING/d' -i CMakeLists.txt || die +} + +src_configure() { + local mycmakeargs=( + -DBUILD_DOCUMENTATION=$(usex doc) + -DAvogadro_ENABLE_RPC=$(usex rpc) + -DENABLE_TESTING=$(usex test) + -DUSE_VTK=$(usex vtk) + ) + cmake-utils_src_configure +} diff --git a/sci-chemistry/avogadro2/metadata.xml b/sci-chemistry/avogadro2/metadata.xml new file mode 100644 index 000000000000..a43fe21628c8 --- /dev/null +++ b/sci-chemistry/avogadro2/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="rpc">Enable RPC server</flag> + <flag name="vtk">include vtk support</flag> + </use> + <upstream> + <remote-id type="github">OpenChemistry/avogadroapp</remote-id> + <remote-id type="sourceforge">avogadro</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/azara/Manifest b/sci-chemistry/azara/Manifest new file mode 100644 index 000000000000..d356c0818ea0 --- /dev/null +++ b/sci-chemistry/azara/Manifest @@ -0,0 +1,9 @@ +AUX 2.8-64bit.patch 2919 SHA256 857d4200ab3f59c535e620a577788995dec5aa889cdf73582d6bee374a9df50d SHA512 f2c42875f7c4aaa2110376fae252e53feb19e82c003ce44f9ba4df0c6bff1e0bcf0d55c91faf3480831c7a8c0b868ea29cb59b209aa4d747513b8d20db2a3b7f WHIRLPOOL 50c819365068948d2699bc0cc42e4f46d68a14b8fa977caaee90574fb61079cc82fbeeec3075db0bd17fe83d5697310e6a121b7781c3a45fe191ad6d79d6a6b3 +AUX 2.8-impl-dec.patch 5172 SHA256 a99cd51a1cdbc010760bb35ffc5f74c0f70ce10c874e4392f0e1dffc5559b410 SHA512 31dd75bb75427a37691cdacd2caee10ec5ee540daef52131eaf7102ec13f06101649a6bfbe6ee47503ef02986816a3c957b19cdb1308ea7c90ce1c22a02b6d05 WHIRLPOOL 8bec275ab95472d84dcbb91ebcb4972dc32bce633639c2e679a44c3ce04b03d007472b9a4dea2f419695b0e0b623c9a60ba39e614bce148a152830f8b291a32a +AUX 2.8-prll.patch 8764 SHA256 79a8efb86f1a8162c943a02dae2ba49688648dac07525aec3516fe619e4937ba SHA512 4868cae8d7fe425136728ca751d59a0d8bb2a7906946a004cee1d017ab60f27075199953122bc81873ca4ba4cf462fcef1dfc0b93d748da966548a3d9f61cd7d WHIRLPOOL 7d43e3ddc42283bca89678a15c1d92ba7860e6ce7e2e53dde8cfd7c446e49cfcb52703ec095f27056656f8298663665ba8eceee319d77b6ca986e912fd828491 +AUX 2.8-python.patch 962 SHA256 74c04c60763f3dc0286fea59f8fe96aa5d83258fab6f9447f91b8ebf4eaac16e SHA512 d3c1aa38a1b783dba82ec571fd8d9bb7d4981f2957e728b91ca42562c453075e351a5805862f11e3d13e2036297c14f58c8f0bc97f128055870b2d47ce89a631 WHIRLPOOL 068ea87c512b6f4f20ac7a121a1041a1b590d288b983cbc5052d5ee45e09fb069d1dfac77f586333b17c305fb8ffcbe4a33812b7e8f6e55f5b0da69d8063d192 +DIST azara-2.8-src.tgz 638120 SHA256 1f9b86d368ca3b4818c88490c40b2055c7a6d1732e746e4c117e045a73269a98 SHA512 61a913b041f8ed7dade9d452ca0d99804ffcea0c678f23ad8357c1e7188996eecde9402201399306fcb32a504b17c3d61997f50ce57794f876c9f8d492ca500c WHIRLPOOL b7512fe29ad97830d2f96811e71c2ab74e9e71c62354f65a499484a1a57fbe8b74a8ecd27a0b72c48cf0ec5bb48c78148433e32f4f2a880c6317d516f3aa644a +EBUILD azara-2.8-r5.ebuild 2108 SHA256 7e24fa7bc15524e7bbdec6aebcafe7271ec1f80138ee35cdb638704590b4f1f9 SHA512 a21a0dda6ce17bf0ee3bf1aee2397ce5a27d65a57b4e5044f13686eec4f1ad49e2758997605717b6e19a88f130f4dbb669819661a7de4491704739dc73b6e394 WHIRLPOOL 170fd4d77c9cd0177054660d047693caf5157d63d75dae3b283bd6107eebac1a1354f5fa4249594bee4aabb4c6ae91da60ee248883772c376ec8448536164f8c +MISC ChangeLog 2719 SHA256 e9269136b67afae7de81f0118f5b89082907db373ccd5bff567c7a27d4baeac3 SHA512 feb77309c136bc0fa444c2a619b9829268175e30dac87c09b2e877bbdad26967813a10e254f886600a8d3cd428370cee6ac7ab60d161b5a0a0569bf3ae641197 WHIRLPOOL efcede0d019666f11808d3cc8171b4ab04c012ec9b44902f6f192b53b187b40b922f3eea29bc25ef5a3e8032117d888f572be6db0bd3bb77b51127f6b7b38e19 +MISC ChangeLog-2015 2827 SHA256 51f112fe10250db9ae0b72aa949a06fda8b3f69caa3d23eb851da28cd117bf73 SHA512 e837eb936918a9e611af6c09448082f12628377b008a73f5842c96fab14eeb2829d322f5f88edc88ff1f68aa7c620a761f2031e717c1964830862c2af8751675 WHIRLPOOL f853a7c94e410a4241e58c52d3a0505fad4ebb544fdaf648c23422443ce77cd8121b2324159c4bf1ae1abd96df11b80d5cff9e924cab10d9a66e0bda1730cfcd +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/azara/azara-2.8-r5.ebuild b/sci-chemistry/azara/azara-2.8-r5.ebuild new file mode 100644 index 000000000000..4403482cf77e --- /dev/null +++ b/sci-chemistry/azara/azara-2.8-r5.ebuild @@ -0,0 +1,100 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils python-r1 toolchain-funcs + +DESCRIPTION="A suite of programmes to process and view NMR data" +HOMEPAGE="http://www.bio.cam.ac.uk/azara/" +SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${PN}/${P}-src.tgz" + +LICENSE="AZARA" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="xpm X" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + x11-libs/libX11 + x11-libs/motif:0 + ${PYTHON_DEPS} + xpm? ( x11-libs/libXpm )" +DEPEND="${RDEPEND}" + +src_prepare() { + cat > ENVIRONMENT <<- EOF + CC=$(tc-getCC) + CFLAGS = ${CFLAGS} + LFLAGS = ${LDFLAGS} + MATH_LIB = -lm + X11_INCLUDE_DIR = -I"${EPREFIX}/usr/X11R6/include" + MOTIF_INCLUDE_DIR = -I"${EPREFIX}/usr/include" -I../global + X11_LIB_DIR = -L"${EPREFIX}/usr/$(get_libdir)" + MOTIF_LIB_DIR = -L"${EPREFIX}/usr/$(get_libdir)" + X11_LIB = -lX11 + MOTIF_LIB = -lXm -lXt + SHARED_FLAGS = -shared + ENDIAN_FLAG = -DBIG_ENDIAN_DATA -DWRITE_ENDIAN_PAR + PIC = -fPIC + EOF + + use xpm && echo "XPMUSE=\"XPM_FLAG=-DUSE_XPM XPM_LIB=-lXpm\"" >> ENVIRONMENT + + epatch \ + "${FILESDIR}"/${PV}-prll.patch \ + "${FILESDIR}"/${PV}-impl-dec.patch \ + "${FILESDIR}"/${PV}-python.patch \ + "${FILESDIR}"/${PV}-64bit.patch +} + +src_compile() { + local mymake + local makeflags + + mymake="${mymake} help nongui" + use X && mymake="${mymake} gui" + + emake ${mymake} + + compilation() { + python_export PYTHON_CFLAGS PYTHON_LIBS + cd "${BUILD_DIR}" || die + emake DataRows_clean + emake \ + PYTHON_INCLUDE_DIR="${PYTHON_CFLAGS}" \ + PYTHON_LIB="${PYTHON_LIBS}" \ + DataRows + } + python_copy_sources + python_foreach_impl compilation +} + +src_install() { + rm bin/pythonAzara || die + if ! use X; then + rm bin/plot* || die + fi + + dodoc CHANGES* README* + dohtml -r html/* + + cd bin || die + dobin ${PN} + rm ${PN} || die + for bin in *; do + newbin ${bin} ${bin}-${PN} + done + + installation() { + cd "${BUILD_DIR}" || die + python_domodule lib/DataRows.so + } + python_foreach_impl installation +} + +pkg_postinst() { + einfo "Due to collision we moved all binary to *-${PN}" +} diff --git a/sci-chemistry/azara/files/2.8-64bit.patch b/sci-chemistry/azara/files/2.8-64bit.patch new file mode 100644 index 000000000000..c65e075c1d30 --- /dev/null +++ b/sci-chemistry/azara/files/2.8-64bit.patch @@ -0,0 +1,85 @@ +diff --git a/global/par.c b/global/par.c +index ac87c88..fecfe35 100644 +--- a/global/par.c ++++ b/global/par.c +@@ -562,9 +562,9 @@ static Status get_varian_header(FILE *fp, String error_msg) + return OK; + } + +-static long get_varian_long(int offset) ++static int get_varian_int(int offset) + { +- long x; ++ int x; + + if (swapped) + { +@@ -572,7 +572,7 @@ static long get_varian_long(int offset) + SWAP(varian_header[offset+1], varian_header[offset+2], char); + } + +- x = *((long *) (varian_header + offset)); ++ x = *((int *) (varian_header + offset)); + + return x; + } +@@ -591,7 +591,7 @@ static short get_varian_short(int offset) + + static Status check_varian_header(String error_msg) + { +- long nblocks, ntraces, np, ebytes, tbytes, /*bbytes,*/ d; ++ int nblocks, ntraces, np, ebytes, tbytes, /*bbytes,*/ d; + short status; + FILE *fp; + +@@ -605,17 +605,19 @@ static Status check_varian_header(String error_msg) + FCLOSE(fp); + + /* numbers in parentheses are offsets into header */ +- nblocks = get_varian_long(0); /* number of blocks in file */ +- ntraces = get_varian_long(4); /* number of traces per block */ +- np = get_varian_long(8); /* number of elements per trace */ +- ebytes = get_varian_long(12); /* number of bytes per element */ +- tbytes = get_varian_long(16); /* number of bytes per trace */ +- /*bbytes = get_varian_long(20);*/ /* number of bytes per block */ ++ nblocks = get_varian_int(0); /* number of blocks in file */ ++ printf("nblocks = %d\n", nblocks); ++ ntraces = get_varian_int(4); /* number of traces per block */ ++ printf("ntraces = %d\n", ntraces); ++ np = get_varian_int(8); /* number of elements per trace */ ++ ebytes = get_varian_int(12); /* number of bytes per element */ ++ tbytes = get_varian_int(16); /* number of bytes per trace */ ++ /*bbytes = get_varian_int(20);*/ /* number of bytes per block */ + /* short starting at 24 is software version */ + status = get_varian_short(26); /* status of whole file */ + /* long starting at 28 is number of block headers */ + +- if (ntraces != 1L) ++ if (ntraces != 1) + RETURN_ERROR_MSG("can only process Varian data with #traces = 1"); + + if (np != npoints[0]) +@@ -646,12 +648,12 @@ static Status check_varian_header(String error_msg) + + if (integer) + { +- if (ebytes == 2L) ++ if (ebytes == 2) + { + if (status & (1<<2)) + RETURN_ERROR_MSG("Varian header has inconsistent byte information"); + } +- else if (ebytes == 4L) ++ else if (ebytes == 4) + { + if (!(status & (1<<2))) + RETURN_ERROR_MSG("Varian header has inconsistent byte information"); +@@ -666,7 +668,7 @@ static Status check_varian_header(String error_msg) + } + else /* !integer, i.e. floating point */ + { +- if (ebytes != 4L) ++ if (ebytes != 4) + RETURN_ERROR_MSG("Varian header has inconsistent byte information"); + } + diff --git a/sci-chemistry/azara/files/2.8-impl-dec.patch b/sci-chemistry/azara/files/2.8-impl-dec.patch new file mode 100644 index 000000000000..62e8c7d6873b --- /dev/null +++ b/sci-chemistry/azara/files/2.8-impl-dec.patch @@ -0,0 +1,226 @@ +diff --git a/DataRows/data_rows.c b/DataRows/data_rows.c +index 054fa1f..a07eedc 100644 +--- a/DataRows/data_rows.c ++++ b/DataRows/data_rows.c +@@ -1,4 +1,5 @@ + #include "data_rows.h" ++#include "utility.h" + + #include "par.h" + +diff --git a/DataRows/py_data_rows.c b/DataRows/py_data_rows.c +index fc8b3c8..985e6c3 100644 +--- a/DataRows/py_data_rows.c ++++ b/DataRows/py_data_rows.c +@@ -1,4 +1,6 @@ + #include "Python.h" /* Python header files */ ++#include "modsupport.h" ++#include "intobject.h" + + #include "data_rows.h" + +diff --git a/connect/crosspeak.c b/connect/crosspeak.c +index 0de57bf..7b016e1 100644 +--- a/connect/crosspeak.c ++++ b/connect/crosspeak.c +@@ -1,4 +1,5 @@ + #include "crosspeak.h" ++#include "utility.h" + + #include "atom.h" + #include "table.h" +diff --git a/connect/shift.c b/connect/shift.c +index f54ba9f..a880001 100644 +--- a/connect/shift.c ++++ b/connect/shift.c +@@ -1,4 +1,5 @@ + #include "shift.h" ++#include "utility.h" + + #include "atom.h" + #include "table.h" +diff --git a/global/macros.h b/global/macros.h +index 43fc43e..bb1d267 100644 +--- a/global/macros.h ++++ b/global/macros.h +@@ -8,6 +8,7 @@ + #include <math.h> + #include <string.h> + #include <stdlib.h> ++#include <ctype.h> + + #ifdef WIN32 + #include <ctype.h> +diff --git a/global/parser.c b/global/parser.c +index 007d926..0f19575 100644 +--- a/global/parser.c ++++ b/global/parser.c +@@ -1,4 +1,5 @@ + #include "parser.h" ++#include "utility.h" + + #define MAX_NARGS 20 + +diff --git a/peak/fitter.c b/peak/fitter.c +index ba6b175..b58f573 100644 +--- a/peak/fitter.c ++++ b/peak/fitter.c +@@ -1,4 +1,5 @@ + #include "fitter.h" ++#include "data.h" + + #include "nonlinear_model.h" + +diff --git a/peak/peak_fit.c b/peak/peak_fit.c +index 92c69a8..5b9791f 100644 +--- a/peak/peak_fit.c ++++ b/peak/peak_fit.c +@@ -6,6 +6,7 @@ + #include "output.h" + #include "ref.h" + #include "script_fit.h" ++#include "fitter.h" + + #define MEGAWORD (1024 * 1024) + #define DEFAULT_STORE (2 * MEGAWORD) +diff --git a/plot1/draw.c b/plot1/draw.c +index 4fdce96..a2a2e8a 100644 +--- a/plot1/draw.c ++++ b/plot1/draw.c +@@ -1,4 +1,5 @@ + #include "draw.h" ++#include "ticks.h" + + #include "color.h" + #include "data.h" +diff --git a/plot1/object.c b/plot1/object.c +index 973897c..e043a53 100644 +--- a/plot1/object.c ++++ b/plot1/object.c +@@ -1,4 +1,5 @@ + #include "object.h" ++#include "script.h" + + #include "color.h" + #include "parser.h" +diff --git a/plot1/output_popup.c b/plot1/output_popup.c +index 0794584..e73976e 100644 +--- a/plot1/output_popup.c ++++ b/plot1/output_popup.c +@@ -1,4 +1,5 @@ + #include "output_popup.h" ++#include "script.h" + + #include "output.hlp" + +diff --git a/plot1/plots.c b/plot1/plots.c +index 3790f5b..7ac58df 100644 +--- a/plot1/plots.c ++++ b/plot1/plots.c +@@ -1,4 +1,5 @@ + #include "plots.h" ++#include "script.h" + + #include "data.h" + #include "input.h" +diff --git a/plot1/region_popup.c b/plot1/region_popup.c +index 68b3930..f049d29 100644 +--- a/plot1/region_popup.c ++++ b/plot1/region_popup.c +@@ -1,4 +1,5 @@ + #include "region_popup.h" ++#include "data.h" + + #include "region.hlp" + +diff --git a/plot2/data_popup.c b/plot2/data_popup.c +index 851b1d4..1c9026e 100644 +--- a/plot2/data_popup.c ++++ b/plot2/data_popup.c +@@ -1,4 +1,5 @@ + #include "data_popup.h" ++#include "rowcol_popup.h" + + #include "data.hlp" + +diff --git a/plot2/extract_popup.c b/plot2/extract_popup.c +index 416aab0..a7fcbf3 100644 +--- a/plot2/extract_popup.c ++++ b/plot2/extract_popup.c +@@ -1,4 +1,5 @@ + #include "extract_popup.h" ++#include "script.h" + + #include "extract.hlp" + +diff --git a/plot2/levels_popup.c b/plot2/levels_popup.c +index 197cf2c..e1ac22c 100644 +--- a/plot2/levels_popup.c ++++ b/plot2/levels_popup.c +@@ -1,4 +1,5 @@ + #include "levels_popup.h" ++#include "levels_func.h" + + #include "levels.hlp" + +diff --git a/plot2/plot2.c b/plot2/plot2.c +index 9ca91c3..0c10d5a 100644 +--- a/plot2/plot2.c ++++ b/plot2/plot2.c +@@ -1,4 +1,6 @@ + #include "plot2.h" ++#include "object_popup.h" ++#include "prop_popup.h" + + #include "baseline_popup.h" + #include "callback.h" +diff --git a/plot2/rowcol_popup.c b/plot2/rowcol_popup.c +index e9f4843..6c50426 100644 +--- a/plot2/rowcol_popup.c ++++ b/plot2/rowcol_popup.c +@@ -1,4 +1,5 @@ + #include "rowcol_popup.h" ++#include "ref_popup.h" + + #include "rowcol.hlp" + +diff --git a/plot2/script.c b/plot2/script.c +index 2f55182..d7d886f 100644 +--- a/plot2/script.c ++++ b/plot2/script.c +@@ -1,4 +1,5 @@ + #include "script.h" ++#include "macros.h" + + #include "param.h" + #include "stack.h" +diff --git a/plot2/slice_popup.c b/plot2/slice_popup.c +index b601834..1b1e686 100644 +--- a/plot2/slice_popup.c ++++ b/plot2/slice_popup.c +@@ -1,4 +1,5 @@ + #include "slice_popup.h" ++#include "rowcol_func.h" + + #include "baseline.h" + #include "baseline_popup.h" +diff --git a/process/files.c b/process/files.c +index e09127e..d95d681 100644 +--- a/process/files.c ++++ b/process/files.c +@@ -1,4 +1,5 @@ + #include "files.h" ++#include "macros.h" + + #include <sys/types.h> + #include <sys/stat.h> +diff --git a/project/project.c b/project/project.c +index 92b70e3..a3e6d94 100644 +--- a/project/project.c ++++ b/project/project.c +@@ -1,4 +1,5 @@ + #include "project.h" ++#include "utility.h" + + #include "block.h" + #include "par.h" diff --git a/sci-chemistry/azara/files/2.8-prll.patch b/sci-chemistry/azara/files/2.8-prll.patch new file mode 100644 index 000000000000..4720bb659445 --- /dev/null +++ b/sci-chemistry/azara/files/2.8-prll.patch @@ -0,0 +1,387 @@ +diff --git a/DataRows/makefile b/DataRows/makefile +index 587e710..4e0a312 100644 +--- a/DataRows/makefile ++++ b/DataRows/makefile +@@ -28,7 +28,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-DataRows.so: locals globals ++DataRows.so: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) $(SHARED_FLAGS) -o $@ $(CFLAGS) $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) +diff --git a/azara/makefile b/azara/makefile +index 3ba0cd9..f7b4ce5 100644 +--- a/azara/makefile ++++ b/azara/makefile +@@ -12,7 +12,7 @@ LOCAL_OBJS = \ + GLOBAL_OBJS = \ + $(GLOBAL_DIR)/help.o + +-azara: locals globals ++azara: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/combine/makefile b/combine/makefile +index a855236..7a83d8f 100644 +--- a/combine/makefile ++++ b/combine/makefile +@@ -20,7 +20,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-combine: locals globals ++combine: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/connect/makefile b/connect/makefile +index d75e7da..d238507 100644 +--- a/connect/makefile ++++ b/connect/makefile +@@ -23,7 +23,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-connect: locals globals ++connect: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/contours/makefile b/contours/makefile +index 5b832b8..49175dd 100644 +--- a/contours/makefile ++++ b/contours/makefile +@@ -19,7 +19,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-contours: locals globals ++contours: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/deflate/makefile b/deflate/makefile +index 4c4e02e..42d5c30 100644 +--- a/deflate/makefile ++++ b/deflate/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-deflate: locals globals ++deflate: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/extract/makefile b/extract/makefile +index 3212cb9..fed874b 100644 +--- a/extract/makefile ++++ b/extract/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-extract: locals globals ++extract: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/global/makefile b/global/makefile +index 364fa41..5272a31 100644 +--- a/global/makefile ++++ b/global/makefile +@@ -42,6 +42,31 @@ LINPACK_OBJS = \ + AZARA_OBJS = \ + help.o + ++all: \ ++ azara_objects \ ++ decay_objects \ ++ simulate_objects \ ++ viewer_objects \ ++ components_objects \ ++ shuffle_objects \ ++ connect_objects \ ++ slides_objects \ ++ peak_find_objects \ ++ peak_fit_objects \ ++ plot1_objects \ ++ reflate_objects \ ++ deflate_objects \ ++ combine_objects \ ++ unblock_objects \ ++ extract_objects \ ++ project_objects \ ++ contours_objects \ ++ plot2_nog_objects \ ++ plot2_objects \ ++ process_objects \ ++ python_objects \ ++ integrate_objects ++ + azara_objects: $(AZARA_OBJS) + + DECAY_OBJS = \ +diff --git a/help/makefile b/help/makefile +index 9e99a7c..59a86a3 100644 +--- a/help/makefile ++++ b/help/makefile +@@ -39,7 +39,7 @@ globals: + + .c.o:; $(CC) -c $(CFLAGS) $< + +-hlp: ++hlp: txt2hlp + $(TXT2HLP) azara + $(TXT2HLP) combine + $(TXT2HLP) connect +@@ -78,7 +78,7 @@ hlp: + $(TXT2HLP) plot1/text + $(TXT2HLP) DataRows + +-html: ++html: txt2html + $(TXT2HTML) azara + $(TXT2HTML) combine + $(TXT2HTML) connect +diff --git a/makefile b/makefile +index 9965b07..f4383af 100644 +--- a/makefile ++++ b/makefile +@@ -14,7 +14,7 @@ all: help nongui DataRows gui + help: \ + help_program + +-nongui: \ ++nongui: help \ + process_program \ + plot2_nog_program \ + peak_program \ +@@ -29,63 +29,66 @@ nongui: \ + connect_program \ + azara_program + +-gui: \ ++gui: help \ + plot2_program \ + plot1_program + +-DataRows: \ ++DataRows: help \ + DataRows + +-process_program: +- cd process; $(MAKE) ++global: ++ $(MAKE) -C global + +-plot2_program: +- cd plot2; $(MAKE) plot2 ++process_program: global ++ $(MAKE) -C process + +-plot2_nog_program: +- cd plot2; $(MAKE) plot2_nog ++plot2_program: global ++ $(MAKE) -C plot2 + +-plot1_program: +- cd plot1; $(MAKE) ++plot2_nog_program: global ++ $(MAKE) -C plot2 plot2_nog + +-peak_program: +- cd peak; $(MAKE) ++plot1_program: global ++ $(MAKE) -C plot1 + +-extract_program: +- cd extract; $(MAKE) ++peak_program: global process_program ++ $(MAKE) -C peak + +-project_program: +- cd project; $(MAKE) ++extract_program: global ++ $(MAKE) -C extract + +-unblock_program: +- cd unblock; $(MAKE) ++project_program: global ++ $(MAKE) -C project + +-contours_program: +- cd contours; $(MAKE) ++unblock_program: global ++ $(MAKE) -C unblock + +-combine_program: +- cd combine; $(MAKE) ++contours_program: global ++ $(MAKE) -C contours + +-deflate_program: +- cd deflate; $(MAKE) ++combine_program: global ++ $(MAKE) -C combine + +-reflate_program: +- cd reflate; $(MAKE) ++deflate_program: global ++ $(MAKE) -C deflate + +-utility_program: +- cd utility; $(MAKE) ++reflate_program: global ++ $(MAKE) -C reflate + +-connect_program: +- cd connect; $(MAKE) ++utility_program: global ++ $(MAKE) -C utility + +-help_program: +- cd help; $(MAKE) ++connect_program: global ++ $(MAKE) -C connect + +-azara_program: +- cd azara; $(MAKE) ++help_program: global ++ $(MAKE) -C help + +-DataRows: +- cd DataRows; $(MAKE) ++azara_program: global ++ $(MAKE) -C azara ++ ++DataRows: global ++ $(MAKE) -C DataRows + + clean: \ + global_clean \ +@@ -227,3 +230,5 @@ azara_realclean: + DataRows_realclean: + cd DataRows; $(MAKE) realclean + ++ ++.PHONY: global process_program +diff --git a/peak/makefile b/peak/makefile +index f3c13b7..4211221 100644 +--- a/peak/makefile ++++ b/peak/makefile +@@ -97,13 +97,13 @@ COMMAND_OBJS = \ + + all: peak_find peak_fit + +-peak_find: local_find global_find ++peak_find: $(LOCAL_FIND_OBJS) $(GLOBAL_FIND_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_FIND_OBJS) \ + $(GLOBAL_FIND_OBJS) \ + $(LIB) $(MATH_LIB) + +-peak_fit: local_fit global_fit commands ++peak_fit: $(LOCAL_FIT_OBJS) $(GLOBAL_FIT_OBJS) $(COMMAND_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_FIT_OBJS) \ + $(GLOBAL_FIT_OBJS) \ +diff --git a/plot1/makefile b/plot1/makefile +index d1dce2d..e729443 100644 +--- a/plot1/makefile ++++ b/plot1/makefile +@@ -95,7 +95,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/utility.o \ + $(GLOBAL_DIR)/window.o + +-plot1: locals globals ++plot1: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +@@ -110,7 +110,7 @@ locals: + globals: + cd $(GLOBAL_DIR); $(MAKE) plot1_objects + +-.c.o:; $(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) $< ++.c.o:; $(CC) $(X11_INCLUDE_DIR) $(MOTIF_INCLUDE_DIR) -c $(CFLAGS) -I../plot2 $< + + clean: + rm -f *.o +diff --git a/plot2/makefile b/plot2/makefile +index a6b7b4a..98e286e 100644 +--- a/plot2/makefile ++++ b/plot2/makefile +@@ -129,7 +129,7 @@ GLOBAL_PLOT2_NOG_OBJS = \ + + all: plot2 plot2_nog + +-plot2: local_plot2 global_plot2 ++plot2: $(LOCAL_PLOT2_OBJS) $(GLOBAL_PLOT2_OBJS) + $(CC) -o $@ $(CFLAGS) $(LFLAGS) \ + $(LOCAL_PLOT2_OBJS) \ + $(GLOBAL_PLOT2_OBJS) \ +@@ -137,7 +137,7 @@ plot2: local_plot2 global_plot2 + $(LIB) $(MATH_LIB) \ + $(MOTIF_LIB) $(X11_LIB) $(XPM_LIB) + +-plot2_nog: local_plot2_nog global_plot2_nog ++plot2_nog: $(LOCAL_PLOT2_NOG_OBJS) $(GLOBAL_PLOT2_NOG_OBJS) + $(CC) -o $@ $(CFLAGS) $(LFLAGS) \ + $(LOCAL_PLOT2_NOG_OBJS) \ + $(GLOBAL_PLOT2_NOG_OBJS) \ +diff --git a/process/makefile b/process/makefile +index 22ceeed..72d587b 100644 +--- a/process/makefile ++++ b/process/makefile +@@ -72,7 +72,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/utility.o \ + $(LINPACK_OBJS) + +-process: locals globals ++process: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/project/makefile b/project/makefile +index 78143fc..ed0f296 100644 +--- a/project/makefile ++++ b/project/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-project: locals globals ++project: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/reflate/makefile b/reflate/makefile +index 079a3fc..01ec311 100644 +--- a/reflate/makefile ++++ b/reflate/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-reflate: locals globals ++reflate: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ +diff --git a/unblock/makefile b/unblock/makefile +index 510dc9e..d9a0f2b 100644 +--- a/unblock/makefile ++++ b/unblock/makefile +@@ -18,7 +18,7 @@ GLOBAL_OBJS = \ + $(GLOBAL_DIR)/ref.o \ + $(GLOBAL_DIR)/utility.o + +-unblock: locals globals ++unblock: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) -o $@ $(LFLAGS) \ + $(LOCAL_OBJS) \ + $(GLOBAL_OBJS) \ diff --git a/sci-chemistry/azara/files/2.8-python.patch b/sci-chemistry/azara/files/2.8-python.patch new file mode 100644 index 000000000000..9834c77a77dc --- /dev/null +++ b/sci-chemistry/azara/files/2.8-python.patch @@ -0,0 +1,44 @@ +diff --git a/DataRows/makefile b/DataRows/makefile +index 4e0a312..ce261ab 100644 +--- a/DataRows/makefile ++++ b/DataRows/makefile +@@ -22,16 +22,17 @@ LOCAL_OBJS = \ + data_rows.o + + GLOBAL_OBJS = \ +- $(GLOBAL_DIR)/block_io.o \ +- $(GLOBAL_DIR)/par.o \ +- $(GLOBAL_DIR)/parse.o \ +- $(GLOBAL_DIR)/ref.o \ +- $(GLOBAL_DIR)/utility.o ++ block_io.o \ ++ par.o \ ++ parse.o \ ++ ref.o \ ++ utility.o + + DataRows.so: $(LOCAL_OBJS) $(GLOBAL_OBJS) + $(CC) $(SHARED_FLAGS) -o $@ $(CFLAGS) $(LFLAGS) \ + $(LOCAL_OBJS) \ +- $(GLOBAL_OBJS) ++ $(GLOBAL_OBJS) \ ++ $(PYTHON_LIB) + + local_objects: $(LOCAL_OBJS) + +@@ -42,9 +43,13 @@ globals: + cd $(GLOBAL_DIR); $(MAKE) python_objects + + py_data_rows.o: py_data_rows.c +- $(CC) -c $(CFLAGS) $(PYTHON_INCLUDE_DIR) $< ++ $(CC) -c $(CFLAGS) $(PIC) $(PYTHON_INCLUDE_DIR) $< + +-.c.o:; $(CC) -c $(CFLAGS) $< ++data_rows.o: data_rows.c ++ $(CC) -c $(CFLAGS) $(PIC) $< ++ ++%.o: $(GLOBAL_DIR)/%.c ++ $(CC) -c $(CFLAGS) $(PIC) $< + + clean: + rm -f *.o diff --git a/sci-chemistry/azara/metadata.xml b/sci-chemistry/azara/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/azara/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/ball/Manifest b/sci-chemistry/ball/Manifest new file mode 100644 index 000000000000..9e17eba2056c --- /dev/null +++ b/sci-chemistry/ball/Manifest @@ -0,0 +1,15 @@ +AUX ball-1.4.1-BondOrder.xml.patch 1675 SHA256 8aaecb9dc1bc729a0446c350b423b47779b8d82a3b00f570a55e4b4f0b7b02c3 SHA512 77e04209bebff5057ad549d1c1d7b638391fb063efb8635a72b46287a4c4975c2d0940267bce9002f3c9dc0f6fab7e21a3099506f57a44e0a325149ee134b2e0 WHIRLPOOL db3ecb2587e607f8257348d9e6dc558e2795807fd8c62e3fecf82bb426b54d18efba510c2b8990dd6fd74781b048be1e69373678977f723c11ed6624ad774d78 +AUX ball-1.4.1-missing-signed.patch 985 SHA256 5bdeb4613e775e83bf219661f0e494f7556322aac7af3b4dfab593203c6dea7b SHA512 ea50bbceb38e80416e4f49a247816ccaf1318c45676669388f681eca5be525b5ed6d472c1b20afe37d3d95ae5334d90831269c77bce922207b515e8c5a46f20a WHIRLPOOL d6311ba93396e7b4dceb3cdf39d35d736fc8c87f52309d258673f71244903f860199c0cab55cbda81fadf11b82e60361e82c737871e2632c1c5006bdac929b10 +AUX ball-1.4.1-multilib.patch 1585 SHA256 ee246df89ca6f1559df359fb6af93462fda9c93fa8a81977f6a5b92190d6ceb5 SHA512 5eebfdce5fba25967c252d0c83f6187079efc55c9481045d6c9e111930e1bb2bed31666b913eb12f46a723aa875559b54f658460efd7be10bbbe4c7cd2982341 WHIRLPOOL f4240a867e4ae503f49bffb986e8bd8a69e1914d6e770e7ae7cb7c03efd23eec3fa095c837e5874785ec4b6bf326c9fec15e16c746f48b89d9afe173f19eb0df +AUX ball-1.4.2-Fix-compilation-of-sipModularWidget.patch 1565 SHA256 3644269518b8444d08de7348f799ba0dedaf644d84c89a55afefdfb64822dfff SHA512 15cc7b8583b5dfcefa152dac0fcf300ad2369f147dc4bb4061fd06586eea403a67442389b2eecca93144b02f73c0eb252794604b87348e63dddcaa03d2775882 WHIRLPOOL e184f70ec3d06e2ef1dc918f0b6e7390b01ce9695ec6bc6cb2ee8f9a637657d18fe74c34ef240d4f721e3d4d74953c9f6d080da7af3d41286d681ef83107e49d +AUX ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch 1011 SHA256 7231441f971d95ec4845cd899d1d9c3c5c6adedc91156a312c1c76d6d8a096c0 SHA512 f99d0b42b6798b0f97aeb93f9aedf9dfd68c62f948dabab4cc1e7b6a4251b10ec8b4e109936f86456f77b1faecad5eff05bb40200d55490c7f82787b3f6951a1 WHIRLPOOL b54bfc73d6b4f674a7c3830ba142a9e55a13c5775d8174ea24c47759299f00b590df958e9213be892be103064e62f7e095ef543429c2a92884c1468f1660bd9c +AUX ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch 1470 SHA256 be30e8dba38a385d53604c887436bae090aaae46bed97d87b02dd12083f8c19e SHA512 18cd445e4867878f73d74afef1ae74d02bb3a118fdeb379beb2463cef501a79eacfa9c5d487fa2656993f652cc0a7432c7d139a2df101416cc6d7139dc4af034 WHIRLPOOL 5a35d821789ddebe11d45f99866e052d345972d43193888346fbb5cf036288655a92d46c6b8d82291ba4ac6d3f8a57b350a5a71412ecd90b3ea1b4fcca00cbdb +AUX ball-1.4.2-fix-python-bindings.patch 643 SHA256 e922d2bbe70da2d7a4c52848c5d54462c2fcdcd85d2c6633758ed3cdc108ac78 SHA512 af1d61a2f4b6b1a0e567e0257e575ffe75f62bb0d0a49379bc08861d0c5bb9dee458a254966a88ecb62eefcd3c6fbb9426b734265627bf7a936111df0f7e61ef WHIRLPOOL 63c37700908f41c3ffa798bdf4af3ea570d65c0bfda4a1d0fd38d44218908dd5d6c0b37073654cb457aa18cc5948781c067ffce362e471a93eb9ede4575f48f4 +AUX ball-1.4.2-std-namespace-isnan.patch 716 SHA256 ca00219aad60b5581c8d6398e93d3a325068a38e6ca7bfbd599c666d94b010da SHA512 2fb87783e7d97d12c4841e9e475eb8d99c2a20b0e162f37394182236a6c1ca3c24c0193110671c296dbb2ae244aab720680b17b0862c3da54ab65061f49be9d2 WHIRLPOOL 2985085ba1066a274abd389030263a0f66ba52cb41b08f4665517d016f07420fc352181be4c5ae9fca8ae21221d14f24591da8bf6598a9187aa950360303f4d5 +AUX ball-1.4.2-struct-swap-attribute.patch 1997 SHA256 d1b561edddcd15d6130dc272448dcfef9737f8854b736b2ee0d5877f372cd8de SHA512 a8b7e2eaf094a97008fb69030549a4c4bb2eabaf3d06ee5191ae5512c3af73198f88c26dca5e0b63cc19d9e3b1e21c323494017f81339b4a30caf1ae8f0f98f0 WHIRLPOOL c7b8f780746207b873021e467be4690da373da5beca4ef67d49256e78616b3ce217912881440bc0533b6a07af75278a1ecca0418c03fad3f5aecb0ed9a806298 +AUX ball-1.4.2-underlinking.patch 665 SHA256 634613f8f820f6b25e6a3f914b4d0c963a7253ba72d95bd21bef8f355a552c2d SHA512 b122e4f6e87be39642355869a42730263ec9d5e66d9887af5e2c4040eef4fce1306a57b106731bba8136197eecc3f72ca99b863aead70f89825ae6724268c688 WHIRLPOOL a519d166b62775b3760395992564e2848c76fab949eca45f19ef4b3f7f35ab0d82b455cd2c74307c80e3664235a11ad36fe991622ac54a28258de8356cb1a111 +DIST BALL-1.4.2.tar.xz 16080664 SHA256 053931b2e050d7d5bceaa21ad3617a1ad0af00f94de56076ce02d544383cbf91 SHA512 c719af4ef2dc1076818d59b72350b704fbffea06bd44737519fb50d88da113ea509333d407f2330aa59bf1c4e6b81adfd3d28e05459f66d7c9707f8d85db7a87 WHIRLPOOL ba7ae340833ea5703d047a9dbc0ce50d9b9dc2b0047a0c6d9f9a17946956c684a09e0860f25c7214a2aa0adee9beb1d01eac38b0ab08259a2934f97cbef91379 +EBUILD ball-1.4.2-r2.ebuild 2037 SHA256 c5218b0291adce02ed4195d81dc83b087014b26d8ff297c1bb90b2252be2c0f6 SHA512 81f51cdb2e6d7d988aa7f180bf506804d8eb76e2e8a5a297ed50068afc536ece9b42b381123b1bfddc2f69c315aa3cbdba4fe7b60912d82907c0f5ed6ae02479 WHIRLPOOL a737d1ba8627f201d9c6d96b99f4020557a6de7ffcaccd499c6626324ecc8c6a47fab2268874f11c67b2d4345523dacdd59f66ecc869c70d60d36766a1163a9c +MISC ChangeLog 3477 SHA256 5e0f4466c72c5783d50b6d30507447420d48ef7d92189765a1ca8f0fa575665b SHA512 83a16a4b125e367df6b1d2495a0f8c6f4a002e303b118e3220d16ee347be22240879070cd6e002d03a9567b778fbfd8c9f3ea4449924bb551d53eb9a8407184c WHIRLPOOL 5501f254ce7dcfba461fb04af335035ae50c49eed87f51261d4c581bb360224bc2cf02063eb7d391f6e987a4d0e7e3012d1d68ef49637cd54ab7f203f8ea5a57 +MISC ChangeLog-2015 3655 SHA256 9cd762f20a05231449c99a932e893c038f1a68c7fa3700398d2bb0eb4722d3c2 SHA512 4846b75ed695e81b9cb3f4795d8d817ea7dcaa2a2a5c0772f95a13a26c11c58326c2a6742508f72f8268ac923679a240d15da7340a8fc9e1e24a052ea75ec8e1 WHIRLPOOL 382e9c74992e878360d3a492ea9af6fae0a5442b42868fb6e0c2b48919d9cf96c47786d06d6b9ffd14d03a1a050892903f1ebb47580ee8374f30a95c8d2a16f6 +MISC metadata.xml 1431 SHA256 b61214d60e181d3094c9a22de31bf43ce1da55924a624cb9f956fbe037343c21 SHA512 c12eaa309bc4e2f6fb51415b943144974a23a92e0705dd7368e402c1be7244485b66bf2d1f0dc11a6b2b673be7189b2543b999924e5ecb94ca00ec9bd1ba32b2 WHIRLPOOL 39d3dbe2c48625c785c327999b7e20c7493e4021b50ef2230263f64651e8f6737efc3fed731aa81901cfdcc36f75c618030735b76ab2b278894b54b36f8d9290 diff --git a/sci-chemistry/ball/ball-1.4.2-r2.ebuild b/sci-chemistry/ball/ball-1.4.2-r2.ebuild new file mode 100644 index 000000000000..89c96a194b67 --- /dev/null +++ b/sci-chemistry/ball/ball-1.4.2-r2.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils python-single-r1 + +DESCRIPTION="Biochemical Algorithms Library" +HOMEPAGE="http://www.ball-project.org/" +SRC_URI="http://www.ball-project.org/Downloads/v${PV}/BALL-${PV}.tar.xz" + +SLOT="0" +LICENSE="LGPL-2 GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cuda mpi +python sql test +threads" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + dev-cpp/eigen:3 + dev-libs/boost:= + dev-qt/qtcore:4 + dev-qt/qtgui:4 + dev-qt/qtopengl:4 + dev-qt/qttest:4 + media-libs/glew:0 + sci-libs/fftw:3.0[threads?] + sci-libs/gsl + sci-libs/libsvm + sci-mathematics/lpsolve + virtual/opengl + x11-libs/libX11 + cuda? ( dev-util/nvidia-cuda-toolkit ) + mpi? ( virtual/mpi ) + python? ( ${PYTHON_DEPS} ) + sql? ( dev-qt/qtsql:4 )" +DEPEND="${RDEPEND} + dev-python/sip + sys-devel/bison + virtual/yacc" + +S="${WORKDIR}"/BALL-${PV} + +PATCHES=( + "${FILESDIR}"/${PN}-1.4.1-multilib.patch + "${FILESDIR}"/${PN}-1.4.1-missing-signed.patch + "${FILESDIR}"/${P}-PDBFile-Fix-compilation-with-gcc-4.8.patch + "${FILESDIR}"/${P}-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch + "${FILESDIR}"/${PN}-1.4.1-BondOrder.xml.patch + "${FILESDIR}"/${P}-Fix-compilation-of-sipModularWidget.patch + "${FILESDIR}"/${P}-underlinking.patch + "${FILESDIR}"/${P}-fix-python-bindings.patch + "${FILESDIR}"/${P}-std-namespace-isnan.patch + "${FILESDIR}"/${P}-struct-swap-attribute.patch +) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_configure() { + local mycmakeargs=( + -DUSE_FFTW_THREADS=$(usex threads) + -DMT_ENABLE_CUDA=$(usex cuda) + -DMT_ENABLE_MPI=$(usex mpi) + -DBALL_HAS_QTSQL=$(usex sql) + -DBALL_PYTHON_SUPPORT=$(usex python) + ) + cmake-utils_src_configure + + local i + for i in "${S}"/data/*; do + ln -sf "${i}" "${BUILD_DIR}"/source/TEST/ || die + ln -sf "${i}" "${S}"/source/TEST/ || die + done +} + +src_compile() { + cmake-utils_src_compile + use test && cmake-utils_src_make build_tests +} diff --git a/sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch b/sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch new file mode 100644 index 000000000000..51e592806999 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch @@ -0,0 +1,30 @@ + source/STRUCTURE/assignBondOrderProcessor.C | 2 +- + source/TEST/AssignBondOrderProcessor_test.C | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/source/STRUCTURE/assignBondOrderProcessor.C b/source/STRUCTURE/assignBondOrderProcessor.C +index f8acc4f..035fffc 100644 +--- a/source/STRUCTURE/assignBondOrderProcessor.C ++++ b/source/STRUCTURE/assignBondOrderProcessor.C +@@ -100,7 +100,7 @@ namespace BALL + const bool AssignBondOrderProcessor::Default::KEKULIZE_RINGS = true; + + const char* AssignBondOrderProcessor::Option::INIFile = "iniFile"; +- const String AssignBondOrderProcessor::Default::INIFile = "/bond_lengths/BondOrder.xml"; ++ const String AssignBondOrderProcessor::Default::INIFile = "bond_lengths/BondOrder.xml"; + + const char* AssignBondOrderProcessor::Option::MAX_BOND_ORDER = "max_bond_order"; + const int AssignBondOrderProcessor::Default::MAX_BOND_ORDER = 3; +diff --git a/source/TEST/AssignBondOrderProcessor_test.C b/source/TEST/AssignBondOrderProcessor_test.C +index 6dfafcc..3405ef5 100644 +--- a/source/TEST/AssignBondOrderProcessor_test.C ++++ b/source/TEST/AssignBondOrderProcessor_test.C +@@ -1834,7 +1834,7 @@ CHECK(Option::INIFile) + // There is really not much we can test here, so we just execute the processor + // to have a chance of catching bugs with valgrind if they sneak in + AssignBondOrderProcessor abop; +- abop.options.set(AssignBondOrderProcessor::Option::INIFile, "/bond_lengths/BondOrderGAFF.xml"); ++ abop.options.set(AssignBondOrderProcessor::Option::INIFile, "bond_lengths/BondOrderGAFF.xml"); + + System sys40; + MOL2File mol40(BALL_TEST_DATA_PATH(AssignBondOrderProcessor_test_C4_input.mol2), std::ios::in); diff --git a/sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch b/sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch new file mode 100644 index 000000000000..6868871b3dc4 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch @@ -0,0 +1,26 @@ +Index: ball/include/BALL/DATATYPE/hashGrid.h +=================================================================== +--- ball.orig/include/BALL/DATATYPE/hashGrid.h 2011-12-09 13:49:26.000000000 +0100 ++++ ball/include/BALL/DATATYPE/hashGrid.h 2011-12-09 13:51:09.000000000 +0100 +@@ -37,7 +37,7 @@ + { + namespace __private + { +- extern const char BALL_EXPORT neighbour_table_[27][3]; ++ extern const signed char BALL_EXPORT neighbour_table_[27][3]; + } + + template <typename Item> class HashGrid3; +Index: ball/source/DATATYPE/hashGrid.C +=================================================================== +--- ball.orig/source/DATATYPE/hashGrid.C 2011-12-09 13:49:26.000000000 +0100 ++++ ball/source/DATATYPE/hashGrid.C 2011-12-09 13:50:49.000000000 +0100 +@@ -9,7 +9,7 @@ + { + namespace __private + { +- const char neighbour_table_[27][3] = ++ const signed char neighbour_table_[27][3] = + { + { 0, 0, 0 }, { 0, 0, -1 }, { 0, 0, 1 }, + { 0, -1, -1 }, { 0, -1, 0 }, { 0, -1, 1 }, diff --git a/sci-chemistry/ball/files/ball-1.4.1-multilib.patch b/sci-chemistry/ball/files/ball-1.4.1-multilib.patch new file mode 100644 index 000000000000..317c4029c678 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.1-multilib.patch @@ -0,0 +1,39 @@ +From 5b8f4e58b4e54bcdfa6f287e01f91d9dfd4e5a14 Mon Sep 17 00:00:00 2001 +From: Justin Lecher <jlec@gentoo.org> +Date: Sun, 25 Mar 2012 14:12:21 +0200 +Subject: [PATCH] Correct path for multilib installation. + +Libraries should go into lib64 not lib on native 64bit. Therefore we can use the LIBDIR detected by cmake. +--- + CMakeLists.txt | 8 ++++---- + 1 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 940ebf4..7eb3db4 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -426,8 +426,8 @@ SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/bin") + ## These variables are used in all install-targets + IF (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + SET(BALL_RUNTIME_INSTALL_DIRECTORY "bin") +- SET(BALL_LIBRARY_INSTALL_DIRECTORY "lib") +- SET(BALL_ARCHIVE_INSTALL_DIRECTORY "lib") ++ SET(BALL_LIBRARY_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) ++ SET(BALL_ARCHIVE_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) + SET(BALL_HEADER_INSTALL_DIRECTORY ".") + SET(BALL_DATA_INSTALL_DIRECTORY "share/BALL") + SET(BALL_DOCUMENTATION_INSTALL_DIRECTORY "share/BALL/doc") +@@ -435,8 +435,8 @@ IF (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + SET(BALL_PYTHON_INSTALL_DIRECTORY "bin") + SET(BALL_PLUGIN_INSTALL_DIRECTORY "bin") + ELSE() +- SET(BALL_PYTHON_INSTALL_DIRECTORY "lib") +- SET(BALL_PLUGIN_INSTALL_DIRECTORY "lib") ++ SET(BALL_PYTHON_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) ++ SET(BALL_PLUGIN_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) + ENDIF() + ELSE() + SET(BALL_BUNDLE_INSTALL_DIRECTORY "Applications") +-- +1.7.8.5 + diff --git a/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch b/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch new file mode 100644 index 000000000000..3ec2f6e983a8 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch @@ -0,0 +1,40 @@ +From da49802f8620562f91ac2c947520dccd223ee26b Mon Sep 17 00:00:00 2001 +From: Andreas Hildebrandt <andreas.hildebrandt@uni-mainz.de> +Date: Wed, 15 Jan 2014 17:42:01 +0100 +Subject: [PATCH] Fix compilation of sipModularWidget + +--- + source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip | 10 +++++----- + 1 file changed, 5 insertions(+), 5 deletions(-) + +diff --git a/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip b/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip +index 522b0ed..7b8ba3e 100644 +--- a/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip ++++ b/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip +@@ -22,18 +22,18 @@ class ModularWidget + static Size countInstances(); + static ModularWidget* getInstance(Position); + +- ModularWidget(const char* = "<ModularWidget>") throw(); +- ModularWidget(const ModularWidget&) throw(); ++ ModularWidget(const char* = "<ModularWidget>"); ++ ModularWidget(const ModularWidget&); + ~ModularWidget() throw(); + +- virtual void destroy() throw(); +- virtual void clear() throw(); ++// virtual void destroy(); ++ virtual void clear(); + + static void registerWidget(ModularWidget*) throw(NullPointer); + // virtual void initializeWidget(MainControl&); + // virtual void finalizeWidget(MainControl&); + virtual void checkMenu(MainControl&) throw(); +-// virtual void initializePreferencesTab(Preferences&) throw(); ++// virtual void initializePreferencesTab(Preferences&); + // virtual void finalizePreferencesTab(Preferences&) throw(); + virtual void applyPreferences() throw(); + virtual void fetchPreferences(INIFile&) throw(); +-- +1.9.1 + diff --git a/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch b/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch new file mode 100644 index 000000000000..f6b8ff45fa7f --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch @@ -0,0 +1,28 @@ +From e7cc50705bed20e160bd4b637b23f57270f580a8 Mon Sep 17 00:00:00 2001 +From: Daniel Stoeckel <dstoeckel@bioinf.uni-sb.de> +Date: Sat, 6 Apr 2013 01:06:55 +0200 +Subject: [PATCH] PDBFile:Fix compilation with gcc 4.8 + +Apparently the automatic conversion from boost::shared_ptr<CrystalInfo> +to boost::shared_ptr<PersistentObject> is no longer supported. +Just change the type of the pointer and work around this issue. +--- + source/FORMAT/PDBFileDetails.C | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/source/FORMAT/PDBFileDetails.C b/source/FORMAT/PDBFileDetails.C +index 97c2572..aedc5db 100644 +--- a/source/FORMAT/PDBFileDetails.C ++++ b/source/FORMAT/PDBFileDetails.C +@@ -901,7 +901,7 @@ namespace BALL + { + if (!(current_protein_->hasProperty("CRYSTALINFO"))) + { +- boost::shared_ptr<CrystalInfo> temp_ptr(new CrystalInfo()); ++ boost::shared_ptr<PersistentObject> temp_ptr(new CrystalInfo()); + current_protein_->setProperty(NamedProperty("CRYSTALINFO", temp_ptr)); + } + +-- +1.9.1 + diff --git a/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch b/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch new file mode 100644 index 000000000000..615a92290805 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch @@ -0,0 +1,44 @@ +From 1e76c9cb1920e9176b725269985c7eb43126d188 Mon Sep 17 00:00:00 2001 +From: Luis de la Garza <delagarza@informatik.uni-tuebingen.de> +Date: Fri, 22 Nov 2013 15:18:55 +0100 +Subject: [PATCH] QT4_EXTRACT_OPTIONS CMake macro changed in CMake 2.8.12; + fixed BALLMacros.cmake + +--- + cmake/BALLMacros.cmake | 14 ++++++++++---- + 1 file changed, 10 insertions(+), 4 deletions(-) + +diff --git a/cmake/BALLMacros.cmake b/cmake/BALLMacros.cmake +index f81ab89..0ac1b87 100644 +--- a/cmake/BALLMacros.cmake ++++ b/cmake/BALLMacros.cmake +@@ -6,16 +6,22 @@ + ### minor modifications (marked with ## BALL ###) + ### + MACRO(QT4_WRAP_UI_BALL outfiles ) +- QT4_EXTRACT_OPTIONS(ui_files ui_options ${ARGN}) +- +- ### BALL ### ++ # since 2.8.12 qt4_extract_options has an additional argument ++ # copied fix from OpenMS ++ IF(${CMAKE_VERSION} VERSION_LESS "2.8.12") ++ QT4_EXTRACT_OPTIONS(ui_files ui_options ${ARGN}) ++ ELSE() ++ QT4_EXTRACT_OPTIONS(ui_files ui_options ui_target ${ARGN}) ++ ENDIF() ++ ++ ### BALL ### + # create output directory (will not exist for out-of-source builds) + FILE(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/include/BALL/VIEW/UIC/) + + FOREACH (it ${ui_files}) + GET_FILENAME_COMPONENT(outfile ${it} NAME_WE) + GET_FILENAME_COMPONENT(infile ${it} ABSOLUTE) +- ### BALL ### ++ ### BALL ### + SET(outfile ${PROJECT_BINARY_DIR}/include/BALL/VIEW/UIC/ui_${outfile}.h) + ADD_CUSTOM_COMMAND(OUTPUT ${outfile} + COMMAND ${QT_UIC_EXECUTABLE} +-- +1.9.1 + diff --git a/sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch b/sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch new file mode 100644 index 000000000000..a13ea2f36ec0 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch @@ -0,0 +1,22 @@ +From 38a955ad9588817073a330c79d4b4476afcf69d5 Mon Sep 17 00:00:00 2001 +From: Daniel Stoeckel <dstoeckel@bioinf.uni-sb.de> +Date: Thu, 14 Apr 2016 19:30:04 +0200 +Subject: [PATCH] Fix Python bindings for Box + +--- + source/PYTHON/EXTENSIONS/VIEW/box.sip | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/source/PYTHON/EXTENSIONS/VIEW/box.sip b/source/PYTHON/EXTENSIONS/VIEW/box.sip +index 341b1a4..592765e 100644 +--- a/source/PYTHON/EXTENSIONS/VIEW/box.sip ++++ b/source/PYTHON/EXTENSIONS/VIEW/box.sip +@@ -6,7 +6,7 @@ + + class Box + : GeometricObject, +- Vertex2 ++ Box3 + { + %TypeHeaderCode + #include <BALL/VIEW/PRIMITIVES/box.h> diff --git a/sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch b/sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch new file mode 100644 index 000000000000..cea6377b6a20 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch @@ -0,0 +1,16 @@ +Fix C++11 changes to isnan(): +* /var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/source/MOLMEC/MINIMIZATION/shiftedLVMM.C:769:46: required from here +* /var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/include/BALL/MATHS/common.h:175:18: error: ‘isnan’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] +* return (isnan(t) != 0); + +--- BALL-1.4.2/include/BALL/MATHS/common.h ++++ BALL-1.4.2/include/BALL/MATHS/common.h +@@ -172,7 +172,7 @@ + #elif defined(BALL_OS_DARWIN) + return ( __inline_isnand(t) != 0); + #else +- return (isnan(t) != 0); ++ return (std::isnan(t) != 0); + #endif + } + diff --git a/sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch b/sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch new file mode 100644 index 000000000000..da334915f410 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch @@ -0,0 +1,80 @@ +Silence warning pollution due to misplaced attributes: +* /var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/include/BALL/COMMON/logStream.h:165:22: note: attribute for ‘struct BALL::LogStreamBuf::StreamStruct’ must follow the ‘struct’ keyword + +--- BALL-1.4.2/include/BALL/COMMON/logStream.h ++++ BALL-1.4.2/include/BALL/COMMON/logStream.h +@@ -162,7 +162,7 @@ + virtual int overflow(int c = -1); + //@} + +- BALL_EXPORT struct StreamStruct ++ struct BALL_EXPORT StreamStruct + { + std::ostream* stream; + string prefix; +--- BALL-1.4.2/include/BALL/FORMAT/MOL2File.h ++++ BALL-1.4.2/include/BALL/FORMAT/MOL2File.h +@@ -33,7 +33,7 @@ + public: + + /// A class used for storing TRIPOS sets +- BALL_EXPORT struct SetStruct ++ struct BALL_EXPORT SetStruct + { + String name; + bool is_static; +@@ -136,7 +136,7 @@ + + bool containsAtomChilds_(AtomContainerConstIterator& frag_it); + +- BALL_EXPORT struct AtomStruct ++ struct BALL_EXPORT AtomStruct + { + String name; + Vector3 position; +@@ -146,14 +146,14 @@ + float charge; + }; + +- BALL_EXPORT struct BondStruct ++ struct BALL_EXPORT BondStruct + { + Position atom1; + Position atom2; + String type; + }; + +- BALL_EXPORT struct MoleculeStruct ++ struct BALL_EXPORT MoleculeStruct + { + String name; + Size number_of_atoms; +@@ -166,7 +166,7 @@ + String comment; + }; + +- BALL_EXPORT struct SubstructureStruct ++ struct BALL_EXPORT SubstructureStruct + { + String name; + Size root_atom; +@@ -178,7 +178,7 @@ + String comment; + }; + +- BALL_EXPORT struct CommentStruct ++ struct BALL_EXPORT CommentStruct + { + String name; + String value; +--- BALL-1.4.2/include/BALL/FORMAT/MOLFile.h ++++ BALL-1.4.2/include/BALL/FORMAT/MOLFile.h +@@ -41,7 +41,7 @@ + @see PropertyManager::setProperty + @see PropertyManager::getProperty + */ +- BALL_EXPORT struct Property ++ struct BALL_EXPORT Property + { + /// + static const String ATOM_MASS_DIFFERENCE; diff --git a/sci-chemistry/ball/files/ball-1.4.2-underlinking.patch b/sci-chemistry/ball/files/ball-1.4.2-underlinking.patch new file mode 100644 index 000000000000..825f41978c13 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-underlinking.patch @@ -0,0 +1,16 @@ + source/APPLICATIONS/BALLVIEW/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/source/APPLICATIONS/BALLVIEW/CMakeLists.txt b/source/APPLICATIONS/BALLVIEW/CMakeLists.txt +index 6d16212..f94ce76 100644 +--- a/source/APPLICATIONS/BALLVIEW/CMakeLists.txt ++++ b/source/APPLICATIONS/BALLVIEW/CMakeLists.txt +@@ -85,7 +85,7 @@ IF (UNIX) + LIST(APPEND BALLVIEW_SUPPORT_LIBRARIES "pthread") + ENDIF () + +-TARGET_LINK_LIBRARIES(BALLView BALL VIEW ${BALLVIEW_SUPPORT_LIBRARIES}) ++TARGET_LINK_LIBRARIES(BALLView BALL VIEW ${BALLVIEW_SUPPORT_LIBRARIES} X11) + + #Setup the translations + INCLUDE(${CMAKE_SOURCE_DIR}/cmake/BALLViewTranslations.cmake) diff --git a/sci-chemistry/ball/metadata.xml b/sci-chemistry/ball/metadata.xml new file mode 100644 index 000000000000..72d683b18460 --- /dev/null +++ b/sci-chemistry/ball/metadata.xml @@ -0,0 +1,31 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +Rapid Software Prototyping can significantly reduce development times in the +field of Computational Molecular Biology and Molecular Modeling. +BALL (Biochemical Algorithms Library) is an application framework in C++ that +has been specifically designed for this purpose. It provides an extensive set +of data structures as well as classes for Molecular Mechanics, advanced +solvation methods, comparison and analysis of protein structures, file +import/export, and visualization . + +BALL has been carefully designed to be robust, easy to use, and open to +extensions. Especially its extensibility which results from an object-oriented +and generic programming approach distinguishes it from other software packages. +BALL is well suited to serve as a public repository for reliable data +structures and algorithms. + +Based on BALL we have developed a stand-alone tool for molecular visualization, +BALLView . BALLView makes the broad functionality available through an +integrated user-friendly GUI. +</longdescription> + <use> + <flag name="sql">Include SQL database support</flag> + <flag name="cuda">Include cuda support</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/bkchem/Manifest b/sci-chemistry/bkchem/Manifest new file mode 100644 index 000000000000..6d2432b89d1d --- /dev/null +++ b/sci-chemistry/bkchem/Manifest @@ -0,0 +1,6 @@ +AUX bkchem-0.14.0_pre2-nolauncher.patch 2967 SHA256 91f95fedb29a3d6be3581a2aa056dc961176af0296d2fdbd1c0d0ba28e321312 SHA512 dbd7b8eef583c3b64dfc1755a3b5eae5eb8ab222454936636147de64e021166e29f915655f1acf2d7252983bf4873dc8f2fb69ca58b56955ab1ce07e8ec82789 WHIRLPOOL 2f4c410a30d08d7d7bb472a97afaa5969046e164098b1a9bd6cca03de0dd622e9ee9c150f2cc3b05cff4e4a2d9a63d6bb9b1f5503d012f7b4172ee2da708b35a +DIST bkchem-0.14.0-pre2.tar.gz 998916 SHA256 65b93128932959b394eff8e5a8018a19b30d26ee1ae44345e8bb87167303ed26 SHA512 7fc3bbd7bfe27bc91cf69a98c347a3fb92f4ea25b45a13debd0646a6b02d7a40c5729ae1b2a9ac33c1049d6b90e38355c3cd80e06660a0a2fcc5dafb3514ef20 WHIRLPOOL 732bc45913248aa3df5929933f2072d09d90a46cdc3b3e22f1849adf391d7fd62704e71a98e24649bd74e1ebe96b30d7d398dadabffc0fcd114d8c13922241c6 +EBUILD bkchem-0.14.0_pre2-r1.ebuild 892 SHA256 9de4a30312a4b763f3508bbd6bfbeb4d374f5873f0ea15a2a955fa3483b8162e SHA512 32b82b62e7b190595a2a28cd2e7ae76d55d9cddd13646a01d472808eb75d6edd89dc3828794f8c070199b6d77461d4e4911bda69aea3ff03339219ba3313962b WHIRLPOOL be05f521c005505b50d404206f2daf041170d66d41ffc6c2c4d1e72f7018fec22a51601b3c2fc109bef1d53d82977272c606ecc716795ec54059d59bd1aab948 +MISC ChangeLog 2683 SHA256 c71c3912adfe474ef74a6e517e9000c224df212712260ff8c5f844e23dc08161 SHA512 ee9900aa765475b17b8e77f0b987fa497ebc7c4f78b082588edd6191fd3b63d2ef846da6a73f7881db0b1696a5bef5f5c0b4564b2b3e8ceb283b72f0ff01d34f WHIRLPOOL dda78e54e38bde0eb86de2d432313e26493c1ffadce523a4a01da52b306e1ac13d8c61e293ec9324e0593b14dc9ff48356356ed810b2f44fc9a0d5095c8f8f1a +MISC ChangeLog-2015 1485 SHA256 900b36366bc55b134110ccee4b046df0cfb9e12175b8f4f50a22eb42964d82a9 SHA512 ff44c6d6b8702cab41b44ad5300aa199fe9c7a383372fa28c44f0ee2e6949e8867e1263f98696afe504a925df700c9d72a571ce0a1d893eab72b836469398261 WHIRLPOOL a53a5e234f143cccd36493f881e94f4ed27f09a7e2883a2c4029c3c0077778539389591c3c4718627698a1bfaabd5ef4e02b9d338ff3db7e0377fdf6cbaab1da +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/bkchem/bkchem-0.14.0_pre2-r1.ebuild b/sci-chemistry/bkchem/bkchem-0.14.0_pre2-r1.ebuild new file mode 100644 index 000000000000..35fa24221e61 --- /dev/null +++ b/sci-chemistry/bkchem/bkchem-0.14.0_pre2-r1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +PYTHON_REQ_USE="tk" + +inherit distutils-r1 eutils versionator + +MY_P="${PN}-$(replace_version_separator 3 -)" + +DESCRIPTION="Chemical drawing program" +HOMEPAGE="http://bkchem.zirael.org/" +SRC_URI="http://bkchem.zirael.org/download/${MY_P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~x86" +LICENSE="GPL-2" +IUSE="cairo" + +DEPEND="cairo? ( dev-python/pycairo[svg,${PYTHON_USEDEP}] )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/${MY_P} + +PATCHES=( + "${FILESDIR}"/${P}-nolauncher.patch +) + +python_install() { + distutils-r1_python_install "--strip=${ED}/_${EPYTHON}" +} + +python_install_all() { + distutils-r1_python_install_all + python_foreach_impl python_newscript ${PN}/${PN}.py ${PN} + make_desktop_entry bkchem BKChem "${EPREFIX}"/usr/share/${PN}/images/${PN}.png Science +} diff --git a/sci-chemistry/bkchem/files/bkchem-0.14.0_pre2-nolauncher.patch b/sci-chemistry/bkchem/files/bkchem-0.14.0_pre2-nolauncher.patch new file mode 100644 index 000000000000..202c47a9c74f --- /dev/null +++ b/sci-chemistry/bkchem/files/bkchem-0.14.0_pre2-nolauncher.patch @@ -0,0 +1,106 @@ + bkchem/bkchem.py | 24 +++++++++++++----------- + setup.py | 23 ----------------------- + 2 files changed, 13 insertions(+), 34 deletions(-) + +diff --git a/bkchem/bkchem.py b/bkchem/bkchem.py +index b336b9c..bcb68b0 100644 +--- a/bkchem/bkchem.py ++++ b/bkchem/bkchem.py +@@ -1,3 +1,4 @@ ++#!/usr/bin/env python2 + #-------------------------------------------------------------------------- + # This file is part of BKChem - a chemical drawing program + # Copyright (C) 2002-2009 Beda Kosata <beda@zirael.org> +@@ -18,18 +19,19 @@ + #-------------------------------------------------------------------------- + + +-"""this is just a starter of the application""" ++#"""this is just a starter of the application""" + + ## support for loading from outside of bkchem dir + +-import os_support, sys ++from bkchem import os_support ++import sys + sys.path.insert( 1, os_support.get_module_path()) + + + ### now starting for real + +-from singleton_store import Store +-import pref_manager ++from bkchem.singleton_store import Store ++from bkchem import pref_manager + + # at first preference manager + Store.pm = pref_manager.pref_manager( +@@ -78,13 +80,13 @@ else: + + + +-import config ++from bkchem import config + + if not config.debug: + # checking of important modules availability + # import modules +- import import_checker +- import messages ++ from bkchem import import_checker ++ from bkchem import messages + + # we need sets from the 2.3 version + if not import_checker.python_version_ok: +@@ -103,16 +105,16 @@ if not config.debug: + + + #import Tkinter +-from main import BKChem +-from splash import Splash +-from singleton_store import Store ++from bkchem.main import BKChem ++from bkchem.splash import Splash ++from bkchem.singleton_store import Store + + myapp = BKChem() + myapp.withdraw() + + if __name__ == '__main__': + +- import messages ++ from bkchem import messages + enc = sys.getfilesystemencoding() + if not enc: + enc = sys.getdefaultencoding() +diff --git a/setup.py b/setup.py +index d4b2a21..2319216 100755 +--- a/setup.py ++++ b/setup.py +@@ -91,26 +91,3 @@ if len( sys.argv) > 1 and sys.argv[1] == 'install' and '--help' not in sys.argv: + print "file %s created" % config_name + + +- # the executable +- if not os.path.isdir( bin_dir): +- try: +- os.mkdir( bin_dir) +- except: +- print "ERROR: could not create directory %s" % bin_dir +- sys.exit( 201) +- exec_name = os.path.join( bin_dir, 'bkchem') +- try: +- file = open( exec_name, 'w') +- except: +- print "ERROR: couldn't open the file %s for write" % exec_name +- sys.exit( 201) +- file.write( "#!/bin/sh\n") +- file.write( 'python %s "$@"\n' % strip_path( os.path.join( py_dir, "bkchem", "bkchem.py"))) +- file.close() +- print "file %s created" % exec_name +- try: +- os.chmod( os.path.join( bin_dir, 'bkchem'), 5+5*8+7*8*8) +- except: +- print "ERROR: failed to make %s executable" % exec_name +- sys.exit( 201) +- print "file %s made executable" % exec_name diff --git a/sci-chemistry/bkchem/metadata.xml b/sci-chemistry/bkchem/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/bkchem/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/bodr/Manifest b/sci-chemistry/bodr/Manifest new file mode 100644 index 000000000000..34f1e51092c0 --- /dev/null +++ b/sci-chemistry/bodr/Manifest @@ -0,0 +1,7 @@ +DIST bodr-10.tar.bz2 225671 SHA256 738a0f0e263cdc088581d0a67a0ea16ec586ceb424704d0ff73bdb5da5d4ee81 SHA512 a3e0e7195914938d8824127aa4777c4054c302ef7811d82d1e012d9be5d7a13d7f2225d4216f4a30ae7dbf70eb3b0b38571c3ee0dbe1d97af15f04171dd51bec WHIRLPOOL e61db3427f6f994a1a628eec12c1a41cf8d9cdbd1a16814a267363ffe4fa320f3fb9b03f8188c746899774631dc5d0398830b8d779d225f3317158809c182c3e +DIST bodr-9.tar.bz2 210548 SHA256 a7ed30ecc385ff9fe9b2af84710574ac12febea081b5123db6d6337a4a7a4b60 SHA512 5bcdd682729e11a0bc48f9306262e03fa2a3ca3a805633c2b40d7f94608ce6e2e778cc89ed0c57ec3bf6105c2f759204e158ac6f29c9e6ee3aa37190f8f0d772 WHIRLPOOL 78061c24718a4ce5c5694e369d3c97eb90826b2c3b3f694ba9a0f405173ef0efdc565583373b26c96582c853e1606314ee2c5ab3e5cc8e889c0625358f87291b +EBUILD bodr-10.ebuild 587 SHA256 4cde0599b05674e16ef77cee5a5457f36de92b9c53d2598185b20027a1fcb33f SHA512 076d180852dc5f1e312bb817de7f5642410b6d9006f0fc578ba714c43fefee38abe4810ad9ae536b19ac6637dd4acf64c1fc4b4faf606032d8b13181a453718a WHIRLPOOL e521d199a6d6a4e1d3853a9fad1edd91bf33c7f39afcbb1a0e9515b1680851dcc76ad0e5a1a68213a163b65d6debbebec82e5f1b637ac9c7961176dc0d34383c +EBUILD bodr-9-r1.ebuild 587 SHA256 4cde0599b05674e16ef77cee5a5457f36de92b9c53d2598185b20027a1fcb33f SHA512 076d180852dc5f1e312bb817de7f5642410b6d9006f0fc578ba714c43fefee38abe4810ad9ae536b19ac6637dd4acf64c1fc4b4faf606032d8b13181a453718a WHIRLPOOL e521d199a6d6a4e1d3853a9fad1edd91bf33c7f39afcbb1a0e9515b1680851dcc76ad0e5a1a68213a163b65d6debbebec82e5f1b637ac9c7961176dc0d34383c +MISC ChangeLog 2587 SHA256 917c00a65e9490650dc3b32290b2519d701887fedc85a1c375138df6132dccbf SHA512 b821dc805ee52816307b1a6fdd8090784f979042c3630458da05dfc54f803c5b95b93b31661b75aa5954caa6c65145cf9bf5f81fceeaade433476a008934cd30 WHIRLPOOL 10a215bcb90bf3964b3c87ba877adbe02886cf1fa8749996c913a3297cd51bc5e479fab321a65ab2b69c9adcb3ee783ecaf790d659dd8b95e2500b5b383d2c64 +MISC ChangeLog-2015 1593 SHA256 e7b02e75e2a9d4bfb3eaf8073eb8d1f876674853677da06b5f03127d26def790 SHA512 f9e48c0c7b6d9c9e9906378a21a60f9df799d39085e8cdfe9065c34e592a632a085b9da738f4ecb0a0b59f41bf1648113c91df0b1b6c2c4d5946fd73963174e8 WHIRLPOOL c5e8532e460dcdf6005c44d04de7e8ac6c6a8e899c0446e843eecfb44fbe537fc7518229b37cfe4e722d6d44bfe9b9a87c08077c8d189bc011d60c2d64f42792 +MISC metadata.xml 701 SHA256 0b955004c3ae866273a2aa490bca290219b259a701f3ab6a1ab8f888d3ae4591 SHA512 e1671fa590f0f2abee6c99940ebddf2711abd46637d7b9fe715b74d90d478432ed742a1bb25c540d053cc0bd82e69b8ac298b607852e2e4d3b027d110e13cd6a WHIRLPOOL 879d911825a7e8fc529ed83e6c8b0874d976bbd0363085c65ede368e5d79f57f7a1075ac53f4c5be79f889adb5c6266dd3c925c2ff44217141d5de244048879f diff --git a/sci-chemistry/bodr/bodr-10.ebuild b/sci-chemistry/bodr/bodr-10.ebuild new file mode 100644 index 000000000000..1d5763a1ba8a --- /dev/null +++ b/sci-chemistry/bodr/bodr-10.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +DESCRIPTION="The Blue Obelisk Data Repository listing element and isotope properties" +HOMEPAGE="https://sourceforge.net/projects/bodr" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~ppc-macos" +IUSE="" + +DEPEND="dev-libs/libxslt" +RDEPEND="" + +DOCS=( "THANKS" "AUTHORS" "README" "ChangeLog" ) + +src_prepare(){ + sed -i -e "s/COPYING//g" Makefile.* || die +} + +src_configure() { + econf --docdir="${EPREFIX}"/usr/share/doc/${PF} +} diff --git a/sci-chemistry/bodr/bodr-9-r1.ebuild b/sci-chemistry/bodr/bodr-9-r1.ebuild new file mode 100644 index 000000000000..1d5763a1ba8a --- /dev/null +++ b/sci-chemistry/bodr/bodr-9-r1.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +DESCRIPTION="The Blue Obelisk Data Repository listing element and isotope properties" +HOMEPAGE="https://sourceforge.net/projects/bodr" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~ppc-macos" +IUSE="" + +DEPEND="dev-libs/libxslt" +RDEPEND="" + +DOCS=( "THANKS" "AUTHORS" "README" "ChangeLog" ) + +src_prepare(){ + sed -i -e "s/COPYING//g" Makefile.* || die +} + +src_configure() { + econf --docdir="${EPREFIX}"/usr/share/doc/${PF} +} diff --git a/sci-chemistry/bodr/metadata.xml b/sci-chemistry/bodr/metadata.xml new file mode 100644 index 000000000000..bf2f27772f9b --- /dev/null +++ b/sci-chemistry/bodr/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> + Blue Obelisk Data Repository (BODR) is a shared data repository. It lists + many important chemoinformatics data such as elemental properties, atomic + radii, etc. including references to original literature. Software developers + can use this repository on online webpages or in chemistry software for + free. + </longdescription> + <upstream> + <remote-id type="sourceforge">bodr</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/burrow-owl/Manifest b/sci-chemistry/burrow-owl/Manifest new file mode 100644 index 000000000000..7513256adb22 --- /dev/null +++ b/sci-chemistry/burrow-owl/Manifest @@ -0,0 +1,6 @@ +DIST burrow-demos.tar 80896000 SHA256 f93e957889adab0521c6e3234f117cf984b7bb18ba6641a3edbdd30202db4b96 SHA512 76948846b4bff2f5c0814e41ee1745122580d6e28f8de217edbf42c4530bc64fb093dc9c96e9c0c083098755c525300b563ee1368caa12be791b2bea7015ee6b WHIRLPOOL 88ca227d8e808814187630c9568e927620a0dc4fb0eba4131ab14cae842aa778fda6294b32e8ec0e23224fca3b5a2a65609ed7f97a34691267439a557bfa0c42 +DIST burrow-owl-1.5.1.tar.gz 1408249 SHA256 76a4ab0746b1b945e0177d441f7ced8042063d4ff2c9171343ea20ddc19a9bbb SHA512 38b428c8b40cdca6caabc7ed9d247118dbf67b537afaec3af14909353d6b138fdf98a33dee6241ce5224631e16c4dbce11b9aadcfe01fecf92f1aae692ce71e1 WHIRLPOOL e165b0508b28e03a47c77ee72ea0d2347ef9088fe33df9788935e3ec0906efd511f77eebe27d74ed79a913f420cde015a39faebdc3195edc1d279ac0d607d39b +EBUILD burrow-owl-1.5.1.ebuild 1129 SHA256 3547c40528c0abd7a485a8fd82813e74c9da1e4d1bd78e80e4a5315cc6e4eb8d SHA512 e91387bd3edaf679d6e1cadac56433f6384d1cad657d1bc1ab11775f5c00cd3fcc988764915eddcbdb07b3c0b1042e8f9267f045e10cf57222ca6991e2aae28b WHIRLPOOL 2357a698961b2bebde1da75a5621b0d83b685e12e696998a37e524039cc21da16ea5a5be2ec8b18baf2b05fd07d0b9b4d9f719df90356a23de046e5f29f72f4b +MISC ChangeLog 2532 SHA256 bc9b1bc4172a4e794e1a016f6175756c7de838810f023632c03a5be408670d10 SHA512 a59a79ccf3f7cb58e22f9e87e94e77235935e466c524625e9ab043d5255dac4366159c8caa18dc3e81948c7372e653a6d2e82e5ccd323ef388d7d09f108e6260 WHIRLPOOL 52f41ab7211f68f4695ac2deabcbc8866630f03655d3fb695bd64d98957b7ebb3c6690c40e2adb4eb3e825a8127b4ffd0ad4ff95830240c1a8d1f71ca8e891f9 +MISC ChangeLog-2015 1928 SHA256 aca4321f3b970e322ffea2b9b610a5164f8d1c965e5c897efc7f503851ff2a70 SHA512 d899a0fe9aab8112ff11f2c4a948e70d5a6a312863c4fceff7259a153353dbc2f5b59424b85c5f625801a9abd599c1a43a93d567321858f5f7fcc8bb26ec9ffc WHIRLPOOL 05f5eb4674dfed6feb8a64de5beb149b750d3e517b829f6b481a68c61ddec20d28b08b6212439ca4956c218100cdc688c78e4c305cf29ecf9a9fd1ebfd83a46b +MISC metadata.xml 355 SHA256 9fca14e9f8f4ff6254db6985a1923793876c96869f05572d4bf96b34eb26f4e7 SHA512 1bba5ea159834c137bdc08622bbd89cf895acde6b8ebce0cee6f6b5f2b754b9a5b0b01ccfb89bf6b4b03ec75925c017716773c0fc4807964c38ddad0dce79f50 WHIRLPOOL 26d31b33afaac96e0aaa4763063cb70f5ed3de8cb29d29c52811f6e582787fb7ed28b3e6f958df1ccfd562fd4417f78c03fe2bf57d13dfc9f59d36b562896ecf diff --git a/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild b/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild new file mode 100644 index 000000000000..106ba29bba2e --- /dev/null +++ b/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils virtualx + +DESCRIPTION="Visualize multidimensional nuclear magnetic resonance (NMR) spectra" +HOMEPAGE="http://burrow-owl.sourceforge.net/" +SRC_URI=" + mirror://sourceforge/${PN}/${P}.tar.gz + examples? ( mirror://sourceforge/${PN}/burrow-demos.tar )" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc examples static-libs" + +RDEPEND=" + dev-libs/g-wrap + dev-libs/glib:2 + dev-scheme/guile[networking,regex] + dev-scheme/guile-cairo + dev-scheme/guile-gnome-platform + sci-libs/starparse + x11-libs/gtk+:2" +DEPEND="${RDEPEND} + dev-util/indent + virtual/pkgconfig + doc? ( app-doc/doxygen ) +" + +src_configure() { + local myeconfargs=( + $(use_with doc doxygen doxygen) + ) + autotools-utils_src_configure +} + +src_test () { + cd "${AUTOTOOLS_BUILD_DIR}" || die + virtualmake -C test-suite check +} + +src_install() { + use doc && HTML_DOCS=( "${AUTOTOOLS_BUILD_DIR}/doc/api/html/." ) + autotools-utils_src_install + + use examples && \ + insinto /usr/share/${PN} && \ + doins -r "${WORKDIR}"/burrow-demos/* +} diff --git a/sci-chemistry/burrow-owl/metadata.xml b/sci-chemistry/burrow-owl/metadata.xml new file mode 100644 index 000000000000..776713a5da1a --- /dev/null +++ b/sci-chemistry/burrow-owl/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">burrow-owl</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/cara-bin/Manifest b/sci-chemistry/cara-bin/Manifest new file mode 100644 index 000000000000..e031e2ba670d --- /dev/null +++ b/sci-chemistry/cara-bin/Manifest @@ -0,0 +1,6 @@ +DIST Start1.2.cara.xz 43124 SHA256 c28321b051902bc020ea04a46b33ceb19b1b3d902264956474c90798f2d60d25 SHA512 26874d634491558dc593a0ec32e83d5cfceedc69bbf901f4d25d6b9515b84aebffbf495d1ac34b3664b8b5822954edf62c5b88dcca6bcfcb152715caa88f5f03 WHIRLPOOL 034e8b73354e7244e4fcc21c03da7b99c02019ebef1e0754dd9cb8249fe68b82be1e78db9848912fc48c8625b0f2acf0f41242d83949a117f0b8a648a930445e +DIST cara_1.8.4_linux.gz 6677463 SHA256 5ba34cc8b0782e1791186cde5a02ec036665769df7f5c559db27377b6f3cc6d6 SHA512 e264cfbef640f267132dfd48b940203a319c8f34de71c5b786c6bfc2ab561bdf3fbd79516d619ca52b2aca64a2887f770fabfabedb76433c5f78aa02c65f898f WHIRLPOOL 5619c70bc31dfb328a72233c8fc3e3d8dcfdccc3db4e5a67430f0ebe8a0a474f998abb2a0ec56f4a3c2e6e4b95e324ec3c667864c81cb3531a1e162439c780da +EBUILD cara-bin-1.8.4-r1.ebuild 1183 SHA256 f7c4cd51d7bac15e9b6b86bf65cbd5eddd9036438787b9f3b48ae76fe39f6414 SHA512 410fb11a71f2e6184496c67c62b2fc09b0ecf78c19b3a3c8fc6257b25c093560135fdd959297b654f708724dd05037bc65471f0f725779b4bf28c5b406167731 WHIRLPOOL 1243e15f856ef61e507f82f99d3a1ef83834033fb5af9b73dff6fcd53cd9ef2c32e418f1b88c88a3ba9f6c0e1d28a9225712b140058ece9e99f82bd526f22d27 +MISC ChangeLog 2609 SHA256 ec49f6d9047f8d3e996c57cec34737f4040fb7e0d3ca965ffb58612391c11b7d SHA512 0309c2694499bd9257502239861a7e0fe81e4c87f81530c09fdba022a124e9410d1a19ef5b8317f8253a2828b97907a739b81683357217cf29bb11c94f15feb8 WHIRLPOOL cbe2c4e59da1dedbd84b71449b5ebd6274fe563b4e1d45f1729887a92fa307d3ab6b8e880e50b2c965822c20ea328e56b7ba1a4ac0b53ad915ac0adb7d819c43 +MISC ChangeLog-2015 1858 SHA256 bd5f777f204b61c4ca0002101cdb2228ca4dfd1c2a9c3479601bbef5b38690f4 SHA512 b97f6a4be36f201e4336193038608f8b41eea50ef76c05383de5affee66d568c7ace9f8251ebaecbf3b334843b5c00df4a76c5de48bbc6dd409f380963f2170e WHIRLPOOL 06ac3d523a6c37ff99b37d16aa2c9f0876c1644d22e0b74d879299a010cba1e38adf270ff4c93bc8dc5ce948984d93defb3a1e0bb9c5e55b50520994bf140fd2 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/cara-bin/cara-bin-1.8.4-r1.ebuild b/sci-chemistry/cara-bin/cara-bin-1.8.4-r1.ebuild new file mode 100644 index 000000000000..97142d2b1873 --- /dev/null +++ b/sci-chemistry/cara-bin/cara-bin-1.8.4-r1.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +MY_PN="${PN%%-bin}" +MY_P="${MY_PN}_${PV}" + +DESCRIPTION="Analysis of NMR spectra and Computer Aided Resonance Assignment" +SRC_URI=" + http://www.cara.nmr-software.org/downloads/${MY_P}_linux.gz + https://dev.gentoo.org/~jlec/distfiles//Start1.2.cara.xz" +HOMEPAGE="http://www.nmr.ch" + +LICENSE="CARA" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="lua" + +RDEPEND=" + !prefix? ( + >=media-libs/fontconfig-2.10.92[abi_x86_32(-)] + >=media-libs/freetype-2.5.0.1[abi_x86_32(-)] + >=x11-libs/libICE-1.0.8-r1[abi_x86_32(-)] + >=x11-libs/libSM-1.2.1-r1[abi_x86_32(-)] + >=x11-libs/libX11-1.6.2[abi_x86_32(-)] + >=x11-libs/libXcursor-1.1.14[abi_x86_32(-)] + >=x11-libs/libXext-1.3.2[abi_x86_32(-)] + >=x11-libs/libXi-1.7.2[abi_x86_32(-)] + >=x11-libs/libXrandr-1.4.2[abi_x86_32(-)] + >=x11-libs/libXrender-0.9.8[abi_x86_32(-)] + ) + virtual/libstdc++ + lua? ( dev-lang/lua )" +DEPEND="" + +RESTRICT="mirror" + +QA_PREBUILT="opt/cara/*" + +S="${WORKDIR}" + +src_install() { + exeinto /opt/cara + doexe ${MY_P}_linux + dosym ../cara/${MY_P}_linux /opt/bin/cara + dodoc Start1.2.cara +} diff --git a/sci-chemistry/cara-bin/metadata.xml b/sci-chemistry/cara-bin/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/cara-bin/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest new file mode 100644 index 000000000000..8c09b2a6d39a --- /dev/null +++ b/sci-chemistry/ccpn/Manifest @@ -0,0 +1,24 @@ +AUX 2.3.1-parallel.patch 850 SHA256 38f796a18c75b2ffb1168d22d1e1453faa480e4c8b0e3d75db2b0603ac4d6788 SHA512 0597e21c03baa27e2342249814fc0700b73cf2800173468574ef704d48f7e6e042ac6ae552bbb9e27fd4baca36cfaf60a1eac9813354916b3e8295a35b64dcdf WHIRLPOOL 7fec03d065add264de91aa07c211003e2471e77035f36c497c325c4319e999d83c06ef6f496ebab966d0877c89101e26ec7ce86ea8b740973c0254ad118e3e26 +AUX analysis 283 SHA256 f348aa9c9a5f7f380836b0dc62d8a1c053f69e60a441c7ae4abc45f9d8374a7b SHA512 f2dd8216021201b0f9307f8bb82033c3ebb1c9f21450ae206e59ad6442b0cf0f8fc6e4817d4347eb78a9528ba1ef60bd5395708067352d11330215e5ce2568ff WHIRLPOOL 52b60235b6a0421c985d06e28622b88106f9f24395dd9598e83d956f3c619d67248f7c71ac8c211167e06f0540a8aed16c2ce1f8369730c6fbb62269f7384fcd +AUX dangle 279 SHA256 650da642809c8e65d7bed46465b557b4388c9b04556d860d8fbb07e35c960b7b SHA512 21fca09578aa13819a20f08ff414ca2b8d08d177a1ab09f8d85c53ae20fc6f38ab46e2933d72c239029b37ec5eebc3162f0c8e99f1ca1dd20aaa49277fac4e7d WHIRLPOOL f9b768f524a1c25e340e5738aef293140c39e49c8f287788fd8f6a2d921c9d72f3ab4333493cc4428d71b4942864801e23e46e1e72976c50e1325e58a257f9df +AUX dataShifter 282 SHA256 f2db9793af0578e2f3e5ecf740b5178f303f5bb66bf7f307969018a0615e3a3f SHA512 f1c4a87d0d4d1a613ce8c9eacd9e3ba5047f1205404140c0c68a354bb790397b7ec49426660a48601a305906b60a8957d218dbc5ad1d6d48beb7030772a199b7 WHIRLPOOL fad840da2aca6805baedf61e4a24fdbaa3d011e0844f3b199feadaa2e6e86f65cf30349fb462f480fe54aa5ab4106a738f6051f83b2ff4c614053311c6bec19f +AUX depositionFileImporter 286 SHA256 a22f158a85a3cbd546ffdb4c53cc60bd8d634296a86f552d69ec77cbf63e1289 SHA512 f7d7caa4b2b2d91eb5dc27ec0ccd6251dab94f6d8e318190b2f2b1b997f825d6cee1e3a38ee77f9358102dcdaf7d93c4d18c7250855446580abd459db31eec6d WHIRLPOOL 582dce9b6717ba6afbb9e6a5c917882ef6efd7dc05fe828a391e46274e1e095457e058a4ec016b105966cca8564afbf0c1eb77e0d313da3ebf2eab3db3dc54a0 +AUX eci 267 SHA256 1747e087c2c87f68fc7a9d2e42adb37048758377d60d0de0ea6a8ee2cb42a60b SHA512 800b2624fe21c706a1bc30bc8fd4fefb9f4c18cb795266cb8afcb3db09776600785a453eed656b4b25b34fc5e39a0e7a599bff2417bedbd0ac6945d2ad900080 WHIRLPOOL 3a04e6057743c672298a2e9ecc4a396131101b5699c8d8ca965c24fd3ac3db541a3b0b7a53ba87a91f5f3a1d2be7e8ef349013f3d9cb33f8addef05de6709693 +AUX extendNmr 266 SHA256 c13cd4d468e8b35d554f0b623e956f67fd5ac6131defa6535f3a3b810ef48920 SHA512 b94d480c776bc2da31ed12419df1c3364036299553697b7d50eb0ebf073126041e8acd3f1c30051dc1dbc44fef9662001e718a29b8c7fcfc2ca19c0da90125ce WHIRLPOOL 440e453390682bce4a6021d5d9119f985dd7b72cb7083852362228305d6860fd65e1e79c5a06c518677eb9b73d2530624ec5b6f4a7a4a690612f47cf02d665b8 +AUX formatConverter 286 SHA256 a7e501e118c52dbde7d7bf85b80520963e30b9e3babc202e4d2d0ff6a84406e6 SHA512 a987b73b10614a2616b62589004ae1e321903af08efea62f6c74f2cf5b1e7053454a382107056250824373bce9f281ad0af2e8f6928cdf2e556e9638646cfcda WHIRLPOOL 452eee87cc1a9c45c9fce54d3029e6464cb91795ea2ab9d1312661b856145f10956556f97ad13b2a1db649d1e62a5a77885b74a952057c0f81aa6d597dfcb222 +AUX pipe2azara 290 SHA256 d656e61005b0a5e49fdf835febac8ad334fa946fadf577072ed6999d7d8f3159 SHA512 6f90a1720dc786d84576029cf77271e8eeb0b5c38506e93227064aafba1152a86762125d3bb9f26a741dcc215da87cf96ba9b8926568db79b56159f8839e8a80 WHIRLPOOL 6eedb142d8433b9c85f3804105d69ac024981e263fdf552417741d31300cab2ae4fb4ac40a0770d75725775a77449c70d9ae5aba8f1742ebb45d2d95bba81bda +AUX xeasy2azara 288 SHA256 e116e19f3cb7bb10a75b75608ae6efb93dfb710e86fece357f3003913673f14a SHA512 e9a3dedc155f9f7b163eead73099532653454a7f5f12042348abf87a4e8930cb8b0b66fd87ef9fcc3b395c92d7e4942829ec8f5e7a1c28c7b3ce51022b8fce6b WHIRLPOOL e021756a059dfdf0f7dfdbac0f1740ec90a31d1b0f2b70d588d7574a0fe4f0607ecfc52b58a7e3f5140ff4e7fc4054f8fa11fa467aa41a2ad09ac99a24678979 +DIST analysis2.4.1.tar.gz 36088236 SHA256 1cb089dcc739e8536d938a68536f556094f5d728907b251fe337758ba5bef106 SHA512 db44468c360d51815614fe0055505001c0a7a722f980c2c049c00524672bdfd4a507134ce1d68b29ebf622ffe94e0c9bb9685fea5b3441790b997a64f78c0dc1 WHIRLPOOL b53fc0438a878a8f8ce0244f5c1ce9edb616665149a699364e3bcd38c5db548c22b80ef67b4183ad5321b71b69a3b85aecc7d912893bba947700003a411651ac +DIST analysis2.4.2.tar.gz 36390919 SHA256 14941131033cbd4b0b13d6d4fe3f9253360a7c2ace8ece9194be00c1fe4b2903 SHA512 694faefd3c085b559b6bb4729141a9ab885334f578bfbb0ebf260366dbca38c31738d5f5af50b5c7ea16b304b27adf80411082859796a5afeec630c36d56bd8b WHIRLPOOL 4499dcb074d445bfc972f9dea43e6f3e3c28722d513dce0fec4e1b2b5dab8be098f53f82565d86a4e7935f0595ef303465668230aa61021cf88e13cce8606214 +DIST ccpn-update-2.4.1-150226.patch.xz 10732 SHA256 74e8723d310d336cd4215ed4e9a1a1c0b2c0efdb4c03aaacba7ecd0575b38287 SHA512 60eb4acf6179f80207a72076ff5d5d733d3c3e804c1ce0a48701dd6e923146af49cd6759a529c8125f4b26eb3f8f83b35acc0c48b88a3e3034b25b5438a04feb WHIRLPOOL 3a2357d4fcb086206d45edd5b9cc807313b5f62be2f2a70e8f011f5521cf8729371b8c7149837c4ea1f6f059e26a49c1d20492f338a844e15f38ccf543faf6e1 +DIST ccpn-update-2.4.2-150325.patch.xz 2096 SHA256 d33676fd93aaa5814aa43179f221df69f4bae9b8ec98ce5b6cc57ce6aacab732 SHA512 c544e0a4a93d0e3275a22d07d21bf3bb5ed90cf041f40bf08fbc687b431640ad5c56180eadd4b43e4023b08ef42afe5a874423becc6f9313a0b1f642a4b97873 WHIRLPOOL f2e9780eb3216185cc6b89ca490e14c2de1130393eda4308fc71e6a2eb0460fc97f83ab3c92fb6a488a1926ba2f3099c7ae5f0a4bd216f8ffa24bfd87e360838 +DIST ccpn-update-2.4.2-150413.patch.xz 3132 SHA256 c0796e1f739f799003304c8b8d23ea0ee42b2e0a6dd59b292cb2a1167b5725f5 SHA512 99893ca009ff76b015017b29cfd97e0ae935ed2d62aa5a99d52dd9a5f22cf0d369e5019273fe3c3811c28b32568721fb64f71c5927eb57d0cc91dcea44b0288d WHIRLPOOL 48a355ef4824d41517d618178be4cd4efc42a6f5e190bac88348041504da0807aa1b34bafbc3937d7f6fc3b5b52fe469431fb6ce9df40bb1c56d7faad88cfe51 +DIST ccpn-update-2.4.2-150421.patch.xz 3788 SHA256 df8f7dd81281f3f7ddd266b8bd90a089f61a9e8f0cda3bcba8b495a6f4be6238 SHA512 0e8a10b6d9721b52574cd2fe0413dca0fac32a948eb31d3db6e2c4d4f7d85c341e8d53d70954341792ea598a37ec87e4392a615e1c2f6f8bbfc0e42a750be648 WHIRLPOOL 2673ac33b2eca1a3fb873567784f1d77937e7ec6aec3ab7eef6065f9322513326993786bd3865a50c50c58e05bf874ba25df02d15083f50aef9acb404ca4e1ef +EBUILD ccpn-2.4.1_p150226.ebuild 4568 SHA256 8850f5fa03dbbc6059609d3f6609abd0a4bed16955bef16ada876f130dd5770c SHA512 d69103a9da8022f9b37e9f995728fc7eeb2d7692e6c7de11816bae521dcfcd74aabbf0758646575f9cad67149204e3a79b4c8ec45afae9e28a7fcb6c659632d0 WHIRLPOOL 6954dfe36d792ea22215288d61ac2384e50ed164036fb60e2ce8ef814f7fa7cfd400d8a3934cf4b60fa12d05bf53f921efba364c4bb78d136e5fd8bf11bf5402 +EBUILD ccpn-2.4.2.ebuild 4569 SHA256 e83678571f3379583dd89671db0f9e7a94e64e4a571346931562b763653f9512 SHA512 f780549f9a4802482fdf47b963bfe0a7fce49fd029ebe1e1117500dcf2a296489da71e47e8c19ad6bb3a84d778f34bb0faff619b34259baae9f0d841a16ce827 WHIRLPOOL 116e4ae6b0403b4ab200ec220271f54eb431e9acbb4fad0955665612f454b9b6861bf71e75ca9baf442f7448534633fc8d6db9199424f3e14e06f394405017ac +EBUILD ccpn-2.4.2_p150325.ebuild 4568 SHA256 8850f5fa03dbbc6059609d3f6609abd0a4bed16955bef16ada876f130dd5770c SHA512 d69103a9da8022f9b37e9f995728fc7eeb2d7692e6c7de11816bae521dcfcd74aabbf0758646575f9cad67149204e3a79b4c8ec45afae9e28a7fcb6c659632d0 WHIRLPOOL 6954dfe36d792ea22215288d61ac2384e50ed164036fb60e2ce8ef814f7fa7cfd400d8a3934cf4b60fa12d05bf53f921efba364c4bb78d136e5fd8bf11bf5402 +EBUILD ccpn-2.4.2_p150413.ebuild 4568 SHA256 8850f5fa03dbbc6059609d3f6609abd0a4bed16955bef16ada876f130dd5770c SHA512 d69103a9da8022f9b37e9f995728fc7eeb2d7692e6c7de11816bae521dcfcd74aabbf0758646575f9cad67149204e3a79b4c8ec45afae9e28a7fcb6c659632d0 WHIRLPOOL 6954dfe36d792ea22215288d61ac2384e50ed164036fb60e2ce8ef814f7fa7cfd400d8a3934cf4b60fa12d05bf53f921efba364c4bb78d136e5fd8bf11bf5402 +EBUILD ccpn-2.4.2_p150421.ebuild 4568 SHA256 8850f5fa03dbbc6059609d3f6609abd0a4bed16955bef16ada876f130dd5770c SHA512 d69103a9da8022f9b37e9f995728fc7eeb2d7692e6c7de11816bae521dcfcd74aabbf0758646575f9cad67149204e3a79b4c8ec45afae9e28a7fcb6c659632d0 WHIRLPOOL 6954dfe36d792ea22215288d61ac2384e50ed164036fb60e2ce8ef814f7fa7cfd400d8a3934cf4b60fa12d05bf53f921efba364c4bb78d136e5fd8bf11bf5402 +MISC ChangeLog 3178 SHA256 7988018e0161cf5c930d120b4218e2eb83468bbfea8709f299dae1b4572d4012 SHA512 2e6e422d5856972cd8a08fb11d80d6cac59dccbbafb6514421207bb7f1a88f8c53821c9378b28e1faf5e87fb901b046a0e93a1754698b09ecf513486fe105b61 WHIRLPOOL b74144a4d0361bba2933ad126bf5c88939267beacd29a4035a3205f468c4bec21342291f69de2723d1073f66882595cc13e8947d8e2ec64cb289dcab68352604 +MISC ChangeLog-2015 31557 SHA256 042c0bc173a82407f009a4fca2a0104631a6b468bad8c7cccdcebc13d2af3d7d SHA512 7ed05524d32beab53d2f5436af7f7f737b10f482ca2d04b94bd0f9e8d6554a579ce59404e8c366b42e3f7debb35981242a6579ebebe9a135ecb5efe6c91c299e WHIRLPOOL e486e6dce0ce4080dd7f3084b3c5743cb03f3f871b1b638d7b5ae4c6eeac986e1b0aafb2d49015d02990816e4968b8098b9b1bf2e9a47ce9a8abdd0be1d78d29 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild b/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild new file mode 100644 index 000000000000..a1755eca7d7d --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.1_p150226.ebuild @@ -0,0 +1,165 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" + + if use opengl; then + GLUT_NEED_INIT="-DNEED_GLUT_INIT" + IGNORE_GL_FLAG="" + GL_FLAG="-DUSE_GL_TRUE" + GL_DIR="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2.ebuild new file mode 100644 index 000000000000..6303b8d42837 --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.2.ebuild @@ -0,0 +1,165 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +#PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" + + if use opengl; then + GLUT_NEED_INIT="-DNEED_GLUT_INIT" + IGNORE_GL_FLAG="" + GL_FLAG="-DUSE_GL_TRUE" + GL_DIR="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild new file mode 100644 index 000000000000..a1755eca7d7d --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.2_p150325.ebuild @@ -0,0 +1,165 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" + + if use opengl; then + GLUT_NEED_INIT="-DNEED_GLUT_INIT" + IGNORE_GL_FLAG="" + GL_FLAG="-DUSE_GL_TRUE" + GL_DIR="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild new file mode 100644 index 000000000000..a1755eca7d7d --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.2_p150413.ebuild @@ -0,0 +1,165 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" + + if use opengl; then + GLUT_NEED_INIT="-DNEED_GLUT_INIT" + IGNORE_GL_FLAG="" + GL_FLAG="-DUSE_GL_TRUE" + GL_DIR="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} diff --git a/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild b/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild new file mode 100644 index 000000000000..a1755eca7d7d --- /dev/null +++ b/sci-chemistry/ccpn/ccpn-2.4.2_p150421.ebuild @@ -0,0 +1,165 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="ssl,tk" + +inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator + +PATCHSET="${PV##*_p}" +MY_PN="${PN}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR" +HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" +SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] \ + && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+opengl" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/tk:0=[threads] + dev-python/numpy[${PYTHON_USEDEP}] + dev-tcltk/tix + =sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}] + sci-biology/psipred + x11-libs/libXext + x11-libs/libX11 + opengl? ( + media-libs/freeglut + dev-python/pyglet[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2) + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + + epatch "${FILESDIR}"/2.3.1-parallel.patch + + append-lfs-flags + + sed \ + -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \ + -e "s:weights_s:weights:g" \ + -i python/ccpnmr/analysis/wrappers/Psipred.py || die + + local tk_ver + local myconf + + tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)" + + if use opengl; then + GLUT_NEED_INIT="-DNEED_GLUT_INIT" + IGNORE_GL_FLAG="" + GL_FLAG="-DUSE_GL_TRUE" + GL_DIR="${EPREFIX}/usr" + GL_LIB="-lglut -lGLU -lGL" + GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include" + GL_LIB_FLAGS="" + else + IGNORE_GL_FLAG="-DIGNORE_GL" + GL_FLAG="-DUSE_GL_FALSE" + fi + + GLUT_NOT_IN_GL="" + GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)" + + rm -rf data model doc license || die + + sed \ + -e "s|/usr|${EPREFIX}/usr|g" \ + -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \ + -e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \ + -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \ + -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \ + -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \ + -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \ + -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \ + -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \ + -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \ + -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \ + -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \ + -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(TK_LIB =\).*|\1 -ltk|g" \ + -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \ + -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \ + -e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \ + c/environment_default.txt > c/environment.txt || die + + sed \ + -e 's:ln -s:cp -f:g' \ + -i $(find python -name linkSharedObjs) || die +} + +src_compile() { + emake -C c all + emake -C c links +} + +src_install() { + local libdir + local tkver + local _wrapper + + find . -name "*.pyc" -type f -delete || die + + libdir=$(get_libdir) + tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + + _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr" + for wrapper in ${_wrapper}; do + sed \ + -e "s|gentoo_sitedir|$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${EPYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ + "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}" + dobin "${T}"/${wrapper} + done + + local in_path=$(python_get_sitedir)/${PN} + local files + local pydocs + + pydocs="$(find python -name doc -type d)" + rm -rf ${pydocs} || die + + for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do + sed \ + -e 's|#from __future__|from __future__|g' \ + -i ${i} || die + done + + dodir ${in_path#${EPREFIX}}/c + + ebegin "Installing main files" + python_moduleinto ${PN} + python_domodule python + eend + + ebegin "Adjusting permissions" + for _file in $(find "${ED}" -type f -name "*so"); do + chmod 755 ${_file} + done + eend + python_optimize +} diff --git a/sci-chemistry/ccpn/files/2.3.1-parallel.patch b/sci-chemistry/ccpn/files/2.3.1-parallel.patch new file mode 100644 index 000000000000..fcf44707e082 --- /dev/null +++ b/sci-chemistry/ccpn/files/2.3.1-parallel.patch @@ -0,0 +1,38 @@ +diff --git a/ccpnmr2.3/c/Makefile b/ccpnmr2.3/c/Makefile +index 01fb25a..8e8e1fe 100644 +--- a/ccpnmr2.3/c/Makefile ++++ b/ccpnmr2.3/c/Makefile +@@ -5,22 +5,22 @@ all: compile + compile: global structure analysis clouds dynamics bayes + + global: +- cd memops/global && $(MAKE) ++ $(MAKE) -C memops/global + +-structure: +- cd ccp/structure && $(MAKE) ++structure: global ++ $(MAKE) -C ccp/structure + +-analysis: +- cd ccpnmr/analysis && $(MAKE) ++analysis: global ++ $(MAKE) -C ccpnmr/analysis + +-clouds: +- cd ccpnmr/clouds && $(MAKE) ++clouds: global ++ $(MAKE) -C ccpnmr/clouds + +-dynamics: +- cd ccpnmr/dynamics && $(MAKE) ++dynamics: global ++ $(MAKE) -C ccpnmr/dynamics + +-bayes: +- cd other/cambridge/bayes && $(MAKE) ++bayes: global ++ $(MAKE) -C other/cambridge/bayes + + clean: global_clean structure_clean analysis_clean clouds_clean dynamics_clean bayes_clean + diff --git a/sci-chemistry/ccpn/files/analysis b/sci-chemistry/ccpn/files/analysis new file mode 100644 index 000000000000..828ed4e64ae9 --- /dev/null +++ b/sci-chemistry/ccpn/files/analysis @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -i -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/analysis/AnalysisGui.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/dangle b/sci-chemistry/ccpn/files/dangle new file mode 100644 index 000000000000..6d8a42e615de --- /dev/null +++ b/sci-chemistry/ccpn/files/dangle @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/cambridge/dangle/DangleGui.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/dataShifter b/sci-chemistry/ccpn/files/dataShifter new file mode 100644 index 000000000000..c083960f2f60 --- /dev/null +++ b/sci-chemistry/ccpn/files/dataShifter @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/DataShifter.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/depositionFileImporter b/sci-chemistry/ccpn/files/depositionFileImporter new file mode 100644 index 000000000000..09505ccc4925 --- /dev/null +++ b/sci-chemistry/ccpn/files/depositionFileImporter @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/pdbe/deposition/dataFileImport/dataFileImportGui.py $@ diff --git a/sci-chemistry/ccpn/files/eci b/sci-chemistry/ccpn/files/eci new file mode 100644 index 000000000000..54d913348718 --- /dev/null +++ b/sci-chemistry/ccpn/files/eci @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/eci/EntryCompletionGui.py $* diff --git a/sci-chemistry/ccpn/files/extendNmr b/sci-chemistry/ccpn/files/extendNmr new file mode 100644 index 000000000000..a2fe4c997c7c --- /dev/null +++ b/sci-chemistry/ccpn/files/extendNmr @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O -i -O ${CCPNMR_TOP_DIR}/ccpn/python/extendNmr/ExtendNmrGui.py $@ diff --git a/sci-chemistry/ccpn/files/formatConverter b/sci-chemistry/ccpn/files/formatConverter new file mode 100644 index 000000000000..6cb273612352 --- /dev/null +++ b/sci-chemistry/ccpn/files/formatConverter @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccpnmr/format/gui/FormatConverter.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/pipe2azara b/sci-chemistry/ccpn/files/pipe2azara new file mode 100644 index 000000000000..5a3710a134a7 --- /dev/null +++ b/sci-chemistry/ccpn/files/pipe2azara @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/NmrPipeData.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/files/xeasy2azara b/sci-chemistry/ccpn/files/xeasy2azara new file mode 100644 index 000000000000..7b73714c2fa5 --- /dev/null +++ b/sci-chemistry/ccpn/files/xeasy2azara @@ -0,0 +1,8 @@ +#!/bin/bash + +export CCPNMR_TOP_DIR=gentoo_sitedir +export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python +export TCL_LIBRARY=gentootcl +export TK_LIBRARY=gentootk +export PSIPRED_DIR=gentoousr +gentoopython -O ${CCPNMR_TOP_DIR}/ccpn/python/ccp/format/spectra/params/XeasyData.py $1 $2 $3 $4 $5 $6 diff --git a/sci-chemistry/ccpn/metadata.xml b/sci-chemistry/ccpn/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/ccpn/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/chemical-mime-data/Manifest b/sci-chemistry/chemical-mime-data/Manifest new file mode 100644 index 000000000000..4a5e36fc2c8b --- /dev/null +++ b/sci-chemistry/chemical-mime-data/Manifest @@ -0,0 +1,10 @@ +AUX chemical-mime-data-0.1.94-namespace-svg.patch 798 SHA256 d22f61f87f3042c0f66a3e4a9c5d8c0b1355ef8b92557dc6811a1626f4905323 SHA512 64addfac817a7f056f381515561b4311936410dc46385a3ded8c65f8fbc3d5dda731c4ec02e9369299c8122e7c43a6dc53005a4957e4165bbf958f683708513d WHIRLPOOL 797d22b29caf2b804f08310db66ecc61a09f1f012c60d37600bf4080e73d6488fcbf7ac7a2944c7e8c03b2e02bf03b5fd7e17551d0c670af66045e157d985fa7 +AUX chemical-mime-data-0.1.94-pigz.patch 481 SHA256 af97f7048e8618c3134a695e907af39a61dafaec4901f664cd0271d670980dac SHA512 a16839c1b88486ed26b4987a22594d0c3d45254d31157560135bdba008e5caa0a372d11e7db858564f1eca75452d2e43509899a91c2a8872465ea06277a1fb6c WHIRLPOOL df23df58a0f96dcd94e98d2c03073aa211322a9bdc9f7edc490ef1343e7ff2188be243be39f7e007bde70548a67c37762b91fdf4520e5a70e9959ae10efce1ad +AUX chemical-mime-data-0.1.94-rsvg-convert.patch 1039 SHA256 e30a3903585570d0ec9360638e2972ff145efef51f394f9c39ca34f821cc2613 SHA512 9c12f96f16e7982a5ba11fc546293a2e74f8918ef6eb274e3b1a618fc28aff244402c9b28ffebc2e01c8f6eb0e9e2516da82852bd0f9142c10e97f027670e60d WHIRLPOOL 2bebab7b2f67e4b249396af59ef5578981a97a73d63d864d66555b78c188c80f7bdfad5dd3f90b60acc2508d38f9e24be2ed8a3fd70b2656a5da0f3022e9595a +AUX chemical-mime-data-0.1.94-turbomole.patch 2451 SHA256 1fc2ca2eeb840a6ba16b32306deffb7ad67d5c2890ed196d304a3a197668dfd8 SHA512 1bfa8818d159f0f917a24a06b0bfe926f0854f4242d8c2dbbedcd4210ffd38a459298862dc1d1aedbbe648a933db99c5d647c5409af74f88b03dd3033946df54 WHIRLPOOL 247e1eeb5eaa42261d9112065e2d3d01bf4afe5736a5bf1fe42613175338b074676407a68ea751eaa4225bf54a4585fd6460207c0341489720fee0003b63c619 +DIST chemical-mime-data-0.1.94.tar.bz2 146077 SHA256 4907cdf60e9edca0a453f6f24e9179ae9da085b67168e932ba44a4280316bff1 SHA512 7f3d967149f27ab1de53c948dc055959e661e1be9d778e3d56d06bea95769da7770ab5fb66afab6607747ef91ffb1dbbcf921e5f06e3303351781968594b5f00 WHIRLPOOL 2e601b37ca22cc1d2b77b5d82713e756dea380fcb0a01c517513be0271162df6e19e7cc7dbc0af8f25e579bb809e0768cc2ee394124c91c296ed0d4c38cfa213 +EBUILD chemical-mime-data-0.1.94-r2.ebuild 1340 SHA256 9ad0f9d012212a546af1a51cdd13023b7758aec932d17a6e0387859d71c2f5b0 SHA512 bbbdb5aea48fef9f226fb2b7c94a9bc126e72647a94054ec58c307c159609855c655a070ddb8bb5fe110a77ec82b2cfeed965ff9ad8fd9c8d7a66aba9de9a8cc WHIRLPOOL 15f1964f8856f732c71273fc61b275b702009969c44f7a3af04702cdcf3fac48f2c27455e88ded00058cc78683a4c64eaf73708e01f1f5752218bf0cc0ad6fd0 +EBUILD chemical-mime-data-0.1.94-r3.ebuild 1000 SHA256 b49111ece8e84eddf0b3ec424323781c245fd4858e75e185cb53923f1c1c8f4a SHA512 86c723dbc3d8ab4753a103e74771b5ead0fb312cffa5e277e474358dc214beecc309ff527e7c4f53a257e40e4ca82edcdf41fd934eaac0ab36fd33d7179cb27b WHIRLPOOL 3a4f92fe0aa48b01da667e16c3f41f7b9b04102212a4464be8e3b94d11c581998a1083cb51952e22faf5c1df3e6fa88c474a6a68e25f6499bd359ec49a7dc2a9 +MISC ChangeLog 4270 SHA256 45308e98f37866ffe75ab48db7dec57885b8ab4767eeaaa37126048da1e4c05b SHA512 7405847da5e582d15ad04d510a9ba14701b26553ac6215e0cee36563ff875d011859d220cbf039b4a8d3af667d81e40c7daefcfe43776367d3e9463a90b30899 WHIRLPOOL 654a03bd80c780e5c09b88bbc7f55361a29c186c6e62eb0b397fa03487d9c799fc07b5b564f9f1b2a8d5fbb6d4531b90c7204c6bfec8e606d27eb6ddeb1f73b9 +MISC ChangeLog-2015 1942 SHA256 fbdb6d124f4b9374ba912e58ad8b7d713a9a2b71e4e473b868b0937e038a1d48 SHA512 2b62aafb60a5f7b1ba03360a061a30e72e43ed8b75211691617564469576ac15cd169560d3b7e03481e687c054119cddcd265c721566ae2d15f633dab82532ce WHIRLPOOL d65a815de44f777f37fc9e36a6cbeffc3ec3188c9ebcfe0258fcd6d81a9a75b6682382b4c72da7f29530ea2e611d439aab96cfdec5ab293e73f443f043c99b53 +MISC metadata.xml 474 SHA256 fe1f26b7fafcaf892d4b578e492626459bc6ef84be9a73687d3bd3e16dacf602 SHA512 59cfe759a75bf49fb020652168434fb610c2d5ba56507945253f556b5542a119bc9c9dc4f2b71ceed93f6672b31e5713cc9d76c433e95b0a08c51e9e577bac00 WHIRLPOOL 86b31834eba5f32a09199138d836598aeb6c71cba48675763db1e6f1044443b0201b0023f55adcdb2b7b06c376568ed050e857ee1d5d4216e6d384efc84a75f4 diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r2.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r2.ebuild new file mode 100644 index 000000000000..d9d29973585b --- /dev/null +++ b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r2.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils fdo-mime + +DESCRIPTION="A collection of data files to add support for chemical MIME types" +HOMEPAGE="http://chemical-mime.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN/-data/}/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +RDEPEND=" + gnome-base/gnome-mime-data + x11-misc/shared-mime-info" +DEPEND="${RDEPEND} + dev-util/intltool + dev-util/desktop-file-utils + dev-libs/libxslt + media-gfx/imagemagick[xml,png,svg] + media-gfx/inkscape + virtual/pkgconfig" + +PATCHES=( + "${FILESDIR}"/${P}-turbomole.patch + "${FILESDIR}"/${P}-pigz.patch + "${FILESDIR}"/${P}-namespace-svg.patch + ) + +src_prepare() { + # needed for convert/inkscape #464782 + export XDG_CONFIG_HOME=$HOME/.config + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-update-database + --htmldir=/usr/share/doc/${PF}/html + ) + autotools-utils_src_configure +} + +pkg_postinst() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update + ewarn "You can ignore any 'Unknown media type in type' warnings." +} + +pkg_postrm() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update + ewarn "You can ignore any 'Unknown media type in type' warnings." +} diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r3.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r3.ebuild new file mode 100644 index 000000000000..56b7db9129ac --- /dev/null +++ b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r3.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools xdg + +DESCRIPTION="A collection of data files to add support for chemical MIME types" +HOMEPAGE="http://chemical-mime.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN/-data/}/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="amd64 arm x86" +IUSE="" + +RDEPEND=" + gnome-base/gnome-mime-data + x11-misc/shared-mime-info" +DEPEND="${RDEPEND} + dev-util/intltool + dev-util/desktop-file-utils + dev-libs/libxslt + || ( + gnome-base/librsvg + media-gfx/imagemagick[xml,png,svg] + ) + media-gfx/imagemagick[png] + virtual/pkgconfig" + +PATCHES=( + "${FILESDIR}"/${P}-turbomole.patch + "${FILESDIR}"/${P}-pigz.patch + "${FILESDIR}"/${P}-namespace-svg.patch + "${FILESDIR}"/${P}-rsvg-convert.patch + ) + +src_prepare() { + xdg_src_prepare + eautoreconf +} + +src_configure() { + local myeconfargs=( + --disable-update-database + --htmldir=/usr/share/doc/${PF}/html + ) + econf ${myeconfargs[@]} +} diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-namespace-svg.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-namespace-svg.patch new file mode 100644 index 000000000000..9860261af403 --- /dev/null +++ b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-namespace-svg.patch @@ -0,0 +1,16 @@ + icons/hicolor/gnome-mime-chemical.svg | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/icons/hicolor/gnome-mime-chemical.svg b/icons/hicolor/gnome-mime-chemical.svg +index 1a8d428..804514c 100644 +--- a/icons/hicolor/gnome-mime-chemical.svg ++++ b/icons/hicolor/gnome-mime-chemical.svg +@@ -5,7 +5,7 @@ + <!ENTITY ns_svg "http://www.w3.org/2000/svg"> + <!ENTITY ns_xlink "http://www.w3.org/1999/xlink"> + ]> +-<svg xmlns="&ns_svg;" xmlns:xlink="&ns_xlink;" xmlns:a="http://ns.adobe.com/AdobeSVGViewerExtensions/3.0/" ++<svg xmlns:svg="&ns_svg;" xmlns:xlink="&ns_xlink;" xmlns:a="http://ns.adobe.com/AdobeSVGViewerExtensions/3.0/" + width="128" height="128" viewBox="0 0 128 128" overflow="visible" enable-background="new 0 0 128 128" xml:space="preserve"> + <g id="Layer_1"> + <g> diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-pigz.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-pigz.patch new file mode 100644 index 000000000000..8b5ccfbc3fd9 --- /dev/null +++ b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-pigz.patch @@ -0,0 +1,16 @@ + Makefile.am | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Makefile.am b/Makefile.am +index 96e03ab..ba0847a 100644 +--- a/icons/hicolor/Makefile.am ++++ b/icons/hicolor/Makefile.am +@@ -21,7 +21,7 @@ icon_sizes = 16 22 24 32 36 48 64 72 96 128 192 + if BOOL_HICOLOR_THEME + + .svg.svgz: +- gzip $< -c > $@ ++ gzip -c $< > $@ + for size in $(icon_sizes) ; do \ + if test "x$(RSVG)" != "x" ; then \ + $(RSVG) -w $${size} -h $${size} -f png $< $*_$${size}.png ; \ diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-rsvg-convert.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-rsvg-convert.patch new file mode 100644 index 000000000000..8a92e19e1578 --- /dev/null +++ b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-rsvg-convert.patch @@ -0,0 +1,30 @@ + configure.ac | 2 +- + icons/hicolor/Makefile.am | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 6f87a94..a503da4 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -102,7 +102,7 @@ if test "x$enable_convert" != "xyes" -a "x$CONVERT" = "xno" ; then + [RSVG], + [The 'rsvg' binary with path. Use it to define or override the location of 'rsvg'.] + ) +- AC_PATH_PROG([RSVG], [rsvg], [no]) ++ AC_PATH_PROG([RSVG], [rsvg-convert], [no]) + AC_SUBST([RSVG]) + fi + +diff --git a/icons/hicolor/Makefile.am b/icons/hicolor/Makefile.am +index ba0847a..f2e0a84 100644 +--- a/icons/hicolor/Makefile.am ++++ b/icons/hicolor/Makefile.am +@@ -24,7 +24,7 @@ if BOOL_HICOLOR_THEME + gzip -c $< > $@ + for size in $(icon_sizes) ; do \ + if test "x$(RSVG)" != "x" ; then \ +- $(RSVG) -w $${size} -h $${size} -f png $< $*_$${size}.png ; \ ++ $(RSVG) -w $${size} -h $${size} -f png $< --output $*_$${size}.png ; \ + else \ + $(CONVERT) $< -resize $${size}x$${size} $*_$${size}.png ; \ + fi \ diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-turbomole.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-turbomole.patch new file mode 100644 index 000000000000..852d6b0605be --- /dev/null +++ b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-turbomole.patch @@ -0,0 +1,57 @@ +diff -up chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in +--- chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in.turbomole 2009-08-10 09:37:06.000000000 +0200 ++++ chemical-mime-data-0.1.94/src/chemical-mime-database.xml.in 2009-08-10 09:40:57.000000000 +0200 +@@ -1290,7 +1290,7 @@ + <specification url="http://ca.expasy.org/sprot/userman.html"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-basis" support="no"> ++ <mime-type type="chemical/x-turbomole-basis" support="yes"> + <_comment>Turbomole Basis Set File</_comment> + <glob pattern="basis"/> + <sub-class-of type="text/plain"/> +@@ -1304,7 +1304,7 @@ + <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-control" support="no"> ++ <mime-type type="chemical/x-turbomole-control" support="yes"> + <_comment>Turbomole Control File</_comment> + <glob pattern="control"/> + <sub-class-of type="text/plain"/> +@@ -1320,7 +1320,7 @@ + <specification url="http://www.cosmologic.de/data/DOK_HTML/node230.html"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-coord" support="no"> ++ <mime-type type="chemical/x-turbomole-coord" support="yes"> + <_comment>Turbomole Coordinate File</_comment> + <glob pattern="coord"/> + <glob pattern="*.tmol"/> +@@ -1335,7 +1335,7 @@ + <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-grad" support="no"> ++ <mime-type type="chemical/x-turbomole-grad" support="yes"> + <_comment>Turbomole Gradient File</_comment> + <glob pattern="gradient"/> + <sub-class-of type="text/plain"/> +@@ -1383,7 +1383,7 @@ + <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-scfmo" support="no"> ++ <mime-type type="chemical/x-turbomole-scfmo" support="yes"> + <_comment>Turbomole SCF Molecular Orbital File</_comment> + <acronym>MO</acronym> + <expanded-acronym>Molecular Orbital</expanded-acronym> +@@ -1401,7 +1401,7 @@ + <specification url="http://www.cosmologic.de/data/DOK_HTML/"/> + </mime-type> + +- <mime-type type="chemical/x-turbomole-vibrational" support="no"> ++ <mime-type type="chemical/x-turbomole-vibrational" support="yes"> + <_comment>Turbomole Vibrational Data File</_comment> + <glob pattern="???"/> + <sub-class-of type="text/plain"/> diff --git a/sci-chemistry/chemical-mime-data/metadata.xml b/sci-chemistry/chemical-mime-data/metadata.xml new file mode 100644 index 000000000000..fa1ab91bf749 --- /dev/null +++ b/sci-chemistry/chemical-mime-data/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription lang="en"> +A collection of data files to add support for chemical MIME types. +</longdescription> + <upstream> + <remote-id type="sourceforge">chemical-mime</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/chemtool/Manifest b/sci-chemistry/chemtool/Manifest new file mode 100644 index 000000000000..0f3eeb0a6283 --- /dev/null +++ b/sci-chemistry/chemtool/Manifest @@ -0,0 +1,8 @@ +AUX 1.6.13-no-underlinking.patch 2251 SHA256 49cd82280ac80e06bb92fd521be85b1b38998e1d1831ed64d2e447315c78141e SHA512 42d623e2875118350a3c4a1979483ccd1de535f8a6ceec7fb9554661a8f91c3403d2cfc207891ac1f71ae7fda4486e48c74bc6621dc76eb2740a7c5f68caaeb9 WHIRLPOOL b36eca2f2232da77d95ba2e1f1edc0389a2591dd6e0fc57ed0d2c1bf5053363fbdea78caaf6bb72d8f3a719bbeeeb7a84e0b25d4b9f3e0c7d59d49e43b864a60 +DIST chemtool-1.6.13.tar.gz 838868 SHA256 31a07683f55305c3e0c4d7af3bc3d1d3a9a2eff4d836455fe1e382962f0aa0c8 SHA512 6c248321f73b6eab4ad21e810639a1f0b14cc30db9c9fdc8fe66ee218bd88ead5e74f1f047f5badcb91b515827c2eddc64b28ead380d9b14ab5b76777e7134dd WHIRLPOOL c7158a75480e9b98eb2ed5c16d73c4d5e5fa05375009ac1778b7e9bf0e9a2ef9092032557d46ea506a6503c0799676998a6fcb80063ed56a7ae8d360c1f273bc +DIST chemtool-1.6.14.tar.gz 817735 SHA256 86161a0461386b334a5ffb17cdf094a491941884678272f45749813514ddafcb SHA512 066c83c61aced3134b081767e788143a047889a2fee4b6535c2b0a3166bccc73d75981e1cf35b7bcaa5b8fe2e0227b28693b659decd82f7783cb4082ac6ed2bd WHIRLPOOL 41a2bd4662c06307a94281e6a54d4e129b407bc597c7d08c8a9f976332cb727f3e195d1d85429716ac22a34ea1dae03b724167bbb5444c03dcb24131cc20ae1d +EBUILD chemtool-1.6.13.ebuild 1169 SHA256 052457b1f6c2aff5366cc9c6d2c0cc4d79b5b3b2397e70d85794c8efd1dd1d30 SHA512 d3135ea531d93cf3e0465e3350e78da8cd9e4acda8517bbd29fb1547fd4f8dce3b7acbde0c6b9cd535c74834129a53e79dd72a3ee39d40348f9bbb7bd07eaf71 WHIRLPOOL 421d68155ea1a366bcfc86321f0ef80ff09d7282c99e0362138698318c9391dba5e5ae1028995f05e6aa401c17d06661648df46076bc7bd97d0706f28e0982fb +EBUILD chemtool-1.6.14.ebuild 1172 SHA256 1f977fb3725f46898bcf335076b80ba02bdcf04c9378d1ecb8556f8ea08c060a SHA512 25684162b9f93c42ce81b69f22f71d112acc5d65fef1e26bbf6c980887c852e0130d0c9fb0babc360c1c5e3b41391cf4473cce0dba0d88400e99a6fe87114b72 WHIRLPOOL 312666c2212c4d9a1b11f5aeb73e42150ba00051666630294b0225ebb7a2633f61944d314a23e5485082058ca3598228a009415b2e8a2682e6c6621bd333987e +MISC ChangeLog 2530 SHA256 213257d2b418500f28768251ffb200004ad0be8cdc211cc96e82f0b52f4d9544 SHA512 bda3b88e7d7c2f7f8ff54f55b303ab14e7e256cedae38a76f681e6e190949f670b76c3038aba8b0aae2e3ef79066e86dbe87936f0b4e6568161443d142c0fdee WHIRLPOOL ef4ba177acdb4846c9de46bd2844be3af08b0a0088a805ad1efd1a6a4fe089a85380a7324f38c279ad23b547cc2d23fcf46618ea7e4b69725b8da2a0e6d263f7 +MISC ChangeLog-2015 7979 SHA256 925546a14e6e180c8eb7bb27300d223427d52878adcaa5f4e61cc178674eedcb SHA512 ba9387f37bcfa8ae63c05500bee400386d407549101ae28bf64737ded4d3aeea939a12c6034a06e70e31e0578d5cedbdc083967810e9b9917541d3fa2f577cb3 WHIRLPOOL 68e6ed950a1b819f7f1f145d80a42797295f459445040d8624228503444618bcb0edf79ed88ea5400567fd283573e0091f9595366cfaf41fca179c4fb53f44b4 +MISC metadata.xml 335 SHA256 110bd3d7bb6168051ad520d63f01b4ff89fb71dc63b8f49d1ba20fc318624743 SHA512 b02a3fd1101bd4ffb01ffd327b307f802fdb126492eea9dd98b86a87a367e669ba5ed4d94d5fecc4528c94abfd90d41e6215c91a34a64b95d0a2e7c2060a76b7 WHIRLPOOL 95d320faffd72369c8669bcf9ea6fb2d2191661914f1d947d62d000a32e93178636e06837f5661fa1c25b3ed56c2d07a12b6581e9084a695c34070c84e23f828 diff --git a/sci-chemistry/chemtool/chemtool-1.6.13.ebuild b/sci-chemistry/chemtool/chemtool-1.6.13.ebuild new file mode 100644 index 000000000000..8eb6ec996db2 --- /dev/null +++ b/sci-chemistry/chemtool/chemtool-1.6.13.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils eutils + +DESCRIPTION="A GTK program for drawing organic molecules" +HOMEPAGE="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/" +SRC_URI="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc x86" +IUSE="emf gnome nls" + +RDEPEND=" + dev-libs/glib:2 + media-gfx/transfig + x11-libs/gtk+:2 + x11-libs/libX11 + x11-libs/pango + emf? ( media-libs/libemf )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +PATCHES=( + "${FILESDIR}"/${PV}-no-underlinking.patch + ) + +src_configure() { + local myeconfargs=( + --without-kdedir + $(use_with gnome gnomedir /usr) + $(use_enable emf) + --enable-undo + --enable-menu + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + + insinto /usr/share/${PN}/examples + doins "${S}"/examples/* + if ! use nls; then rm -rf "${ED}"/usr/share/locale || die; fi + + insinto /usr/share/pixmaps + doins chemtool.xpm + make_desktop_entry ${PN} Chemtool ${PN} "Education;Science;Chemistry" +} diff --git a/sci-chemistry/chemtool/chemtool-1.6.14.ebuild b/sci-chemistry/chemtool/chemtool-1.6.14.ebuild new file mode 100644 index 000000000000..58a5d56b105e --- /dev/null +++ b/sci-chemistry/chemtool/chemtool-1.6.14.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils eutils + +DESCRIPTION="A GTK program for drawing organic molecules" +HOMEPAGE="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/" +SRC_URI="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="emf gnome nls" + +RDEPEND=" + dev-libs/glib:2 + media-gfx/transfig + x11-libs/gtk+:2 + x11-libs/libX11 + x11-libs/pango + emf? ( media-libs/libemf )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +PATCHES=( + "${FILESDIR}"/1.6.13-no-underlinking.patch +) + +src_configure() { + local myeconfargs=( + --without-kdedir + $(use_with gnome gnomedir /usr) + $(use_enable emf) + --enable-undo + --enable-menu + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + + insinto /usr/share/${PN}/examples + doins "${S}"/examples/* + if ! use nls; then rm -rf "${ED}"/usr/share/locale || die; fi + + insinto /usr/share/pixmaps + doins chemtool.xpm + make_desktop_entry ${PN} Chemtool ${PN} "Education;Science;Chemistry" +} diff --git a/sci-chemistry/chemtool/files/1.6.13-no-underlinking.patch b/sci-chemistry/chemtool/files/1.6.13-no-underlinking.patch new file mode 100644 index 000000000000..5d2fe36d6bf1 --- /dev/null +++ b/sci-chemistry/chemtool/files/1.6.13-no-underlinking.patch @@ -0,0 +1,78 @@ + Makefile.am | 6 ++++-- + configure.ac | 24 ++++-------------------- + 2 files changed, 8 insertions(+), 22 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index 99dbf8c..931ba16 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -22,10 +22,12 @@ localedir = $(datadir)/locale + DEFS = -DLOCALEDIR=\"$(localedir)\" @DEFS@ + + # Make sure the gettext.h include file is found. +-AM_CPPFLAGS = -I. -I$(srcdir) @GTK_CFLAGS@ ++AM_CPPFLAGS = -I. -I$(srcdir) @GTK_CFLAGS@ @EMFINCL@ + + # Link time dependencies. +-LDADD = @LIBINTL@ @GTK_LIBS@ @EMFLIBS@ ++LDADD = @LIBINTL@ @GTK_LIBS@ @EMFLIBS@ -lX11 ++ ++AM_CFLAGS = -DGTK2 + + # Additional files to be distributed. + EXTRA_DIST = autogen.sh autoclean.sh +diff --git a/configure.ac b/configure.ac +index 6d8c45a..c5fab42 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -32,32 +32,14 @@ AC_PATH_PROG(PKG_CONFIG, pkg-config, no) + + AC_MSG_CHECKING([for GTK version and compile options ]) + +-if test x$PKG_CONFIG = xno -o x$enable_gtk1 = xyes ; then +-AM_PATH_GTK(1.0.2, , exit 1) +-else +-if $PKG_CONFIG gtk+-2.0 --cflags ; then +- GTK_CFLAGS="-DGTK2 `$PKG_CONFIG gtk+-2.0 --cflags` " +- GTK_LIBS=`$PKG_CONFIG gtk+-2.0 --libs` +-dnl use_gtk2=yes +- AC_DEFINE([GTK2], [1], [the GTK2 library]) +- enable_stockgtk=yes +-else +-if $PKG_CONFIG --cflags gtk+ ; then +- GTK_CFLAGS=`$PKG_CONFIG gtk+ --cflags` +- GTK_LIBS=`$PKG_CONFIG gtk+ --libs` +-dnl use_gtk2=no +-fi +-fi +-fi +- +-dnl AC_MSG_RESULT using GTK2 : $use_gtk2 ++PKG_CHECK_MODULES([GTK],[gtk+-2.0]) + + dnl Checks for header files. + AC_PATH_XTRA + AC_HEADER_DIRENT + AC_HEADER_STDC + +-LDFLAGS="$X_LIBS" ++LDFLAGS+="$X_LIBS" + AC_CHECK_LIB([X11],[XOpenDisplay]) + dnl just an ugly hack to work around the more aggressive header checks + dnl in recent autoconf. Not sure if we should really rely on include +@@ -184,6 +166,7 @@ if test x$enable_emf = xyes; then + AC_MSG_RESULT(yes) + AC_DEFINE([EMF], [1], [use optional libEMF instead of fig2dev for EMF output]) + EMFLIBS="-lEMF -lstdc++" ++ EMFINCL="-I${includedir}libEMF" + else + AC_MSG_RESULT(no) + EMFLIBS="" +@@ -221,6 +204,7 @@ AC_SUBST(localedir) + AC_SUBST(kdemimedir) + AC_SUBST(gnomemimedir) + AC_SUBST(EMFLIBS) ++AC_SUBST(EMFINCL) + AC_SUBST(MYGTKSRCS) + AC_SUBST(MYGTKOBJS) + AC_SUBST(GTK_CFLAGS) diff --git a/sci-chemistry/chemtool/metadata.xml b/sci-chemistry/chemtool/metadata.xml new file mode 100644 index 000000000000..8b1591478bcf --- /dev/null +++ b/sci-chemistry/chemtool/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="emf">EMF export support</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/clashlist/Manifest b/sci-chemistry/clashlist/Manifest new file mode 100644 index 000000000000..4a46ed5b9da2 --- /dev/null +++ b/sci-chemistry/clashlist/Manifest @@ -0,0 +1,5 @@ +DIST molprobity-3.17.tgz 26429898 SHA256 2e70814efb4f566a522762a626f69669c09285cbb6fc26444eb947fde9b30f25 SHA512 a6e986f285ff7e8d167e2d1c935a55b080446c9809d352c95e2ffa32265892b59cd1611730e75ca88aa28387495d3ebd84226e1a9cdd33f0b27b1a8a1b6a469f WHIRLPOOL 3981522eeacaa589530e7d268cda786bebeaf676f7fa5c26508798022126bd1a1c8ea193f65e3c5c739fb3b516b26c3cf24ac0e7898e764a9cffab6637dcd5a9 +EBUILD clashlist-3.17-r1.ebuild 652 SHA256 54e5b295af091ef3369bb776ec51207856e50b015d4d50523568425ca2d569d7 SHA512 600b5dca240537ca83fb374c72e73f205bb2ce320cbccd03b5c922f5163b43a059dc2f6fab481f0b54d066d3ed1a7f06c125b95ba7f05a2065b62395193961c9 WHIRLPOOL 70ae99b92b50097e2defe14b6119c6936667f808f76ce21025d9fac861aa54aea09d59b04adeeec7069134384cbb0421a1283a08480390c2a4b9ac014a34ea89 +MISC ChangeLog 2991 SHA256 f2b0bc389e6616710e285c8a7ce620955c971ee2de498ab71b49f85c0e3e3bdb SHA512 cc649db5aefb47069cb102bf049435fe33640b18455dbb4675822a0dadb6b0c8bcbfb9ca208e1284e04a3899f2514e9abdd2d946dbdc52105e08127431eaa011 WHIRLPOOL f48681fe57ae70437ecfc191946532478643866909b34020c071923fd31b5857ac7b8d937265c75ffb70358f299fd5590b06e25cca6898da77ba674f3cd3c0c6 +MISC ChangeLog-2015 861 SHA256 156e5d08c3dfaed508204a770285c79804d9e616fa4cea9d280a37cd0e7383cd SHA512 d2004c9aeba4f67b4094512a8a859d78d1e3f391c3229c33d26958a98ef1c5783d3c9b0874d0fa80c5c09da06bd654e764fcee8d060b8302f52ef13725a406a4 WHIRLPOOL dc22f22fe88e11b51e82e2e209f93ab47ab8753b2d260c177916d3f73e033c1feadbcb2b83c190e109abedc7641bb412eef1e619b89685fe065085edd9ff444b +MISC metadata.xml 723 SHA256 52cbea9f4cff708f8a89d5a23093425858b3800d22d5676039cae31d97ba6b3c SHA512 7da0ab5c03d802eac05b84e5f47fecdaf990ace2789f0f88c69e730155c9a9637ce23d5ede6633c6e6f7cf9c2cdf3e7b7c82de169caa291bd8facab327577e16 WHIRLPOOL 377be4ed02487c1dbd61f62483c260953f620c6513343ff34ba578f58aa8b440064d0d7ed58a5124afb30968d89e86d2c3b11fe0f696e01009865f5905255966 diff --git a/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild b/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild new file mode 100644 index 000000000000..7028015f5835 --- /dev/null +++ b/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +DESCRIPTION="Build lists of van der Waals clashes from an input PDB file" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php" +SRC_URI="mirror://gentoo/molprobity-${PV}.tgz" + +SLOT="0" +LICENSE="richardson" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + >=sci-chemistry/cluster-1.3.081231-r1 + sci-chemistry/probe" +DEPEND="${RDEPEND}" + +S="${WORKDIR}" + +src_prepare() { + sed \ + -e 's: cluster : molprobity-cluster :g' \ + -i molprobity3/bin/clashlist || die +} + +src_install() { + dobin molprobity3/bin/clashlist +} diff --git a/sci-chemistry/clashlist/metadata.xml b/sci-chemistry/clashlist/metadata.xml new file mode 100644 index 000000000000..a2df83cc0e8b --- /dev/null +++ b/sci-chemistry/clashlist/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +Clashlist is a simple UNIX script which uses the awk facility along with +the programs Probe and Cluster to build lists of van der Waals clashes +from an input PDB-format molecular data file (with H atoms). These lists +are organized such that collections of interacting residues are grouped +together, sorted by the worst clash. For the purposes of this analysis, +a clash is defined as a van der Waals overlap >= 0.4 A. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/cluster/Manifest b/sci-chemistry/cluster/Manifest new file mode 100644 index 000000000000..0834ad49df66 --- /dev/null +++ b/sci-chemistry/cluster/Manifest @@ -0,0 +1,8 @@ +AUX 1.3.081231-includes.patch 245 SHA256 a4ab35ecef5f3bc2146823f6bd611f2a7dc0dc1fa299cb60f2c8a94ff64e78ae SHA512 a1261ed2b3f867fe464e1501fa9bc0b1f2909eaf736475e717da95ddbc34ae2938346c0044f7b6d84264a0d85ea5f7b1214caf1c2b12c544876912ff10e2302a WHIRLPOOL b39276b9aa98fd9c81b0bfbfddcc7573c3c43d1b3638556b8a911be66006cb81b15d9f8f05cfdc0b073c32950e70c4d115f8122cd7e4d3b8c6ef55e5beb51271 +AUX 1.3.081231-ldflags.patch 842 SHA256 32d3d0821d1366af28553c1f3a28f5e6f9b1ea593b7c21efb30d478080219f2f SHA512 9937f88e65ae94595ba2889e7f57d3b295e025d2ebd83817300a7f74a674fab84358e3b7fc9619ba473c586c51bd106e303b096cdb267d8fda05670f7815e9e4 WHIRLPOOL 7af94b4a1d1375785e200ebe4bdcd91e4ba2ee6aca0d19188cb924465c29a02ee4775326aea4bdef11fbe9fe068312d4c248ef2b56c2357217a64d2c658166c2 +DIST cluster.1.3.081231.src.tgz 8860 SHA256 4e0986d5ff124936b5fff4b6f8989dd04be11180d6552fddc34b2c10dfcc870f SHA512 af5851ef467458d45ee5f2309c6344ae16145ac371a1b9d0a3d8b5769a18b98877cf7cb65b85f71108d927b0e6c363e06b85a67e7cb2e5e0b41af375cb2db7ac WHIRLPOOL 2f02de20b323792360b28d5a42d233d06be529414e29796a39a439651fee9e8ba73bdd05033907ac7434890bfa2a31aaf57ab98bbe59964d06a2d63646833f5f +EBUILD cluster-1.3.081231-r1.ebuild 664 SHA256 1e4f87963d752f207938865011496e5ec461b69614e561d2cf57582f5042c5e4 SHA512 2179d4beb99e86945b2afa8b0951da4f2c59ad13a0070429d7c0a24e0d363ee0a7f12a3710655305be332cec4744e3b22167e1c99986fcb1e22dec2fc46e6d59 WHIRLPOOL 820b6e31cb52ef88027a7e2c62524d4ef03d5de900921c8e6fd8873af7a94e0fe3927f2b00449a7375f800cea640ebec82141cdaab24b3605fbdc2d9a0a3f304 +EBUILD cluster-1.3.081231.ebuild 646 SHA256 c11080dcd466c8346e3f0a709fec5a0edd289eedea63ece008683ea8ee14a46c SHA512 2bafc4cec0e46ad3749a5b005f629340bc2b0ec8e3fd062da5f20edcccb67597c6a3b1cb5c7045a2d3796de3b488f78ca7b53678c911d63f9dfaf0ff290f9a73 WHIRLPOOL 9818aacf36464c6a282f7468c0f3c17261a85760dbc0f82032cddd7daf63b37c960fe5e2754695bc2ce978916e8d0fb9ee3d6e277604c54cfa53bb1322b2e0db +MISC ChangeLog 2721 SHA256 b8594c90a8f6d0985eb00aa67d89994a5c1d39c52f580285b7e8a3866120b630 SHA512 3588e18b2936a2133f1905eeda0f7a51dbbd73748f6693a18ade4dc22d7e22cccfeaaa664029c49d2da2f528acf79ff1280d806737f33b7a09afcfe649504cea WHIRLPOOL c723e15094658deee98aea4011629935ff445890fdad7fe97183d09f4bec60298dd91a91f94d935aeec48cee0342dc283be634a5105eda1db386dfadce41a486 +MISC ChangeLog-2015 1628 SHA256 1f8d4eb64bc6a4286abef1c5ff341bab34e634aa44ccede53ddedbfef659436c SHA512 836be8b404b2322513fad122319a5a73dcca232db1dd328e2d6c7bf3259fdea0ead351274d68c611837fb209ba1e3f4bb70cd3e826a997cfcae4355015a70bf9 WHIRLPOOL e51962bb7b1782f0b813fbd90d6aa4b74fa915cc6a48e6a061a69a91fbfb0abb9a99b248d09ebce1001dd1e811e4c5272ba1f04b3dd37ebdedc75ba106e803e7 +MISC metadata.xml 661 SHA256 5e895ff55256c3017a244b7bfd59dc8a8de3aa6d5601341155aba0468ab3bd2c SHA512 449c8965bd2f3039effcf1d6fc15fea1708cf5987aee36a4b8c470f85b59f7b04884a796a353f17fd890aa9d2e4ee7b1c25ed969febabaa54e577f8be31ed889 WHIRLPOOL edd65cfb23cb24fee72d2c940ad88e5c9186f2b6a1d390d4c29f1d93314a2ef7f068032b72b1d8bbea7d7ca565941eafe8a49715e5ac05d5c0f97dcbf88939f8 diff --git a/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild b/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild new file mode 100644 index 000000000000..955f546926e2 --- /dev/null +++ b/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Build lists of collections of interacting items" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${PN}.${PV}.src.tgz" + +SLOT="0" +LICENSE="richardson" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}"/${PN}1.3src + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-ldflags.patch \ + "${FILESDIR}"/${PV}-includes.patch + tc-export CXX +} + +src_install() { + newbin ${PN} molprobity-${PN} + dodoc README.cluster +} diff --git a/sci-chemistry/cluster/cluster-1.3.081231.ebuild b/sci-chemistry/cluster/cluster-1.3.081231.ebuild new file mode 100644 index 000000000000..e9d3b8999e1e --- /dev/null +++ b/sci-chemistry/cluster/cluster-1.3.081231.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Build lists of collections of interacting items" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${PN}.${PV}.src.tgz" + +SLOT="0" +LICENSE="richardson" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}"/${PN}1.3src + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-ldflags.patch \ + "${FILESDIR}"/${PV}-includes.patch + tc-export CXX +} + +src_install() { + dobin ${PN} + dodoc README.cluster +} diff --git a/sci-chemistry/cluster/files/1.3.081231-includes.patch b/sci-chemistry/cluster/files/1.3.081231-includes.patch new file mode 100644 index 000000000000..a5586a540a4f --- /dev/null +++ b/sci-chemistry/cluster/files/1.3.081231-includes.patch @@ -0,0 +1,12 @@ +diff --git a/cluster.cpp b/cluster.cpp +index 0a8c3c1..1384949 100644 +--- a/cluster.cpp ++++ b/cluster.cpp +@@ -24,6 +24,7 @@ + #include <iostream> + #include <vector> + #include <string> ++#include <cstring> + + #include <iostream> + #include <fstream> diff --git a/sci-chemistry/cluster/files/1.3.081231-ldflags.patch b/sci-chemistry/cluster/files/1.3.081231-ldflags.patch new file mode 100644 index 000000000000..1b99f6d662f2 --- /dev/null +++ b/sci-chemistry/cluster/files/1.3.081231-ldflags.patch @@ -0,0 +1,41 @@ + Makefile | 12 ++++++------ + 1 files changed, 6 insertions(+), 6 deletions(-) + +diff --git a/Makefile b/Makefile +index 7892054..929564b 100644 +--- a/Makefile ++++ b/Makefile +@@ -3,27 +3,27 @@ PROG_FLGS = -D BOOLPREDEFINED + + SRCS = cluster.cpp DisjointSets.cpp utility.cpp + +-CFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) ++CXXFLAGS += $(OPT) $(DEBUG) $(PROG_FLGS) + + LFLAGS = + + OBJLIST = cluster.o DisjointSets.o utility.o + +-CXX = g++ ++CXX ?= g++ + + .cpp.o: +- $(CXX) -c $*.cpp $(CFLAGS) ++ $(CXX) $(CXXFLAGS) -c $*.cpp + +-OPT = -O3 ++OPT = + DEBUG = $(CXXDEBUGFLAGS) + + all: cluster + + cluster: $(OBJLIST) +- $(CXX) -o $@ $(OBJLIST) $(LFLAGS) ++ $(CXX) $(LDFLAGS) -o $@ $(OBJLIST) + + depend: +- makedepend -- $(CFLAGS) -- $(SRCS) ++ makedepend -- $(CXXFLAGS) -- $(SRCS) + + clean: + @rm -rf *.o *.ckp ii_files diff --git a/sci-chemistry/cluster/metadata.xml b/sci-chemistry/cluster/metadata.xml new file mode 100644 index 000000000000..62f5e4eb25ab --- /dev/null +++ b/sci-chemistry/cluster/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +Cluster is a simple UNIX C++ program to build lists of collections +of interacting items from records containing interacting pairs +and larger fragments. + +It reads in lines consisting of two or more names and output +connected clusters of names. Each line of output is +prefixed with a cluster number, the size of the cluster +and an optional name string. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/cns/Manifest b/sci-chemistry/cns/Manifest new file mode 100644 index 000000000000..a02afc4e2f26 --- /dev/null +++ b/sci-chemistry/cns/Manifest @@ -0,0 +1,18 @@ +AUX 1.2.1-allow-gcc-openmp.patch 926 SHA256 8c650b36ef731f7b799397ac9f6abfe9cdf46508df930e7bd3a0f2a0dc2e2275 SHA512 cdaae39096625ff1b84ec76b36d2ec3f2e4e4e532d347fa3f0d3e0aa239e2477301de6c768f14788a9b599694568422009bc1c0298ad677cab28d463e0ea8524 WHIRLPOOL 56af947ac685adb889796416870a365abb4be702b77ca4acf695fc2578e8e876e778376518854fb14e7a2349439fd144def300fe0d45b0fa5f90e4a3b6cdec95 +AUX 1.2.1-aria2.3.patch 658 SHA256 c393799beabda5f61a7dcad9aaa4d211c14eb17b1ffd5200c3306c7ef71d19f3 SHA512 54758723bc4900673dff73e3aa4d9ead803c44ee3af514259b21c73f7495aaa077e29efe381e674d2a6c5c8d888d7c9cf4d4a998b6c4b6d91de488dc4526f7e4 WHIRLPOOL 440bc5066864e90211ea2d8faa8f9758a5472108ad7e33a3157a84d62bf5d3f61af743198205669e520e98aee6d11c720660bf8e088d6c4251cfce6fb230ce90 +AUX 1.2.1-gentoo.patch 2071 SHA256 f7e1f27e68d3b186814ec9f73a86a5ecd589c3d4c4e06b1f08a894556661fde0 SHA512 ecc545e66859d3a88c38cfd40abc278fdd8fca520d63b8d8ab3f2301352962cc70ba436078edec793fda90212fe44c0d333163d64c37afd65e19240f1044feb7 WHIRLPOOL 9069500123cde11a630403f414dd6678224d683f4e790ee79c3d3ec413e0ae9071c8e54828482d14f040682fc3b8719689ba66d6cdd37bb428ee903819e9e06f +AUX 1.2.1-ifort.patch 5346 SHA256 bac35147159fac06fcb3a03a4f09c56224d4ee852b86a771121d98c42f3a9c65 SHA512 738ac365cdf77f5fe0d1b93e1a3b55453b589854822ca18220d32f912c799f8ca133317419f39baf1f8376126b5dc4ea073a19e2c0e05ddb970008bddaed93f3 WHIRLPOOL 74b96c04536806612b5643b4448639bbfd2c75022f6f868656c71bf4514e8907b6ec4c1e34bc96a644a4f1af048e98704d6ca478cc3f67d15bb5e8f31ba9ba21 +AUX 1.2.1-parallel.patch 641 SHA256 7cd3312c35d2dbbd2146fdfa977f9866365c4a7be16787b1ba5d9807ff823d31 SHA512 0d0b43cb055a6d594fcd26d118d1ed9dba86d7e7e99beaf430fa42eb81a1d073622e14cd08377ee9dbd3b68b8b99f80c28ac6c26eb93ffa1ba28ee239a0bdf89 WHIRLPOOL 99340390760dc192db446eb584de8f4e91e61cbc3c156a85dd307db2f65801686b5f86af35b75f18dc8a9e10bc2a5952f29c6e329206d634034c0611bb852633 +AUX 1.3_p7-delete.patch 448 SHA256 aa61180b60fd008e3ba445bab5a4a6b0c4634b34fc5655be94ce07dc45abe958 SHA512 54767ba82bb20190497b92d729b3a3c4ce245fe2b3574a9fef5aa303e19462728953bec7925384fbcf5eb760023fb2b0da19f3162721fe51b1b9733817e7b80a WHIRLPOOL 20259ebde0ccae26175452a0e8d77456f69e7f30eabb6b9edb6f8ed770c0342b54051bf436b7ab646fc1e508a7db8aa740e1438a5c75b04ed33ee36ccc79a2cc +AUX 1.3_p7-gentoo.patch 2581 SHA256 510d62ecd5f98cc0d52c1bfc02cadae648885680b425b40855125e1bdd7a320f SHA512 235b5890c9c0aa9bfac0034e35c3641968b5b1f600bbbfa81240fe405f28910a00184b6fa2ec7a993883ba6db95f1fa9e44cb4b7b9e61ab3d9dcfa26869e1a4c WHIRLPOOL f21ee73b931204aed2c8bb1f8aaae2d2ccd7cea2cb412b3552b062a995cf64b7a0b4314799ab0a44ef0fc9f42562fc7bc03d347de970c9f5c333be86a1139233 +AUX cns_solve_env_sh 7070 SHA256 da571cba2a2244e571870b1783fd6cdce1b595e14234cfb43011e9e9eb50151c SHA512 b012e46706f39d934ff27e4b381907ddd25ca1fbc0112c320b117d68cca3e81f571bfd1821b49477dc16bfd8a0a943c43469fe847cf99e6ab2d08ef238bada31 WHIRLPOOL 4934665fe035ff8cd8d451c8756ead2b7f91da1bb575d5dc55b05868be84f61fbd08e881e4dd1cc315cf2ea681ece1737a70cf2004ebf68f67df76e84d8939d9 +AUX cns_solve_env_sh-1.3_p7 7332 SHA256 88127d99380544e502dfe3b3a7788102a7f6b30e7245b26e5e204b8b611bbc1d SHA512 afe2f24c85eff265659e5b2ba2edab519c3193d30b2dcd815bc91a929fd4f4a9167148f8248237569f809d627a8fa623a46fe82d3e0a2cb1827bed910ce565cb WHIRLPOOL 31dbf0ad952ce1d0f7d105d48bf6a27d510ee8deb2c6e4b0d06387e41a0b4c2b62f88d7b6c87bcecdd6bd17501556ec0c4afa0feec6ab64a2fca6563a2268184 +DIST aria2.3.1.tar.gz 1833973 SHA256 cc45ed2d66182cf0ee197a7cf3bc7edd8d5043d95cdcd19e1cec9aeb82c2fdbc SHA512 79a2cd89e2120acecb04f286a153dbf52c16500e8956c9dad49b1e1ed94a7b2449c7b044bae6f87e0d2b452a1467a2c02de74f0fa85b0eae66042386e2f5e2d5 WHIRLPOOL 2ff003322601b42bec0d2431e2f1f85819b3982f8da612ff778bb404e51f0fcbca3faa6998e9c0635f9e73899609bb1e273420cac182952aa744364c20299723 +DIST aria2.3.2.tar.gz 1836270 SHA256 30727ea8bdc2e3b44e5970545008fcfa07fa59aa28b76824956a2aa71daa9615 SHA512 009a1d0079f5cc162dc732749ddd2b33297268f0d988b2f37bda4ed50c7764ceef7ae5b56b322c7ac79427a4a2a92d1239199891445cb5e2b3d0908ed670e2aa WHIRLPOOL f18af5b751e79c92e04f4dc12b6b806a1c505b269559a2342bdd6280b790f9f0df9bb4afe366af03beaf09af0128c6b68c39bc66603d51ad24914c78b2579cf3 +DIST cns_solve_1.21_all-mp.tar.gz 32748040 SHA256 7ab464e20932eb024ba6378738da77a4a03642d63b0ca9772b612a7cf27baec1 SHA512 383324d771570b501e388fba9bf20789f483a3a4044eb3334c7a7e7835e0c345b784e0d344b22d20a10fe1c33ed21c9013adb1af5912808af480b96abe275857 WHIRLPOOL fecd0b2dfba43e5525a9fcc8543a55867602b376744848ddafd4c132bcdfc32225780f543742fa225b5e0f0ce658c1029a9ca8b80d5ee3f2491b6d63e8ad91b0 +DIST cns_solve_1.3_all.tar.gz 64167735 SHA256 2ee368022c5ecabf66ce7d32059d93cd7d885ad2d684a094b87c64f6b3dfea0d SHA512 4fe73820e96999bb33a59ff6da979794628552f49bc03cdebcb9439b57e6042b92190e04bb7e4079157adf06a6facc5c16b8ae91621bd24a4b35ee382e53ae37 WHIRLPOOL b3cd14ab7a8a29a44f6e6c3cbc22ee2c665eb8c8565969337b24deffb2a1fd007fae11c5eb73ac38ddf9a38e850948e3b2df2548931722a2a383d5e8c72607a1 +EBUILD cns-1.2.1-r8.ebuild 6584 SHA256 0d7c765918227ee2837de23518e19dbbeb62eb128d4c0a83002f233094c164f4 SHA512 1b998dae6f3228bf56d66af3bdaa5fcfbb167de571506d7f1c5037cc73d1eff23f31f49fe89ed1defd05e2289f63f7a718b3b39a63bf06bd68a37fd91bfda832 WHIRLPOOL 172dc72f50fb0c51817a28f0d11d19d02198ddc963f00b7bfd8ec28b3f32098442581cb091fa89d386c2afe6a5132816478a923e89eab4f242d93d55479fe630 +EBUILD cns-1.3_p7-r1.ebuild 5810 SHA256 697c68b0520d164e5ead2098247c456fe1b29a029030dbe62b0db51becb663f1 SHA512 cb0537ba0dd690864019641369dad0b62399a6beed2f60b97b4e46cb83d1451fbf7ceb965db17fc793958c5865de50edb5ca20b34dcd5762c5417a805bfbbb81 WHIRLPOOL 75ee5b15a216ba3e5c39edc3e4305a0634b28d4112d0040099780bff00cc07f32f7fcf12f00d294cebb66f0958646236815267ab0c319769f6c74e2c42aba1bb +MISC ChangeLog 2886 SHA256 2054460a3bb982d22e6ee1b4b74d58292f985ef3ab11958292a0ed4365c8aa94 SHA512 69dbeba7a0dfa1b4d39c5c8c6ea24b1df891a2eeeb71471b388a013e46b8f177d490c6b121c3cbe70553adf76593f10c0aa94b033f286d4aa050449e6e84a21c WHIRLPOOL c2a7e383cb6393f319a759a1897822995a1bf8fb6beb0641e6a9f58928c5e7033ae229fb1cb1179352aa18256e80343da17215df7754f4ccfa64aef0758b5ebe +MISC ChangeLog-2015 9722 SHA256 4da9be48b2e12453d8c733f11b0eabcdb335b34451af4bc17b9d4e1478a491c8 SHA512 07bfd4271134d9a8573b87938f50cae28ed9a289595802d4188bcd3b5a438a1880a15855c3f6af4d7791fe8a05faf03b45e5368e768d08ab6d03930ded72fdda WHIRLPOOL 774446fba9f0ce479d3f9d5bdc9943de6cd8acdf079bc0492e5625eaa1e3025d6f7b5b486d342ca4db6df5060ec2164dbfae600080af290bb80bc362c52bbb8f +MISC metadata.xml 954 SHA256 ddcc792da68b67ef7755cdfe100420fb1b824572d691d71d6e527b15897ab9fa SHA512 af24c501f427f9473a9ef8ec90dfd14b2abb0856e8bde8bb1c664fe49a23032895c4d28d06112791b78880be1ef9b781efe60c26bee5d8e9a40a40b41713159b WHIRLPOOL 616cc6e631cda33b92d46a82cbbe516ed702abff311c897578fefad67c22b16252819f3d7ce22833addd8172eff51223c241d839aa968690b1ea65730880bb6a diff --git a/sci-chemistry/cns/cns-1.2.1-r8.ebuild b/sci-chemistry/cns/cns-1.2.1-r8.ebuild new file mode 100644 index 000000000000..a4b67cba44d3 --- /dev/null +++ b/sci-chemistry/cns/cns-1.2.1-r8.ebuild @@ -0,0 +1,232 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic + +MY_PN="${PN}_solve" +MY_PV="$(delete_version_separator 2)" +MY_P="${MY_PN}_${MY_PV}" + +DESCRIPTION="Crystallography and NMR System" +HOMEPAGE="http://cns.csb.yale.edu/" +SRC_URI=" + ${MY_P}_all-mp.tar.gz + aria? ( aria2.3.2.tar.gz )" + +SLOT="0" +LICENSE="cns" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="aria openmp" + +RDEPEND="app-shells/tcsh" +DEPEND="${RDEPEND}" + +FORTRAN_NEED_OPENMP=1 + +S="${WORKDIR}/${MY_P}" + +RESTRICT="fetch test" + +pkg_nofetch() { + elog "Fill out the form at http://cns.csb.yale.edu/cns_request/" + use aria && elog "and http://aria.pasteur.fr/" + elog "and place these files:" + elog ${A} + elog "in ${DISTDIR}." +} + +get_fcomp() { + case $(tc-getFC) in + *gfortran* ) + FCOMP="gfortran" ;; + ifort ) + FCOMP="ifc" ;; + * ) + FCOMP=$(tc-getFC) ;; + esac +} + +pkg_setup() { + fortran-2_pkg_setup + get_fcomp +} + +get_bitness() { + echo > "${T}"/test.c + $(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o + case $(file "${T}"/test.o) in + *64-bit*|*ppc64*|*x86_64*) export _bitness="64";; + *32-bit*|*ppc*|*i386*) export _bitness="32";; + *) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";; + esac +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-gentoo.patch \ + "${FILESDIR}"/${PV}-parallel.patch + + get_bitness + + if use aria; then + pushd "${WORKDIR}"/aria* >& /dev/null + # Update the cns sources in aria for version 1.2.1 + epatch "${FILESDIR}"/1.2.1-aria2.3.patch + + # Update the code with aria specific things + cp -rf cns/src/* "${S}"/source/ || die + popd >& /dev/null + fi + + # the code uses Intel-compiler-specific directives + if [[ $(tc-getFC) =~ gfortran ]]; then + epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch + use openmp && \ + append-flags -fopenmp && append-ldflags -fopenmp + COMP="gfortran" + [[ ${_bitness} == 64 ]] && \ + append-fflags -fdefault-integer-8 + elif [[ $(tc-getFC) == if* ]]; then + epatch "${FILESDIR}"/${PV}-ifort.patch + use openmp && \ + append-flags -openmp && append-ldflags -openmp + COMP="ifort" + [[ ${_bitness} == 64 ]] && append-fflags -i8 + fi + + [[ ${_bitness} == 64 ]] && \ + append-cflags "-DINTEGER='long long int'" + + # Set up location for the build directory + # Uses obsolete `sort` syntax, so we set _POSIX2_VERSION + cp "${FILESDIR}"/cns_solve_env_sh "${T}"/ || die + sed \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \ + -i "${S}"/cns_solve_env || die + sed \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \ + -i "${T}"/cns_solve_env_sh || die + + einfo "Fixing shebangs..." + find "${S}" -type f \ + -exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' + || die +} + +src_compile() { + local GLOBALS + local MALIGN + if [[ $(tc-getFC) =~ g77 ]]; then + GLOBALS="-fno-globals" + MALIGN='\$(CNS_MALIGN_I86)' + fi + + # Set up the compiler to use + ln -s Makefile.header instlib/machine/unsupported/g77-unix/Makefile.header.${FCOMP} || die + + # make install really means build, since it's expected to be used in-place + # -j1 doesn't mean we do no respect MAKEOPTS! + emake -j1 \ + CC="$(tc-getCC)" \ + F77=$(tc-getFC) \ + LD=$(tc-getFC) \ + CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ + LDFLAGS="${LDFLAGS}" \ + F77OPT="${FCFLAGS} ${MALIGN}" \ + F77STD="${GLOBALS}" \ + OMPLIB="${OMPLIB}" \ + compiler="${COMP}" \ + install +} + +src_test() { + # We need to force on g77 manually, because we can't get aliases working + # when we source in a -c + einfo "Running tests ..." + csh -c \ + "export CNS_G77=ON; source ${S}/cns_solve_env; make run_tests" \ + || die "tests failed" + einfo "Displaying test results ..." + cat "${S}"/*_g77/test/*.diff-test +} + +src_install() { + # Install to locations resembling FHS + sed \ + -e "s:${S}:usr:g" \ + -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT ${EPREFIX}/usr:g" \ + -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/cns:g" \ + -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \ + -e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \ + -e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \ + -e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \ + -e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \ + -e "/^g77on/d" \ + -i "${S}"/cns_solve_env || die + # I don't entirely understand why the sh version requires a leading / + # for CNS_SOLVE and CNS_ROOT, but it does + sed \ + -e "s:${S}:/usr:g" \ + -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=${EPREFIX}/usr:g" \ + -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/cns:g" \ + -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \ + -e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \ + -e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \ + -e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \ + -e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \ + -e "/^g77on/d" \ + -e "/^g77off/d" \ + -i "${T}"/cns_solve_env_sh || die + + # Get rid of setup stuff we don't need in the installed script + sed \ + -e "83,$ d" \ + -e "37,46 d" \ + -i "${S}"/cns_solve_env || die + sed \ + -e "84,$ d" \ + -e "39,50 d" \ + -i "${T}"/cns_solve_env_sh || die + + newbin "${S}"/*linux*/bin/cns_solve* cns_solve + + # Can be run by either cns_solve or cns + dosym cns_solve /usr/bin/cns + + # Don't want to install this + rm -f "${S}"/*linux*/utils/Makefile || die + + dobin "${S}"/*linux*/utils/* + + sed \ + -e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \ + -i "${S}"/bin/cns_web || die + + dobin "${S}"/bin/cns_{edit,header,transfer,web} + + insinto /usr/share/cns + doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib + doins "${S}"/bin/cns_info + + insinto /etc/profile.d + newins "${S}"/cns_solve_env cns_solve_env.csh + newins "${T}"/cns_solve_env_sh cns_solve_env.sh + + dohtml \ + -A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \ + -f all_cns_info_template,omac,def \ + -r doc/html/* + # Conflits with app-text/dos2unix + rm -f "${D}"/usr/bin/dos2unix || die +} + +pkg_postinst() { + if use openmp; then + elog "Set OMP_NUM_THREADS to the number of threads you want." + elog "If you get segfaults on large structures, set the GOMP_STACKSIZE" + elog "variable if using gcc (16384 should be good)." + fi +} diff --git a/sci-chemistry/cns/cns-1.3_p7-r1.ebuild b/sci-chemistry/cns/cns-1.3_p7-r1.ebuild new file mode 100644 index 000000000000..cf86379c44be --- /dev/null +++ b/sci-chemistry/cns/cns-1.3_p7-r1.ebuild @@ -0,0 +1,215 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils fortran-2 toolchain-funcs versionator flag-o-matic + +MY_PN="${PN}_solve" +MY_PV="$(delete_version_separator 2)" +MY_P="${MY_PN}_${MY_PV}" + +DESCRIPTION="Crystallography and NMR System" +HOMEPAGE="http://cns.csb.yale.edu/" +SRC_URI=" + ${MY_P/p7}_all.tar.gz + aria? ( aria2.3.1.tar.gz )" + +SLOT="0" +LICENSE="cns" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="aria openmp" + +RDEPEND="app-shells/tcsh" +DEPEND="${RDEPEND}" + +FORTRAN_NEED_OPENMP=1 + +S="${WORKDIR}/${MY_P/p7}" + +RESTRICT="fetch" + +pkg_nofetch() { + elog "Fill out the form at http://cns.csb.yale.edu/cns_request/" + use aria && elog "and http://aria.pasteur.fr/" + elog "and place these files:" + elog ${A} + elog "in ${DISTDIR}." +} + +get_fcomp() { + case $(tc-getFC) in + *gfortran* ) + FCOMP="gfortran" ;; + ifort ) + FCOMP="ifc" ;; + * ) + FCOMP=$(tc-getFC) ;; + esac +} + +pkg_setup() { + fortran-2_pkg_setup + get_fcomp +} + +get_bitness() { + echo > "${T}"/test.c + $(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o + case $(file "${T}"/test.o) in + *64-bit*|*ppc64*|*x86_64*) export _bitness="64";; + *32-bit*|*ppc*|*i386*) export _bitness="32";; + *) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";; + esac +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-gentoo.patch \ + "${FILESDIR}"/${PV}-delete.patch + + get_bitness + + if use aria; then + pushd "${WORKDIR}"/aria* >& /dev/null + # Update the cns sources in aria for version 1.2.1 + epatch "${FILESDIR}"/1.2.1-aria2.3.patch + + # Update the code with aria specific things + cp -rf cns/src/* "${S}"/source/ || die + popd >& /dev/null + fi + + # the code uses Intel-compiler-specific directives + if [[ $(tc-getFC) =~ gfortran ]]; then + use openmp && \ + append-flags -fopenmp && append-ldflags -fopenmp + COMP="gfortran" + [[ ${_bitness} == 64 ]] && \ + append-fflags -fdefault-integer-8 + elif [[ $(tc-getFC) == if* ]]; then + use openmp && \ + append-flags -openmp && append-ldflags -openmp + COMP="ifort" + [[ ${_bitness} == 64 ]] && append-fflags -i8 + fi + + [[ ${_bitness} == 64 ]] && \ + append-cflags "-DINTEGER='long long int'" + + # Set up location for the build directory + # Uses obsolete `sort` syntax, so we set _POSIX2_VERSION + cp "${FILESDIR}"/cns_solve_env_sh-${PV} "${T}"/cns_solve_env_sh || die + sed \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \ + -i "${S}"/cns_solve_env || die + sed \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \ + -e "s:setenv OMP_STACKSIZE 256m:export OMP_STACKSIZE=256m:g" \ + -e "s:^limit:^ulimit:g" \ + -i "${T}"/cns_solve_env_sh || die + + ebegin "Fixing shebangs..." + find "${S}" -type f \ + -exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' + || die + find . -name "Makefile*" \ + -exec \ + sed \ + -e "s:^SHELL=/bin/sh:SHELL=${EPREFIX}/bin/sh:g" \ + -e "s:/bin/ls:ls:g" \ + -e "s:/bin/rm:rm:g" \ + -i '{}' + || die + eend +} + +src_compile() { + local GLOBALS + local MALIGN + + # Set up the compiler to use + ln -s Makefile.header instlib/machine/unsupported/g77-unix/Makefile.header.${FCOMP} || die + + # make install really means build, since it's expected to be used in-place + # -j1 doesn't mean we do no respect MAKEOPTS! + emake -j1 \ + CC="$(tc-getCC)" \ + CXX="$(tc-getCXX)" \ + F77=$(tc-getFC) \ + LD=$(tc-getFC) \ + CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ + CXXFLAGS="${CXXFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ + LDFLAGS="${LDFLAGS}" \ + F77OPT="${FCFLAGS} ${MALIGN}" \ + F77STD="${GLOBALS}" \ + OMPLIB="${OMPLIB}" \ + compiler="${COMP}" \ + install +} + +src_test() { + # We need to force on g77 manually, because we can't get aliases working + # when we source in a -c + einfo "Running tests ..." + sh -c \ + "export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \ + || die "tests failed" + einfo "Displaying test results ..." + cat "${S}"/*_g77/test/*.diff-test +} + +src_install() { + cat >> "${T}"/66cns <<- EOF + CNS_SOLVE="${EPREFIX}/usr" + CNS_ROOT="${EPREFIX}/usr" + CNS_DATA="${EPREFIX}/usr/share/cns" + CNS_DOC="${EPREFIX}/usr/share/doc/cns-1.3" + CNS_LIB="${EPREFIX}/usr/share/cns/libraries" + CNS_MODULE="${EPREFIX}/usr/share/cns/modules" + CNS_TOPPAR="${EPREFIX}/usr/share/cns/libraries/toppar" + CNS_CONFDB="${EPREFIX}/usr/share/cns/libraries/confdb" + CNS_XTALLIB="${EPREFIX}/usr/share/cns/libraries/xtal" + CNS_NMRLIB="${EPREFIX}/usr/share/cns/libraries/nmr" + CNS_XRAYLIB="${EPREFIX}/usr/share/cns/libraries/xray" + CNS_XTALMODULE="${EPREFIX}/usr/share/cns/modules/xtal" + CNS_NMRMODULE="${EPREFIX}/usr/share/cns/modules/nmr" + CNS_HELPLIB="${EPREFIX}/usr/share/cns/helplib" + EOF + + doenvd "${T}"/66cns || die + + # Don't want to install this + rm -f "${S}"/*linux*/utils/Makefile || die + + sed \ + -e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \ + -i "${S}"/bin/cns_web || die + + newbin "${S}"/*linux*/bin/cns_solve* cns_solve + + # Can be run by either cns_solve or cns + dosym cns_solve /usr/bin/cns + + dobin \ + "${S}"/*linux*/utils/* \ + "${S}"/bin/cns_{edit,header,import_cif,transfer,web} + + insinto /usr/share/cns + doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib "${S}"/bin/cns_info + + dohtml \ + -A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \ + -f all_cns_info_template,omac,def \ + -r doc/html/* + # Conflits with app-text/dos2unix + rm -f "${D}"/usr/bin/dos2unix || die +} + +pkg_postinst() { + if use openmp; then + elog "Set OMP_NUM_THREADS to the number of threads you want." + elog "If you get segfaults on large structures, set the GOMP_STACKSIZE" + elog "variable if using gcc (16384 should be good)." + fi +} diff --git a/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch b/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch new file mode 100644 index 000000000000..42b9b0572231 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch @@ -0,0 +1,20 @@ +--- source/xfft.f.orig 2008-08-03 00:36:52.000000000 -0700 ++++ source/xfft.f 2008-08-03 00:37:06.000000000 -0700 +@@ -514,7 +514,7 @@ + LOGICAL QHERM + DOUBLE PRECISION XRCELL(9), MAPR + C local +-!$ integer omp_get_max_threads, kmp_get_stacksize ++!$ integer omp_get_max_threads + LOGICAL DONE + DOUBLE PRECISION ZERO + PARAMETER (ZERO=0.0D0) +@@ -537,7 +537,7 @@ + NBPP=1 + ! The following command is only relevant for the ifort compiler (if -openmp option is used). + ! If your compiler is not ifort, and gives an error, just comment the next line out: +-!$ if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23) ++! if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23) + ! Explanation: the default KMP_STACKSIZE of ifort is 2**21 bytes (2Mb) for 32bit, + ! and 2**22 bytes (4Mb) for 64bit. + ! This may be low for big structures, which leads to segmentation faults! diff --git a/sci-chemistry/cns/files/1.2.1-aria2.3.patch b/sci-chemistry/cns/files/1.2.1-aria2.3.patch new file mode 100644 index 000000000000..8c6939d8eb92 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-aria2.3.patch @@ -0,0 +1,22 @@ +diff --git a/cns/src/cns.f b/cns/src/cns.f +index a3c2cbe..51a34f8 100644 +--- a/cns/src/cns.f ++++ b/cns/src/cns.f +@@ -470,6 +470,7 @@ C local + INTEGER HNLEN, TMP, PTRSZ, STLEN + CHARACTER*(1) CNSPTMP + CHARACTER*(4) ST ++!$ integer omp_get_max_threads + C + C write header + WRITE(6,'(10X,A)') +@@ -526,6 +527,9 @@ C + WRITE(6,'(10X,7A)') + & ' Running on machine: ',HOSTNM(1:HNLEN), + & ' (',SYSNM(1:TMP),',',ST(1:STLEN),'-bit)' ++!$ write(6,'(31x,a,i3,a)') 'with',omp_get_max_threads(), ++!$ & ' threads' ++!$C (to change use setenv OMP_NUM_THREADS x) + C + CALL GETNAM(USERNM,12,TMP) + WRITE(6,'(10X,2A)') diff --git a/sci-chemistry/cns/files/1.2.1-gentoo.patch b/sci-chemistry/cns/files/1.2.1-gentoo.patch new file mode 100644 index 000000000000..2b47bfcc7d86 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-gentoo.patch @@ -0,0 +1,63 @@ +--- cns_solve_1.21/instlib/source/Makefile.proto 2000-09-07 20:35:33.000000000 +0200 ++++ cns_solve_1.21/instlib/source/Makefile.proto.new 2009-07-14 09:18:37.000000000 +0200 +@@ -11,6 +11,8 @@ + + SHELL=/bin/sh + ++cns_string=`date "+%y%m%d%H%M"` ++ + # commands + RM = /bin/rm + +@@ -25,26 +27,20 @@ + + # rule for the fortran routines + $(OBJS): +- @ echo "compiling: $(@:.o=.f)"; \ +- $(F77) -c $(F77FLAGS) $(@:.o=.f) ++ $(F77) -c $(F77FLAGS) $(@:.o=.f) + + # rule for the dynamic memory allocation C routines + dmemory.o: dmemory.c +- @ echo ; echo "compiling: $?" +- @ $(CC) -c $(CCFLAGS) $? ++ $(CC) -c $(CCFLAGS) $? + + # rule for the machine specific C routines + machine_c.o: machine_c.c +- @ echo ; echo "compiling: $?" +- @ $(CC) -c $(CCFLAGS) $? ++ $(CC) -c $(CCFLAGS) $? + + # rule for the executable itself + ../bin/cns_solve: $(DEPENDS) +- @ echo ; echo "linking: cns_solve"; echo +- @ cns_string=`date "+%y%m%d%H%M"`; \ +- $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ +- $(LDFLAGS) \ +- $(CNS_FFTDIR) $(CNS_FFTLIB); \ ++ $(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ ++ $(CNS_FFTDIR) $(CNS_FFTLIB); \ + if [ -x cns_solve-$$cns_string.exe ]; \ + then echo "created executable file cns_solve-$$cns_string.exe"; \ + echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \ +--- cns_solve_1.21/instlib/utils/Makefile 2004-08-30 00:40:35.000000000 +0200 ++++ cns_solve_1.21/instlib/utils/Makefile.new 2009-07-14 09:50:27.000000000 +0200 +@@ -22,14 +22,14 @@ + make clean + + .f: +- $(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK) ++ $(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK) + + .c: +- $(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK) ++ $(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK) + + .l: + lex $(@).l +- $(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) ++ $(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) + + relink: + @ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile` diff --git a/sci-chemistry/cns/files/1.2.1-ifort.patch b/sci-chemistry/cns/files/1.2.1-ifort.patch new file mode 100644 index 000000000000..ba44bebd1b68 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-ifort.patch @@ -0,0 +1,126 @@ +diff --git a/source/angledb.f b/source/angledb.f +index 28ad657..eaa847d 100644 +--- a/source/angledb.f ++++ b/source/angledb.f +@@ -1416,10 +1416,10 @@ C include files + C local variables + INTEGER COUNT, SPTR, OLDCLASS, OLDMAXANGLEDBS + INTEGER THETYPE, CURPSIS, CURPHIS +- INTEGER CLASSINDEX ++ INTEGER CLASINDEX + DOUBLE PRECISION K1, CUTOFF + CHARACTER*4 THENAME +- CHARACTER*20 CLASSNAME ++ CHARACTER*20 CLASNAME + C begin + C + IF (ANGLEDBFLAG) THEN +@@ -1450,10 +1450,10 @@ C + ELSE IF (WD(1:4).EQ.'CLAS') THEN + OLDCLASS = CURANGLEDBCLASS + CALL NEXTWD('class name =') +- CLASSNAME = WD(1:20) ++ CLASNAME = WD(1:20) + ANGLEDBMODE = NEW + DO COUNT = 1, NANGLEDBCLASSES +- IF (ANGDBCLASSNAMES(COUNT).EQ.CLASSNAME) THEN ++ IF (ANGDBCLASSNAMES(COUNT).EQ.CLASNAME) THEN + ANGLEDBMODE = UPDATE + CURANGLEDBCLASS = COUNT + END IF +@@ -1472,7 +1472,7 @@ C + END IF + NANGLEDBCLASSES = NANGLEDBCLASSES + 1 + CURANGLEDBCLASS = NANGLEDBCLASSES +- ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASSNAME ++ ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASNAME + ANGLEDBASSNDX(CURANGLEDBCLASS) = NANGLEDBS + END IF + C +@@ -1733,16 +1733,16 @@ C + & HEAP(ANGLEDBTPTR)) + ELSE IF (WD(1:4).EQ.'CLAS') THEN + CALL NEXTWD('Class name>') +- CLASSNAME = WD(1:20) +- CLASSINDEX = 0 ++ CLASNAME = WD(1:20) ++ CLASINDEX = 0 + DO COUNT = 1, NANGLEDBCLASSES + IF (ANGDBCLASSNAMES(COUNT).EQ. +- & CLASSNAME) THEN ++ & CLASNAME) THEN + PRINTTHISCLASS(COUNT) = .TRUE. +- CLASSINDEX = COUNT ++ CLASINDEX = COUNT + END IF + END DO +- IF (CLASSINDEX.EQ.0) THEN ++ IF (CLASINDEX.EQ.0) THEN + CALL DSPERR('ANGLEDB', + & 'unknown class. Using first.') + PRINTTHISCLASS(1) = .TRUE. +diff --git a/source/rama.f b/source/rama.f +index c5d14f2..3063e7b 100644 +--- a/source/rama.f ++++ b/source/rama.f +@@ -1468,11 +1468,11 @@ C include files + C local variables + INTEGER COUNT, SPTR, OLDCLASS, OLDMAXRAMAS, + & THETYPE, CURPSIS, CURPHIS, +- & CURCHIS, CURTHTS, CLASSINDEX ++ & CURCHIS, CURTHTS, CLASINDEX + INTEGER CLEN + DOUBLE PRECISION K1, CUTOFF + CHARACTER*4 THENAME +- CHARACTER*50 CLASSNAME ++ CHARACTER*50 CLASNAME + C begin + C + C this is used by READRAMA2 to hold the selection +@@ -1503,10 +1503,10 @@ C + ELSE IF (WD(1:4).EQ.'CLAS') THEN + OLDCLASS = CURRAMACLASS + CALL NEXTWD('class name =') +- CLASSNAME = WD(1:50) ++ CLASNAME = WD(1:50) + RAMAMODE = NEW + DO COUNT = 1, NRAMACLASSES +- IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME) THEN ++ IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME) THEN + RAMAMODE = UPDATE + CURRAMACLASS = COUNT + END IF +@@ -1525,7 +1525,7 @@ C + END IF + NRAMACLASSES = NRAMACLASSES + 1 + CURRAMACLASS = NRAMACLASSES +- RAMACLASSNAMES(CURRAMACLASS) = CLASSNAME ++ RAMACLASSNAMES(CURRAMACLASS) = CLASNAME + END IF + C + C set force constant for current class, +@@ -1954,18 +1954,18 @@ C + & HEAP(RAMAATOMPTR), 0) + ELSE IF (WD(1:4).EQ.'CLAS') THEN + CALL NEXTWD('Class name>') +- CLASSINDEX = 0 ++ CLASINDEX = 0 + DO COUNT = 1, NRAMACLASSES +- IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME) +- & CLASSINDEX = COUNT ++ IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME) ++ & CLASINDEX = COUNT + END DO +- IF (CLASSINDEX.EQ.0) THEN ++ IF (CLASINDEX.EQ.0) THEN + CALL DSPERR('RAMA', + & 'unknown class. Using first.') +- CLASSINDEX = 1 ++ CLASINDEX = 1 + END IF + CALL PRINTRAMAS(CUTOFF, HEAP(CALCRAMAPTR), +- & HEAP(RAMAATOMPTR), CLASSINDEX) ++ & HEAP(RAMAATOMPTR), CLASINDEX) + ELSE + CALL DSPERR('RAMA', + & 'Expected ALL or CLASs.') diff --git a/sci-chemistry/cns/files/1.2.1-parallel.patch b/sci-chemistry/cns/files/1.2.1-parallel.patch new file mode 100644 index 000000000000..dfaa40021d66 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-parallel.patch @@ -0,0 +1,17 @@ +diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto +index 0d0dd3e..ae9e422 100644 +--- a/instlib/source/Makefile.proto ++++ b/instlib/source/Makefile.proto +@@ -19,9 +19,9 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o + + # the default is to make the cns executable + cns_solve: +- @ make -k printflags F77BUG="$(debug)" DEBUG="$(debug)" +- @ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" +- @ make -k exepurge ++ @ make printflags F77BUG="$(debug)" DEBUG="$(debug)" ++ @ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" ++ @ make exepurge + + # rule for the fortran routines + $(OBJS): diff --git a/sci-chemistry/cns/files/1.3_p7-delete.patch b/sci-chemistry/cns/files/1.3_p7-delete.patch new file mode 100644 index 000000000000..cbddf4289158 --- /dev/null +++ b/sci-chemistry/cns/files/1.3_p7-delete.patch @@ -0,0 +1,13 @@ +diff --git a/utils/cluster_struc.cpp b/utils/cluster_struc.cpp +index b64467a..5f727db 100644 +--- a/utils/cluster_struc.cpp ++++ b/utils/cluster_struc.cpp +@@ -173,7 +173,7 @@ int main(int argc, char *argv[]) { + for (int i = 0; i < nrstruc; i++) { + delete[] neighbor[i]; + } +- delete[] neighbor, neighborcount; ++ delete[] neighbor, delete[] neighborcount; + return 5; + } + if (rmsd < cutoff) { diff --git a/sci-chemistry/cns/files/1.3_p7-gentoo.patch b/sci-chemistry/cns/files/1.3_p7-gentoo.patch new file mode 100644 index 000000000000..7942c55abfb9 --- /dev/null +++ b/sci-chemistry/cns/files/1.3_p7-gentoo.patch @@ -0,0 +1,80 @@ +diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto +index 0d0dd3e..dd4b680 100644 +--- a/instlib/source/Makefile.proto ++++ b/instlib/source/Makefile.proto +@@ -11,6 +11,8 @@ + + SHELL=/bin/sh + ++cns_string=`date "+%y%m%d%H%M"` ++ + # commands + RM = /bin/rm + +@@ -19,32 +21,26 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o + + # the default is to make the cns executable + cns_solve: +- @ make -k printflags F77BUG="$(debug)" DEBUG="$(debug)" +- @ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" +- @ make -k exepurge ++ @ make printflags F77BUG="$(debug)" DEBUG="$(debug)" ++ @ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" ++ @ make exepurge + + # rule for the fortran routines + $(OBJS): +- @ echo "compiling: $(@:.o=.f)"; \ +- $(F77) -c $(F77FLAGS) $(@:.o=.f) ++ $(F77) -c $(F77FLAGS) $(@:.o=.f) + + # rule for the dynamic memory allocation C routines + dmemory.o: dmemory.c +- @ echo ; echo "compiling: $?" +- @ $(CC) -c $(CCFLAGS) $? ++ $(CC) -c $(CCFLAGS) $? + + # rule for the machine specific C routines + machine_c.o: machine_c.c +- @ echo ; echo "compiling: $?" +- @ $(CC) -c $(CCFLAGS) $? ++ $(CC) -c $(CCFLAGS) $? + + # rule for the executable itself + ../bin/cns_solve: $(DEPENDS) +- @ echo ; echo "linking: cns_solve"; echo +- @ cns_string=`date "+%y%m%d%H%M"`; \ +- $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ +- $(LDFLAGS) \ +- $(CNS_FFTDIR) $(CNS_FFTLIB); \ ++ $(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \ ++ $(CNS_FFTDIR) $(CNS_FFTLIB); \ + if [ -x cns_solve-$$cns_string.exe ]; \ + then echo "created executable file cns_solve-$$cns_string.exe"; \ + echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \ +diff --git a/instlib/utils/Makefile b/instlib/utils/Makefile +index 98de84f..4f32b34 100644 +--- a/instlib/utils/Makefile ++++ b/instlib/utils/Makefile +@@ -22,17 +22,17 @@ utils: + make clean + + .f: +- $(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK) ++ $(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK) + + .c: +- $(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK) ++ $(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK) + + .cpp: +- $(CPP) -o $@ $(CCFLAGS) $(@).cpp $(CCLINK) ++ $(CXX) $(LDFLAGS) -o $@ $(CXXFLAGS) $(@).cpp $(CCLINK) + + .l: + lex $(@).l +- $(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) ++ $(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB) + + relink: + @ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile` diff --git a/sci-chemistry/cns/files/cns_solve_env_sh b/sci-chemistry/cns/files/cns_solve_env_sh new file mode 100644 index 000000000000..34e1a2b635cf --- /dev/null +++ b/sci-chemistry/cns/files/cns_solve_env_sh @@ -0,0 +1,221 @@ +#!/bin/sh +# +# This file sets up the appropriate environmental variables and paths +# for CNSsolve. In the case of the same machines with different versions +# of the OS, backward compatibility is assumed - ie. a later version will +# be setup for a previous version of the OS if nothing else is available. +# +# written by: Paul Adams +# +# copyright Yale University +# +# ========================================================================== +# +# >>>>>> Important: define the location of the CNSsolve directory <<<<<< +# +# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY + + CNS_SOLVE=_CNSsolve_location_ + +# +# ========================================================================== +# +# full expansion of the CNS_SOLVE variable prior to use. +# +export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE +# +# ========================================================================== +# +# set the number of threads for SGI multiprocessors +# if this causes a problem on other systems it can be commented out +# +export MP_SET_NUMTHREADS; MP_SET_NUMTHREADS=1 +# +# ========================================================================== +# +# get the machine architecture +# +if [ -d $CNS_SOLVE ]; then + if [ ! "$CNS_ARCH" ]; then + export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch` + fi +else + export CNS_ARCH; CNS_ARCH='unknown' +fi +# +# system variables (this is needed for openmp) +# +ulimit -s unlimited +# ========================================================================== +# +# general environmental variables +# +export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries +export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules +export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar +export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb +export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal +export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr +export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray +export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal +export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr +export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib +# +# general user aliases +# +cns_web () { $CNS_SOLVE/bin/cns_web; } +cns_header () { $CNS_SOLVE/bin/cns_header; } +cns_info () { cat $CNS_SOLVE/bin/cns_info; } +cns_transfer () { $CNS_SOLVE/bin/cns_transfer; } +if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then + cns_edit () { $CNS_SOLVE/bin/cns_edit_local; } +else + cns_edit () { $CNS_SOLVE/bin/cns_edit; } +fi +run_tutorial () { "csh -f tutorial.csh"; } +# +# g77 compilation and use +# +g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; } +g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; } +# +# developer aliases +# +run_tests () { $CNS_SOLVE/bin/run_tests; } +run_diffs () { $CNS_SOLVE/bin/run_diffs; } +maketar () { $CNS_SOLVE/bin/maketar; } +create_patch () { $CNS_SOLVE/bin/create_patch; } +# +# +# ========================================================================== +# +# to do expansions - unset noglob just in case user has it otherwise +# +set +f +# +# try to set up appropriate path +# +# first strip off any trailing information (eg. _g77) +# +CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'` +# +cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'` +cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'` +cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'` +cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'` +cns_minor=`echo $cns_major | sed -e 's/\./ /g'` +# +# if we are looking for a specific type of setup then limit search +# +cns_dirs="" +if [ ! "$CNS_G77" ]; then + if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then + cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" + fi +else + CNS_ARCH="${CNS_ARCH}_g77" + if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then + cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" + fi +fi +# +# first look for an exact match (with os version) +# +# +cns_found=0 +if [ -n "$cns_dirs" ]; then + for cns_dir in $cns_dirs ; do + cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'` + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \ + $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + done +# +# +# now look for an exact match (without os version) +# + if [ $cns_found -eq 0 ]; then + for cns_dir in $cns_dirs ; do + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \ + $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + done + fi +# +# now look for a backwards compatible match (with os version major/minor) +# + if [ $cns_found -eq 0 ]; then + for cns_dir in $cns_dirs ; do + if [ $cns_found -eq 0 ]; then + cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'` + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then + osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'` + if [ $osv_test -eq 1 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + fi + fi + done + fi +# +# now look for a wildcard match on cpu +# + if [ $cns_found -eq 0 ]; then + cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'` + cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'` + for cns_dir in $cns_dirs ; do + if [ $cns_found -eq 0 ]; then + cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'` + cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'` + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \ + $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then + cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'` + if [ $cpu_test -eq 1 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + fi + fi + done + fi +fi +# +# if found set environment +# +if [ $cns_found -eq 1 ]; then + # + # set installation and source directory + # + export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv + export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source + # + # path for CNSsolve utility programs + # + if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then + export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils` + fi + # + # path for CNSsolve executable if installed + # + if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then + export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin` + fi +fi +# +unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor +unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same +unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test +# diff --git a/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7 b/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7 new file mode 100644 index 000000000000..12368f87b596 --- /dev/null +++ b/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7 @@ -0,0 +1,229 @@ +#!/bin/sh +# +# This file sets up the appropriate environmental variables and paths +# for CNSsolve. In the case of the same machines with different versions +# of the OS, backward compatibility is assumed - ie. a later version will +# be setup for a previous version of the OS if nothing else is available. +# +# written by: Paul Adams +# +# copyright Yale University +# +# ========================================================================== +# +# >>>>>> Important: define the location of the CNSsolve directory <<<<<< +# +# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY + + CNS_SOLVE=_CNSsolve_location_ + +# +# ========================================================================== +# +# full expansion of the CNS_SOLVE variable prior to use. +# +export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE +# +# ========================================================================== +# +# get the machine architecture +# +if [ -d $CNS_SOLVE ]; then + if [ ! "$CNS_ARCH" ]; then + export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch` + fi +else + export CNS_ARCH; CNS_ARCH='unknown' +fi +# +# ========================================================================== +# +# system variables for OpenMP +# +# The default stack sizes are usually insufficient, especially when +# CNS is compiled using OpenMP. If the stack sizes are too +# small segfaults may occur. Recommended setting for "stacksize": +limit stacksize unlimited +# +# KMP_STACKSIZE is specific for Intel ifort, icc: +##setenv KMP_STACKSIZE 256m +# +# OMP_STACKSIZE is used by all compilers: +setenv OMP_STACKSIZE 256m +# +# Uncomment the following line and change as appropriate to set the number +# of processors (threads) to use. +###setenv OMP_NUM_THREADS 4 +# +# ========================================================================== +# +# general environmental variables +# +export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries +export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules +export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar +export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb +export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal +export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr +export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray +export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal +export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr +export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib +# +# general user aliases +# +cns_web () { $CNS_SOLVE/bin/cns_web; } +cns_header () { $CNS_SOLVE/bin/cns_header; } +cns_info () { cat $CNS_SOLVE/bin/cns_info; } +cns_transfer () { $CNS_SOLVE/bin/cns_transfer; } +if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then + cns_edit () { $CNS_SOLVE/bin/cns_edit_local; } +else + cns_edit () { $CNS_SOLVE/bin/cns_edit; } +fi +# +# g77 compilation and use +# +g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; } +g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; } +# +# developer aliases +# +run_tests () { $CNS_SOLVE/bin/run_tests; } +run_diffs () { $CNS_SOLVE/bin/run_diffs; } +maketar () { $CNS_SOLVE/bin/maketar; } +create_patch () { $CNS_SOLVE/bin/create_patch; } +# +# +# ========================================================================== +# +# to do expansions - unset noglob just in case user has it otherwise +# +set +f +# +# try to set up appropriate path +# +# first strip off any trailing information (eg. _g77) +# +CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'` +# +cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'` +cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'` +cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'` +cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'` +cns_minor=`echo $cns_major | sed -e 's/\./ /g'` +# +# if we are looking for a specific type of setup then limit search +# +cns_dirs="" +if [ ! "$CNS_G77" ]; then + if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then + cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" + fi +else + CNS_ARCH="${CNS_ARCH}_g77" + if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then + cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`" + fi +fi +# +# first look for an exact match (with os version) +# +# +cns_found=0 +if [ -n "$cns_dirs" ]; then + for cns_dir in $cns_dirs ; do + cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'` + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \ + $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + done +# +# +# now look for an exact match (without os version) +# + if [ $cns_found -eq 0 ]; then + for cns_dir in $cns_dirs ; do + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \ + $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + done + fi +# +# now look for a backwards compatible match (with os version major/minor) +# + if [ $cns_found -eq 0 ]; then + for cns_dir in $cns_dirs ; do + if [ $cns_found -eq 0 ]; then + cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'` + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then + osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'` + if [ $osv_test -eq 1 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + fi + fi + done + fi +# +# now look for a wildcard match on cpu +# + if [ $cns_found -eq 0 ]; then + cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'` + cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'` + for cns_dir in $cns_dirs ; do + if [ $cns_found -eq 0 ]; then + cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'` + cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'` + if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then + if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \ + $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then + cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'` + if [ $cpu_test -eq 1 ]; then + cns_archenv=$cns_dir + cns_found=1 + fi + fi + fi + fi + done + fi +fi +# +# if found set environment +# +if [ $cns_found -eq 1 ]; then + # + # set installation and source directory + # + export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv + export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source + # + # path for CNSsolve utility programs + # + if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then + export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils` + fi + # + # path for CNSsolve executable if installed + # + if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then + export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin` + fi +fi +# +unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor +unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same +unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test +# diff --git a/sci-chemistry/cns/metadata.xml b/sci-chemistry/cns/metadata.xml new file mode 100644 index 000000000000..67326b6bd798 --- /dev/null +++ b/sci-chemistry/cns/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="aria"> Support patch for sci-chemistry/aria</flag> + </use> + <longdescription> +Crystallography and NMR System (CNS) is the result of an international +collaborative effort among several research groups. The program has +been designed to provide a flexible multi-level hierachical approach for the +most commonly used algorithms in macromolecular structure determination. +Highlights include heavy atom searching, experimental phasing (including +MAD and MIR), density modification, crystallographic refinement with maximum +likelihood targets, and NMR structure calculation using NOEs, J-coupling, +chemical shift, and dipolar coupling data. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest new file mode 100644 index 000000000000..dd84f840f7ce --- /dev/null +++ b/sci-chemistry/coot/Manifest @@ -0,0 +1,10 @@ +AUX coot-0.8.2-desktop.patch 544 SHA256 6558c17da028f47bec3480afbf85d8457e4c34bb50a6285bf0522de922a6bc89 SHA512 f02b506fe8ba02601e95afa733ea13a24baf0c11a42d6947d4c2cd34c81ef046889a959d76ac66acd0aecf4bd665b656aa8d0138213c3a1e538846a62e53608a WHIRLPOOL 6ce940a32caa7148257f5ffbcb274b6c4762ee6645a2dea80b70aa749c517a50a76098b6f2de0067239cfe787ac06c1385df54e45481ddfe9d9a29d3324bae71 +AUX coot-0.8.2-libguile.patch 776 SHA256 aa1e18d4ef43fb61e85aba05d13797f9aa2beb1da220405f1eb6058ac36eb60b SHA512 96536508d2fec0d13014636f2eb1fa314fe764a78a0d7b4c5a411570c19005e673b32dc4a67551330d56d9af66bed3571d1d5de44fd1741a01180f64d262f3e5 WHIRLPOOL 4c3a95069da1b20c74cc9c87a7bf042aa529af2ff85dcf0071f6759c3d35d3a06c63c0cf2e39376cf4075ec3c10871959122289aa156128bb3b8a0ca0c0d1b3a +AUX coot-0.8.2-libtool.patch 1450 SHA256 e4ba02ad24330e3df3f32772275db47caeb4f36d77d57de882f7a73d7e11e5bf SHA512 d524764fa99e3a5200b1dccc4ac33bccfbb2554c0b66e54f5e7be9a9f21b54e903b67c5109db9c179d53a7bb9624ac291769463cfac2051c6445e5de280b81e7 WHIRLPOOL c9ced4a4c409fbc63769676e7725f7ae990e75ab4d75469cc2d5cc6813a300043b7d31223fe16f4c63bc67594d3d854d24759298248bf01419853233ee46fe77 +AUX coot-0.8.2-sandbox-icons.patch 740 SHA256 b93756a9ab1244573ac24427954c53ac9f14a82e7ec1f115b178897abcab42a8 SHA512 2b45caa89309abe3a4a79ddbcfadf2510b055cbf83e3f8f1ad600db7324562cc9cf8de2bfd25f7ce55c754eb36a08e12bd47a2cb01b769d618a18732dd8d0618 WHIRLPOOL e9eb67a1e75bb9b5508dd555a58490e1313b819e90be09d0703c1663e5d6042e0dce96808997920fad697843630843247f301c85d67925fe72b463da1f26543a +DIST coot-0.8.2-greg-data.tar.gz 8677037 SHA256 d936795853406f3c2a3dfd6f37a07a7df677e96b2d023d9302668aa49b7f06cb SHA512 28396a5fa64af61e8932b565c6593ed27c4708e6a59158d62c94005bea9fa8c46562b6caba97011209a40705e5ec6711b949138dd8a23bb954df2ab4dfa9bb33 WHIRLPOOL cb85234ece76314661bcfa424904224ac554c41fc63655857f3ba1bd2f0bf8e457c55dd1f42ffecffb9a8582ff759277b0fb9a40ca2393bf47b6a09fdd04ce1e +DIST coot-0.8.2.tar.gz 15772937 SHA256 2f5961ded7f2cf06b887560afe964c239aba94f9c4bf8a2a80b3ca4fbc471eee SHA512 a323608df7b63f22eb2d1ac679fc047bba9fe23fe6366ae1d6ae29ca00a567aafb3d29840878e8c5123421037e26b6463f0bb845ef28dcbb4f3647cda2f74575 WHIRLPOOL d84d23aa49404dce63649bd6c5f8149e95ad5776ec4fa6ebdfcf44ebabef56c3a29376da7a1d5f8ee6f8013158a7f5c74f5bd74066036ca750bc3ff7de084791 +EBUILD coot-0.8.2-r1.ebuild 4528 SHA256 432fe66b9b92bfaf7c95a58aa64e6d8150f9155572c9ccb090cd85fc7e88e920 SHA512 25a5f857a6b12af4abaf86f8e23cbfda3db719c57cfe5923e765f9382949b19decf807407762992071b73c1c05fa42d18a46efbd6bac2e830361ca07d2553715 WHIRLPOOL 29fd36513fdbdb5060067652424e9c299397bf52c396f52ccf380c021285286d7f4142d24df5a805ffbe282b078c9e6029f502a5c1f0d528a9e663c23fc3364a +MISC ChangeLog 6137 SHA256 adae0c90ad52a077db47690d046aef91e19918424770a47a2a2d6694ba29c09f SHA512 802d669d07578b149582e2774f6b84c326abf4017d6a04f24abe3291a1ea38addeaa9ba97636b82ba812a4af676a9f6e1c0ccb34a99959ebc28b6e4969cf0fe4 WHIRLPOOL 1eb9e01b9d0772718f7eafe3347cf65d8fa554171e9cbb8421f603f1fd037d1855095f66eaccda0dfcc1b00349da51b50416225a423061cd8fc963367769a7aa +MISC ChangeLog-2015 10693 SHA256 47404a26a7d4c946afd57cea0f31ec8aeca4cd034765419035b3ec3adba0984d SHA512 4549d7da76009495a28c8283a048e0906a3f959da9fcd8278a9287106cc5493b4a0b84cbb731b2d3cb01daf15c369b36f78f734c70c074ffa1d6025add2eeb20 WHIRLPOOL 6c677d0d466f49a73e8573ee393f87fcb5ee82bd1974d9592375f27986065950a7cc0fed787b0f9c9890aedb846b850d4ca957bbbd9f3adb82626df5f32a0015 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/coot/coot-0.8.2-r1.ebuild b/sci-chemistry/coot/coot-0.8.2-r1.ebuild new file mode 100644 index 000000000000..9df6946af852 --- /dev/null +++ b/sci-chemistry/coot/coot-0.8.2-r1.ebuild @@ -0,0 +1,181 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +AUTOTOOLS_AUTORECONF="true" + +inherit autotools-utils python-single-r1 toolchain-funcs versionator + +MY_S2_PV=$(replace_version_separator 2 - ${PV}) +MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1} +MY_S_P=${MY_S2_P}-${PR/r/revision-} +MY_PV=${PV} +MY_P=${PN}-${MY_PV} + +DESCRIPTION="Crystallographic Object-Oriented Toolkit" +HOMEPAGE="https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/" +SRC_URI=" + http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/${MY_P}.tar.gz + test? ( https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/data/greg-data.tar.gz -> ${P}-greg-data.tar.gz )" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+openmp static-libs test" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +SCIDEPS=" + sci-libs/libccp4 + sci-libs/clipper + >=sci-libs/coot-data-2 + >=sci-libs/gsl-1.3 + sci-libs/fftw:2.1= + sci-libs/mmdb:2 + sci-libs/monomer-db + sci-libs/ssm + sci-chemistry/reduce + sci-chemistry/probe" + +XDEPS=" + gnome-base/libgnomecanvas + gnome-base/librsvg:2 + media-libs/libpng:0= + media-libs/freeglut + x11-libs/gtk+:2 + x11-libs/goocanvas:0 + x11-libs/gtkglext + virtual/opengl" + +SCHEMEDEPS=" + <dev-scheme/guile-2 + dev-scheme/net-http + dev-scheme/guile-gui + >=dev-scheme/guile-lib-0.1.6 + dev-scheme/guile-www + >=x11-libs/guile-gtk-2.1" + +RDEPEND=" + ${SCIDEPS} + ${XDEPS} + ${SCHEMEDEPS} + ${PYTHON_DEPS} + dev-db/sqlite:3 + dev-libs/boost:0=[python,${PYTHON_USEDEP}] + dev-libs/glib:2 + >=dev-libs/gmp-4.2.2-r2:0= + dev-python/pygobject:2[${PYTHON_USEDEP}] + dev-python/pygtk:2[${PYTHON_USEDEP}] + >=net-misc/curl-7.19.6 + net-dns/libidn + sys-libs/readline:0= + " +DEPEND="${RDEPEND} + virtual/pkgconfig + >=sys-devel/libtool-2.4-r2 + dev-lang/swig + sys-devel/bc + test? ( dev-scheme/greg )" + +S="${WORKDIR}/${MY_P}" + +pkg_setup() { + if use openmp; then + tc-has-openmp || die "Please use an OPENMP capable compiler" + fi + python-single-r1_pkg_setup +} + +PATCHES=( + "${FILESDIR}"/${P}-desktop.patch + "${FILESDIR}"/${P}-sandbox-icons.patch + "${FILESDIR}"/${P}-libtool.patch + "${FILESDIR}"/${P}-libguile.patch +) + +src_unpack() { + default + if use test; then + cd "${S}" || die + ln -sf ../greg-data || die + fi +} + +src_prepare() { + sed \ + -e '/export LD_LIBRARY/s:^:#:g' \ + -i src/coot.in || die + + sed \ + -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \ + -i configure.ac || die + + autotools-utils_src_prepare +} + +src_configure() { + # All the --with's are used to activate various parts. + # Yes, this is broken behavior. + local myeconfargs=( + --with-goocanvas-prefix="${EPREFIX}/usr" + --with-guile="${EPREFIX}/usr" + --with-python="${EPREFIX}/usr" + --with-guile-gtk + --with-pygtk="${EPREFIX}/usr" + --with-sqlite3 + --with-boost="${EPREFIX}/usr" + ) + autotools-utils_src_configure +} + +src_test() { + source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" + mkdir "${T}"/coot_test || die + + export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb" + export COOT_SCHEME_DIR="${S}/scheme/" + export COOT_RESOURCES_FILE="${S}/cootrc" + export COOT_PIXMAPS_DIR="${S}/pixmaps/" + export COOT_DATA_DIR="${S}/" + export COOT_PYTHON_DIR="${S}/python/" + export PYTHONPATH="${COOT_PYTHON_DIR}:${S}/src:${PYTHONPATH}" + export PYTHONHOME="${EPREFIX}"/usr/ + export CCP4_SCR="${T}"/coot_test/ + export CLIBD_MON="${EPREFIX}/usr/share/data/monomers/" + export COOT_REF_STRUCTS="${EPREFIX}/usr/share/data/monomers/" + export SYMINFO="${S}/syminfo.lib" + + export COOT_TEST_DATA_DIR="${S}"/greg-data/ + + cat > command-line-greg.scm <<- EOF + (use-modules (ice-9 greg)) + (set! greg-tools (list "greg-tests")) + (set! greg-debug #t) + (set! greg-verbose 5) + (let ((r (greg-test-run))) + (if r + (coot-real-exit 0) + (coot-real-exit 1))) + EOF + + einfo "Running test with following paths ..." + einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES" + einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR" + einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE" + einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR" + einfo "COOT_DATA_DIR $COOT_DATA_DIR" + einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR" + einfo "PYTHONPATH $PYTHONPATH" + einfo "PYTHONHOME $PYTHONHOME" + einfo "CCP4_SCR ${CCP4_SCR}" + einfo "CLIBD_MON ${CLIBD_MON}" + einfo "SYMINFO ${SYMINFO}" + + "${S}"/src/coot-bin --no-graphics --script command-line-greg.scm || die + "${S}"/src/coot-bin --no-graphics --script python-tests/coot_unittest.py || die +} diff --git a/sci-chemistry/coot/files/coot-0.8.2-desktop.patch b/sci-chemistry/coot/files/coot-0.8.2-desktop.patch new file mode 100644 index 000000000000..c264dd5a7628 --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.8.2-desktop.patch @@ -0,0 +1,21 @@ + coot.desktop | 7 +++---- + 1 file changed, 3 insertions(+), 4 deletions(-) + +diff --git a/coot.desktop b/coot.desktop +index 74aecf3..8668018 100644 +--- a/coot.desktop ++++ b/coot.desktop +@@ -1,10 +1,9 @@ + [Desktop Entry] + Type=Application +-Encoding=UTF-8 + Name=Coot + Comment=Macromolecular model builder + Exec=coot +-Icon=coot.png ++Icon=coot + Terminal=true +-Categories=Science;Graphics +-MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile ++Categories=Science;Graphics; ++MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile; diff --git a/sci-chemistry/coot/files/coot-0.8.2-libguile.patch b/sci-chemistry/coot/files/coot-0.8.2-libguile.patch new file mode 100644 index 000000000000..cbaccefb2947 --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.8.2-libguile.patch @@ -0,0 +1,29 @@ + src/graphics-info-modelling.cc | 1 + + src/graphics-info.cc | 2 ++ + 2 files changed, 3 insertions(+) + +diff --git a/src/graphics-info-modelling.cc b/src/graphics-info-modelling.cc +index 05a63ad..4b7d129 100644 +--- a/src/graphics-info-modelling.cc ++++ b/src/graphics-info-modelling.cc +@@ -102,6 +102,7 @@ + + #include "utils/coot-utils.hh" + ++#include <libguile.h> + + // Idealize the geometry without considering the map. + // +diff --git a/src/graphics-info.cc b/src/graphics-info.cc +index e2f9d52..76b6769 100644 +--- a/src/graphics-info.cc ++++ b/src/graphics-info.cc +@@ -92,6 +92,8 @@ + #include "cc-interface-scripting.hh" + #endif + ++#include <libguile.h> ++ + // A few non-class members - should be somewhere else, I guess. + // + void initialize_graphics_molecules() { diff --git a/sci-chemistry/coot/files/coot-0.8.2-libtool.patch b/sci-chemistry/coot/files/coot-0.8.2-libtool.patch new file mode 100644 index 000000000000..10c43ad55594 --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.8.2-libtool.patch @@ -0,0 +1,39 @@ + configure.ac | 2 +- + lbg/Makefile.am | 11 ----------- + 2 files changed, 1 insertion(+), 12 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 73d6ed7..b04dcd6 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -69,7 +69,7 @@ AC_LIB_PREPARE_MULTILIB + + AC_SUBST(COOT_STDTYPES) + +-EXPORT_DYNAMIC_FLAG_SPEC=$export_dynamic_flag_spec ++eval EXPORT_DYNAMIC_FLAG_SPEC=\"$export_dynamic_flag_spec\" + AC_SUBST(EXPORT_DYNAMIC_FLAG_SPEC) + + +diff --git a/lbg/Makefile.am b/lbg/Makefile.am +index 1277afe..a79ebe0 100644 +--- a/lbg/Makefile.am ++++ b/lbg/Makefile.am +@@ -43,17 +43,6 @@ pkginclude_HEADERS = lbg.hh wmolecule.hh flev-annotations.hh graphics-c-interfa + lbg-drag-and-drop.hh qed-interface.hh alerts.hh pi-stacking.hh + pkgincludedir = $(includedir)/coot/lbg + +-# 20140521 +-# lidia_LDFLAGS = -Wl,--export-dynamic +-# +-# Now we use EXPORT_DYNAMIC_FLAG_SPEC which usually evaluates to ${wl}--export-dynamic +-# (but not for MacOSX, where it Does The Right Thing (hopefully)). +-# We manually set the value of wl here, but maybe the Right Thing To Do for that is +-# run (eval) $($LIBTOOL --config | grep ^wl). How do I do that here though? +-# I don't understand. Maybe the setting of wl should be done in configure? But then +-# I have to force the output of libtool. Bleugh. Hmm... +-# Anyway, thankyou Gary Vaughan. +-wl=-Wl, + lidia_LDFLAGS = $(EXPORT_DYNAMIC_FLAG_SPEC) + + # res spec output operator means we include libcoot-coord-utils diff --git a/sci-chemistry/coot/files/coot-0.8.2-sandbox-icons.patch b/sci-chemistry/coot/files/coot-0.8.2-sandbox-icons.patch new file mode 100644 index 000000000000..2a9ff2d7177c --- /dev/null +++ b/sci-chemistry/coot/files/coot-0.8.2-sandbox-icons.patch @@ -0,0 +1,16 @@ + pixmaps/icons/Makefile.am | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/pixmaps/icons/Makefile.am b/pixmaps/icons/Makefile.am +index 0c183ae..dddc11a 100644 +--- a/pixmaps/icons/Makefile.am ++++ b/pixmaps/icons/Makefile.am +@@ -11,6 +11,6 @@ install-data-local: + CONTEXT=` echo $$icon | cut -d_ -f2`; \ + SIZE=` echo $$icon | cut -d_ -f3`; \ + ICONFILE=`echo $$icon | cut -d_ -f4`; \ +- mkdir -p $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \ +- $(INSTALL_DATA) $(srcdir)/$$icon $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \ ++ mkdir -p $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \ ++ $(INSTALL_DATA) $(srcdir)/$$icon $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \ + done; diff --git a/sci-chemistry/coot/metadata.xml b/sci-chemistry/coot/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/coot/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/cyana/Manifest b/sci-chemistry/cyana/Manifest new file mode 100644 index 000000000000..1cf1996ce476 --- /dev/null +++ b/sci-chemistry/cyana/Manifest @@ -0,0 +1,9 @@ +AUX 2.1-exec.patch 1959 SHA256 fe8835c6dcdb6a8befa32e6bff1b761c5c6ae6131f73750e18724fb96f9a9623 SHA512 43f04008b623e95e09cc323abd504c4f5bf708bde4771f2e334ae5d4ca59c24cfcaf34a3ad7c5b65ebb4587614343982fe377a226648098e02de8bdaa1c36a1d WHIRLPOOL 5ff8eedecd3e680e0f17917b6bd3c08bca6a0412f4e3e1693163af431eae3e9534d9fd87e574feaa11268988770a6f15ef5b3e070995995200f91521b8f1302a +AUX 2.1-expire.patch 578 SHA256 723d69026e63995b281ae36582f5114562a1c4d6295d311ca2eb2900a1dc7b95 SHA512 7816f284a7af23c5d87a5a464ea36e7a1b09e73516852b85fac0d71bb8376639788f3f9395f8a6fd9365906d2aaadbd060f2194c7af3b68a24927adefcd56c40 WHIRLPOOL 8443238b88c5869225b6d68841a44fcdd618df21df9b07998b35897ad907a0b4e4264ad5925a46d944cfc7996f2ff9618380ac4f14f1b1f55926595eecedcbc2 +AUX 2.1-typo.patch 484 SHA256 ef05c4254cf859e804c44cdfa5774aca5a2f1aa853f0b6c0bccee837db2a5b8b SHA512 298e5053e4261477a11f0dff2339f198e50e92a96b98c5aea82e3a432b806b1ea0baa3638ef6e65dee315be3223510a804e2c849a82fdda0a1cf296de9d89db4 WHIRLPOOL 18b1db0e746630a9c040bd80b9f6cddff1ceaec2e92ce6d5583f6fb830d565012d25cfba284eb194f7b7930c5b01338b302b8dd7be01d56d62a580ac546ad572 +AUX 2.1-xiar.patch 385 SHA256 c8d4daddaafa1388b87c7b107206df873fe98dc418db36ab48bfb2c60b3435e6 SHA512 ce4c27b70d0c432b33f76b4ff76d004f525243269064f1af439bf42ab9783edd9dc19712b277d8e08bb692a28c40db7007040da1635cbd3c432029e4fe6c680f WHIRLPOOL 76d7e103437a7b76a0411fe563e082f90de514d67cf20e0ef0e7e2f9754230ac65a175471ec0685a8a3be9fa2d612a38137f4d03f10014a6e6dd547b4ff37100 +DIST cyana-2.1.tar.gz 2203650 SHA256 4b49d23eda3a327074fa337c7ee13262e93fb2b92cc6feb9139dfb7695bdeded SHA512 20f5369e47198000927ee9a60beda34d265fddcd6be59f0d5d81ac23691b7e870ca674bdd7215a13bc849586411a007ebb1ff46072b55f255a6d796359067be8 WHIRLPOOL dfc60a456c166d98bbdb60227a2dae63d12ea9fb7375dede3d372a6dbf0785bfd0c8b1069d985a6ee775ab136405b553ff9336a2603d139d81d853f0681f5167 +EBUILD cyana-2.1.ebuild 1439 SHA256 f00f45b10735aa60a57b90aa05980382b5b9c8e04569bc5a559a02d4eb0c47af SHA512 47108af1f37d2adb2fd111da3db51f60feedc4d4f7c4da5327b3217626e8d6826b45993e900ca43d252c98d42216e6a878ada5039be7385bd18d2dac67c3891f WHIRLPOOL 57d9b19272cbba10998769f070ee9d0364bd4854575372b7d51a74b9289d42a1659e9b07aea3e02e7e24d02156d2654eafe24e22924b41b5d72f2de72df3ef00 +MISC ChangeLog 2658 SHA256 3ec8746a7c30c9b68e8d8028a52b68404a5335ab7f64c52e4cb24c4a433a6b7d SHA512 08491938901922cea8a9bcc35337eede0a58e21b6ac8dee287b87ae3d080744bba0055afeaac7b1a81b882b2b7a0ef36126109d344b7c13d45b7341c14c50f0a WHIRLPOOL 1b557630f90673b70317bb103e08a86a79855fbd97e99c2fc39c3b57f133e9c06df2aa551afb768e3e4fc7f2803775e20c0180ce99b358da174ca7be63d09716 +MISC ChangeLog-2015 2576 SHA256 9c77e2e9956b062cfab2b1a0d91d4652ff85189fb4f2273676fefe279497e80e SHA512 8c9fa3acaaa16f33d4d2700c1ebeced86f2ec7c3affe27449d92f909fa7a27f23072fa333d9029d74e10bbf9d6e3d3961b2b92b73094be425b3080cfc55c1059 WHIRLPOOL 5beb86e4ad958efc8ba808adf4b4bf1a5062f13acfbc474363a17c3a916f7348e23e420b90d2dd98bd9e17ee543f8233e78e94bc408ff3b16aadb5a043515bf0 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/cyana/cyana-2.1.ebuild b/sci-chemistry/cyana/cyana-2.1.ebuild new file mode 100644 index 000000000000..f017c9af247c --- /dev/null +++ b/sci-chemistry/cyana/cyana-2.1.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils fortran-2 toolchain-funcs + +DESCRIPTION="Combined assignment and dynamics algorithm for NMR applications" +HOMEPAGE="http://www.las.jp/english/products/cyana.html" +SRC_URI="${P}.tar.gz" + +LICENSE="CYANA" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RESTRICT="fetch" + +# we need libg2c for gfortran # 136988 +DEPEND="dev-lang/ifc" +RDEPEND="${DEPEND}" + +pkg_nofetch() { + elog "Please visit" + elog "http://www.las.jp/english/products/cyana.html" + elog "and get a copy of ${A}." + elog "Place it in ${DISTDIR}." +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-typo.patch \ + "${FILESDIR}"/${PV}-exec.patch \ + "${FILESDIR}"/${PV}-expire.patch \ + "${FILESDIR}"/${PV}-xiar.patch + + cat >> etc/config <<- EOF + VERSION=${PV} + SHELL=${EPREFIX}/bin/sh + FC=ifort + FFLAGS=${FFLAGS} -openmp -threads + FFLAGS2=${FFLAGS} -openmp -threads + CC=$(tc-getCC) + AR=xiar + RANLIB=ranlib + FORK=g77fork.o + LDFLAGS=${LDFLAGS} -reentrancy threaded -openmp + LIBS= + DEFS=-Dintel + SYSTEM=intel + EOF +} + +src_compile() { + cd src || die + emake +} + +src_install() { + dobin cyana{job,table,filter,clean} + newbin src/${PN}/${PN}exe.* ${PN} + insinto /usr/share/${PN} + doins -r lib macro help + use examples && doins -r demo + + cat >> "${T}"/20cyana <<- EOF + CYANALIB="${EPREFIX}/usr/share/${PN}" + EOF + + doenvd "${T}"/20cyana +} diff --git a/sci-chemistry/cyana/files/2.1-exec.patch b/sci-chemistry/cyana/files/2.1-exec.patch new file mode 100644 index 000000000000..28cd88d3eee6 --- /dev/null +++ b/sci-chemistry/cyana/files/2.1-exec.patch @@ -0,0 +1,77 @@ +diff --git a/cyana b/cyana +index 4f746cf..a7ff060 100755 +--- a/cyana ++++ b/cyana +@@ -45,16 +45,13 @@ shift `expr $optind - 1` + + if [ "$h" ]; then usage=1; fi + if [ "$usage" ]; then +- echo "Usage: $prog -hctx parameters ..." ++ echo "Usage: $prog -hS parameters ..." + echo + echo " -h help" + echo " -c command command to start program (must contain \$exefile)" + echo " -S run in safe mode, i.e. within one directory" +- echo " -t system explicit system type" +- echo " -x display name of executable without executing it" + exit 2 + fi +-if [ "$c" ]; then cmd="$c"; fi + sys=$t + mode=$x + safe=$S +@@ -65,23 +62,6 @@ safe=$S + eval ${PROG}ARG='$*' + export ${PROG}ARG + +- +-# ------ Set library name ------ +- +-f=$0 +-if [ `echo $f | sed 's,^/.*,+,'` != "+" ]; then f=`which $0`; fi +-odir=`pwd` +-while [ "`ls -l $f | awk '{ print substr($1,1,1) }'`" = "l" ]; do +- l=`ls -l $f | awk '{ i = NF; print $i }'` +- cd `dirname $f`; cd `dirname $l`; l=`pwd`/`basename $l` +- f=$l +-done +-cd `dirname $f` +-libdir=`pwd | sed 's,/src/'${prog}'$,,'` +-cd $odir +-eval ${PROG}LIB=$libdir +-export ${PROG}LIB +- + if [ "$safe" ]; then + CYANAINIT=initsafe; export CYANAINIT + fi +@@ -89,29 +69,4 @@ fi + + # ------ Start the program ------ + +-if [ -d $libdir/src/$prog ]; then +- exe=$libdir/src/$prog/$exe +-else +- exe=$libdir/$exe +-fi +-if [ "$sys" = "" ]; then +- sys=`$libdir/etc/identify` +- files="$exe.$sys* $exe.gnu $exe.*" +-else +- files=$exe.$sys +-fi +-for exefile in $files; do +- if [ -x $exefile ]; then +- if [ "$mode" ]; then +- echo $exefile; exit 0 +- else +- if [ "`echo $cmd | grep -c '\$exefile'`" -gt 0 ]; then +- eval exec $cmd +- else +- eval exec $cmd $exefile +- fi +- fi +- fi +-done +-echo "No executable found in \"`dirname $exe`\"." +-exit 1 ++exec cyana diff --git a/sci-chemistry/cyana/files/2.1-expire.patch b/sci-chemistry/cyana/files/2.1-expire.patch new file mode 100644 index 000000000000..e18008286f68 --- /dev/null +++ b/sci-chemistry/cyana/files/2.1-expire.patch @@ -0,0 +1,15 @@ +--- src/inclan/unix.for.orig 2011-01-05 14:56:46.572193759 +0100 ++++ src/inclan/unix.for 2011-01-05 14:57:27.833627375 +0100 +@@ -206,11 +206,8 @@ + end if + if (iwbeg.lt.0) then + iwbeg=igttim +- iexpir=(julday(12,31,2010)-julday(1,1,1970))*24*3600 +- if (iwbeg.gt.iexpir) call fatmsg ('License expired.') ++ iexpir=iwbeg+100 + j=(iexpir-iwbeg)/(24*3600) +- if (j.lt.1000) +- * call wrnmsg ('License expires in '//plural(j,'day')//'.') + end if + iwall=igttim-iwbeg + c print *,'iwall = ',iwall,iwbeg,idat,itim
\ No newline at end of file diff --git a/sci-chemistry/cyana/files/2.1-typo.patch b/sci-chemistry/cyana/files/2.1-typo.patch new file mode 100644 index 000000000000..3f011a9b2c28 --- /dev/null +++ b/sci-chemistry/cyana/files/2.1-typo.patch @@ -0,0 +1,13 @@ +diff --git a/src/cyana/putpro.f b/src/cyana/putpro.f +index d4080f9..4490225 100644 +--- a/src/cyana/putpro.f ++++ b/src/cyana/putpro.f +@@ -66,7 +66,7 @@ c ------------------------------------------------------ BMRB header + * ' _Mol_residue_sequence', + * ';' + do i=1,nr,20 +- write (iunit,'(20A1))') (rcode(rnam(j)),j=i,min(nr,i+19)) ++ write (iunit,'(20A1)') (rcode(rnam(j)),j=i,min(nr,i+19)) + end do + + write (iunit,'(A)') diff --git a/sci-chemistry/cyana/files/2.1-xiar.patch b/sci-chemistry/cyana/files/2.1-xiar.patch new file mode 100644 index 000000000000..e8393253d7f6 --- /dev/null +++ b/sci-chemistry/cyana/files/2.1-xiar.patch @@ -0,0 +1,16 @@ + src/inclan/Makefile | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/src/inclan/Makefile b/src/inclan/Makefile +index fc5a8bf..482d48f 100644 +--- a/src/inclan/Makefile ++++ b/src/inclan/Makefile +@@ -35,7 +35,7 @@ clean: + + inclan.a: $(OBJS) + rm -f $@ +- ar rc $@ $(OBJS) ++ $(AR) rc $@ $(OBJS) + if [ "$(RANLIB)" ]; then $(RANLIB) $@; fi + + inclan.o: inclan.for diff --git a/sci-chemistry/cyana/metadata.xml b/sci-chemistry/cyana/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/cyana/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest new file mode 100644 index 000000000000..c8f837aea7fe --- /dev/null +++ b/sci-chemistry/dssp/Manifest @@ -0,0 +1,7 @@ +AUX dssp-2.1.0-gentoo.patch 1513 SHA256 76970f86426bcb1e5155117a784541a51e9489b70263a5f66761058c9251ad25 SHA512 7d192019811a6892031c74e14ef9fc7461e77c050a164698f8c72cff08f81a0e6da202e0915b631a5cd6d910a6114a736c706d47b1fd6474ff77c3700efcd9f9 WHIRLPOOL 0834a1d3eae75de760cb361d21a84c39f3c97cdcd11158c7775812506903a3e288720789c1d2880bb3966b29dadea16d81fd66604c1a7559be399153712a5c33 +AUX dssp-2.2.1-boost-1.65-tr1-removal.patch 2126 SHA256 d59a4d7c5c9f1ca1cae2073b554d28edfb36128265dc8dc07fc55b07c3024857 SHA512 8f84c6e163888d6a8192683a6555f7d6003634854f5cde0f6f962744e531165c7e0b2b08c55cbfb9c396d167c44317dd2e7a8290e4defd2c8def0a6511fbbd6c WHIRLPOOL 919ef00d60d9a621e752e6fcc6125318d20e3a424e1b8afdba50f37d28fa695ed61765b99e0fe997ef6ff2df6cd6bbfb5747fe74eae4ab52e63df530e636b5eb +DIST dssp-2.2.1.tgz 47141 SHA256 5fb5e7c085de16c05981e3a72869c8b082911a0b46e6dcc6dbd669c9f267e8e1 SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811 WHIRLPOOL abdb6777ccc06b062e3f20226c555348cd221d9c3e14d2adb9aeb85f14f84db8841c2fbbc4a487f5fa021da6616cddf2e96fde787d7670c419926d24d24944bd +EBUILD dssp-2.2.1-r1.ebuild 962 SHA256 9045f91f7cfdeee3dccd3c02815e84762f91c9f95e430817c66051c88d23f85b SHA512 9488695b51ddfea2127b3b7e02e36095f494ba20f14eeb81b5ab9b6dd4a47bdaae6b517a6f27ad49af75202080f6fa511ea8efdd3aca8a7eee6fe8b7b31ec501 WHIRLPOOL 16f20d85b7f5ef8f803ad326f11719b1db8f541404d194ff3eb9afa8040692ea0ebd5c5a22adf887052261524ec6dd3c7e9114677754fafb813912fb2b5f9cac +MISC ChangeLog 2958 SHA256 bd7a62613a65a005bcd36e23332edfad48515bfa1d34306e0e59e5e83ad3de8b SHA512 1847b40deee64d21d550aadf8650d0f50bb756a4068387392772e7d6f33532827e6a662d3c2b46722a9565a479116190f11c9f3c251d7d198f379346a631da41 WHIRLPOOL bafe24db0f788d1d3fb207912571dcc680f2b7ab2f0894d6c89e43b801f646fb31a4ff16cfb7c3f9de190e8c32ab8871defd19220218d89e496605a57e8faa30 +MISC ChangeLog-2015 2819 SHA256 a422307fec099c15ed41519c373f1f36deff9f2fbe570c2869fa7bf9d62dd9d3 SHA512 81ab13649c11ef7800dae3b85c03a67b9c27f1793a9f4f18c8ec66ce2c3d4294f1647ace9201bb51c44f8799ea2b84ec215d81e8868c9dc3700f1ef90cdb7043 WHIRLPOOL bcf46f6e4e3b7b0d06e04cc76e501eec75ea0483eeef86ec7299b4b4251170231a8eae73f9f4e58174d3d1b558745590e399a0217245309697760f1c55c3984d +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild new file mode 100644 index 000000000000..b660e9ef3c96 --- /dev/null +++ b/sci-chemistry/dssp/dssp-2.2.1-r1.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="The protein secondary structure standard" +HOMEPAGE="http://swift.cmbi.ru.nl/gv/dssp/" +SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/${P}.tgz" + +LICENSE="Boost-1.0" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="dev-libs/boost:=[threads]" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-2.1.0-gentoo.patch + "${FILESDIR}"/${PN}-2.2.1-boost-1.65-tr1-removal.patch +) + +src_configure() { + tc-export CXX + + cat >> make.config <<- EOF || die + BOOST_LIB_SUFFIX = -mt + BOOST_LIB_DIR = "${EPREFIX}/usr/$(get_libdir)" + BOOST_INC_DIR = "${EPREFIX}/usr/include" + EOF +} + +src_install() { + dobin mkdssp + dosym mkdssp /usr/bin/dssp + doman doc/mkdssp.1 + dodoc README.txt changelog + + cat >> "${T}"/30-${PN} <<- EOF || die + DSSP="${EPREFIX}"/usr/bin/${PN} + EOF + doenvd "${T}"/30-${PN} +} diff --git a/sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch b/sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch new file mode 100644 index 000000000000..15198feaea19 --- /dev/null +++ b/sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch @@ -0,0 +1,60 @@ + makefile | 21 +++++++++++---------- + 1 file changed, 11 insertions(+), 10 deletions(-) + +diff --git a/makefile b/makefile +index d6f335e..68736c6 100644 +--- a/makefile ++++ b/makefile +@@ -25,22 +25,23 @@ BOOST_LIBS = thread filesystem program_options iostreams system + LIBS = $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) z bz2 + + DEFINES = USE_COMPRESSION LINUX VERSION='"$(VERSION)"' +-CXX = g++ ++CXX ?= g++ + +-CFLAGS += $(INC_DIR:%=-I%) -iquote src -g -Wall -Wno-multichar -pthread +-LDOPTS += $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -g -pthread ++CPPFLAGS += $(INC_DIR:%=-I%) -iquote src ++CXXFLAGS += -Wall -Wno-multichar -pthread ++LDOPTS += $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -pthread + + OBJ_DIR = obj + + ifeq ($(DEBUG),1) + OBJ_DIR := $(OBJ_DIR).dbg +-CFLAGS += -g3 ++CFLAGS += + else + DEFINES += NDEBUG +-CFLAGS += -O3 ++CFLAGS += + endif + +-CFLAGS += $(DEFINES:%=-D%) ++CPPFLAGS += $(DEFINES:%=-D%) + + DIST_NAME = dssp-$(VERSION) + +@@ -50,18 +51,18 @@ OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ + + mkdssp: $(OBJECTS) + @ echo linking $@ +- @ $(CXX) -static -o $@ $^ $(LDOPTS) ++ $(CXX) $(LDFLAGS) -o $@ $^ $(LDOPTS) + + include $(OBJECTS:%.o=%.d) + + $(OBJECTS:.o=.d): + +-$(OBJ_DIR): ++OBJ_DIR: + @ mkdir -p $(OBJ_DIR) + +-$(OBJ_DIR)/%.o: %.cpp | $(OBJ_DIR) ++$(OBJ_DIR)/%.o: %.cpp OBJ_DIR + @ echo compiling $@ +- @ $(CXX) -MD -c -o $@ $< $(CFLAGS) ++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -MD -c -o $@ $< + + clean: + install -d $(BIN_DIR) $(MAN_DIR) diff --git a/sci-chemistry/dssp/files/dssp-2.2.1-boost-1.65-tr1-removal.patch b/sci-chemistry/dssp/files/dssp-2.2.1-boost-1.65-tr1-removal.patch new file mode 100644 index 000000000000..4eee6b567349 --- /dev/null +++ b/sci-chemistry/dssp/files/dssp-2.2.1-boost-1.65-tr1-removal.patch @@ -0,0 +1,82 @@ +--- a/src/dssp.cpp ++++ b/src/dssp.cpp +@@ -73,7 +73,7 @@ + + double alpha; + char chirality; +- tr1::tie(alpha,chirality) = residue.Alpha(); ++ boost::tie(alpha,chirality) = residue.Alpha(); + + uint32 bp[2] = {}; + char bridgelabel[2] = { ' ', ' ' }; +--- a/src/primitives-3d.cpp ++++ b/src/primitives-3d.cpp +@@ -153,7 +153,7 @@ + + // -------------------------------------------------------------------- + +-tr1::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q) ++boost::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q) + { + if (q.R_component_1() > 1) + q = Normalize(q); +@@ -169,7 +169,7 @@ + + MPoint axis(q.R_component_2() / s, q.R_component_3() / s, q.R_component_4() / s); + +- return tr1::make_tuple(angle, axis); ++ return boost::make_tuple(angle, axis); + } + + MPoint CenterPoints(vector<MPoint>& points) +--- a/src/primitives-3d.h ++++ b/src/primitives-3d.h +@@ -9,7 +9,7 @@ + + #include <vector> + +-#include <boost/tr1/tuple.hpp> ++#include <boost/tuple/tuple.hpp> + #include <boost/math/quaternion.hpp> + + typedef boost::math::quaternion<double> MQuaternion; +@@ -64,7 +64,7 @@ + + MQuaternion Normalize(MQuaternion q); + +-std::tr1::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q); ++boost::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q); + MPoint Centroid(std::vector<MPoint>& points); + MPoint CenterPoints(std::vector<MPoint>& points); + MQuaternion AlignPoints(const std::vector<MPoint>& a, const std::vector<MPoint>& b); +--- a/src/structure.cpp ++++ b/src/structure.cpp +@@ -544,7 +544,7 @@ + return result; + } + +-tr1::tuple<double,char> MResidue::Alpha() const ++boost::tuple<double,char> MResidue::Alpha() const + { + double alhpa = 360; + char chirality = ' '; +@@ -558,7 +558,7 @@ + else + chirality = '+'; + } +- return tr1::make_tuple(alhpa, chirality); ++ return boost::make_tuple(alhpa, chirality); + } + + double MResidue::Kappa() const +--- a/src/structure.h ++++ b/src/structure.h +@@ -168,7 +168,7 @@ + + double Phi() const; + double Psi() const; +- std::tr1::tuple<double,char> ++ boost::tuple<double,char> + Alpha() const; + double Kappa() const; + double TCO() const; diff --git a/sci-chemistry/dssp/metadata.xml b/sci-chemistry/dssp/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/dssp/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/easychem/Manifest b/sci-chemistry/easychem/Manifest new file mode 100644 index 000000000000..f617e757ba12 --- /dev/null +++ b/sci-chemistry/easychem/Manifest @@ -0,0 +1,6 @@ +AUX 0.6-gentoo.patch 1770 SHA256 142c45b63a775aed5563ffffec9230f92ab0f7fe1cc05ca68f49a2c956a9963a SHA512 bf641ed0d0f01d895de9ff5892c475bda14b7d14d44898e02126d3f56bfdad59f425b722031e5e983f7b9633308d6463653422fa16323e06cf22cd3f9b88f261 WHIRLPOOL b6f8f4fdd61c5deab93dae1ed013fffb562949ad7d5d1e50f622eeea5e00017cbc1ec1910ab2c789d18cf174863d363d6a812eaa07c149fbc744ecfd2ae6aa05 +DIST easychem-0.6.tar.gz 265458 SHA256 1dba1a1ed1862c723cd77184a90ee7571a26ebcb0d3c22e7e032af1cbafe284d SHA512 83f877d1813287592a460f4dc3769feda88e45d8f77cd728c4055b60521babe253b4432033941ff429c753cfe675a642714052a01736534147398d6972e47051 WHIRLPOOL 7869025a921b2a6ada516f60c3e79247b1ad74a0bb904f7dd9b7bd993b3b5166ccd3f266f6c2e85198c8bde1ddaf863518a7adea7a6fd9b22bf789e1df7103fe +EBUILD easychem-0.6-r1.ebuild 811 SHA256 1e8a824c90669f0a60cf185d192b31e2a62f75afa4705dc98bfd5fb6467548d3 SHA512 3321fd6357d06960f0d5dd1cdf96cb2db39d362785a1be8dd2571df9a53f1b30fa469d301c6730d7447f35b51fc82069f801af826e20b0eda1c14b113eac8667 WHIRLPOOL 940a121246700c231bd426edbb304b4991a5c1f2b0f7c9bf4e87f7ee9788d5e70e8bc3eb3aebaff87c30582fe74eea258d8252cd2cf5b58bcd4f5a852fb6ee54 +MISC ChangeLog 2498 SHA256 ff265ad724daea5b96563167660761d915e35f23508fa421d9bd49a2654279ab SHA512 4431bd488efc3e47952e9c234231a5a9894fd99239819f4fa6a926da7a7096ebbe783862af7170446b484081ba249b0f998553d26a04b7653b528cca0a55f673 WHIRLPOOL f25c1508a82da359b8b00ee15bfa43dc918e8416d37067452886743f99fee977fe45b95f20ff529ad2220b0477d428d88ec20f1bded9d87bfda9dc7a29f2f7fd +MISC ChangeLog-2015 3585 SHA256 38288ed0c4997bf906a30ab48e8d9f79620c1234f76fcd111f4e5ddff0867e2c SHA512 a3c69093a8d641ec39dcb16d71c161038b2fbaeeb585ae99b38a87d9edb04c4f9c3d51a3f1ab97b7eef04105699ec0e6e9f71fbddcb3450dfdb1b9b7f8c9ae6e WHIRLPOOL 6072e73540a3eca5c220eca37954ff4a06eb57002e259f8d986b1fc6fcf4c29722e71280ab730bbff80856cfb9d2c3e415ef5c57149987bea63dfb813326b49a +MISC metadata.xml 768 SHA256 84d51855f19655ebdc8961027bb8114799107aa379128a6eec269acaae185725 SHA512 d1898532271ade98b1dbde9d4d38d8b9b5750008fd8ebc99e67cfcfa990b86b5f2692dc23f9f8dca4052a0db432be0b8c7130fb52610bf34ddfe00ae77c31e96 WHIRLPOOL 0809931edf09404acd5ceff91203af06a0007fa1390de86f164b5b351d3fc772acb784ddcbdea38c3f9799b024e44fce656c26133e72f61eeff1c507ab5dcc26 diff --git a/sci-chemistry/easychem/easychem-0.6-r1.ebuild b/sci-chemistry/easychem/easychem-0.6-r1.ebuild new file mode 100644 index 000000000000..650c236dfeaf --- /dev/null +++ b/sci-chemistry/easychem/easychem-0.6-r1.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Chemical structure drawing program - focused on presentation" +HOMEPAGE="http://easychem.sourceforge.net/" +SRC_URI="mirror://sourceforge/easychem/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + x11-libs/gtk+:2 + app-text/ghostscript-gpl + media-gfx/pstoedit" +DEPEND="${RDEPEND} + dev-lang/perl + virtual/pkgconfig" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-gentoo.patch + tc-export CC +} + +src_compile() { + ln -s Makefile.linux Makefile || die + DGS_PATH="${EPREFIX}"/usr/bin DPSTOEDIT_PATH="${EPREFIX}"/usr/bin \ + C_FLAGS="${CFLAGS}" emake -e +} + +src_install () { + dobin easychem + dodoc TODO +} diff --git a/sci-chemistry/easychem/files/0.6-gentoo.patch b/sci-chemistry/easychem/files/0.6-gentoo.patch new file mode 100644 index 000000000000..000e4373b3c2 --- /dev/null +++ b/sci-chemistry/easychem/files/0.6-gentoo.patch @@ -0,0 +1,65 @@ +diff --git a/Makefile.linux b/Makefile.linux +index 6638394..5da56b0 100644 +--- a/Makefile.linux ++++ b/Makefile.linux +@@ -1,5 +1,5 @@ + # The C compiler +-CC=gcc ++CC ?= gcc + + # The following line must be uncommented if you want to specify a place + # where the 'gs' (or 'pstoedit') program is. +@@ -25,11 +25,10 @@ GTK_LIBS=`pkg-config --libs gtk+-2.0` + # The list of important files + OBJECTS=auxi.o bonds.o easychem.o export.o dialogs.o detect.o library.o drawing.o + +-all: easychem po/ ++all: easychem po + +-easychem: postscript/ graph/ $(OBJECTS) +- $(CC) -o easychem $(OBJECTS) $(GTK_LIBS) $(C_FLAGS) +- strip easychem ++easychem: postscript graph $(OBJECTS) ++ $(CC) $(C_FLAGS) $(LDFLAGS) -o easychem $(OBJECTS) $(GTK_LIBS) -lm + + clean: FORCE + -cd graph; make clean +@@ -37,7 +36,7 @@ clean: FORCE + -cd po; make clean + -rm $(OBJECTS) easychem + +-export.o: export.c common.h bonds.h postscript/ ++export.o: export.c common.h bonds.h postscript + $(CC) $(GTK_FLAGS) $(C_FLAGS) -c export.c + bonds.o: bonds.c common.h bonds.h + $(CC) $(GTK_FLAGS) $(C_FLAGS) -c bonds.c +@@ -49,20 +48,22 @@ library.o: library.c common.h library.h + $(CC) $(GTK_FLAGS) $(C_FLAGS) -c library.c + drawing.o: drawing.c common.h drawing.h + $(CC) $(GTK_FLAGS) $(C_FLAGS) -c drawing.c +-dialogs.o: dialogs.c common.h dialogs.h graph/ ++dialogs.o: dialogs.c common.h dialogs.h graph + $(CC) $(GTK_FLAGS) $(C_FLAGS) -c dialogs.c + detect.o: detect.c common.h detect.h + $(CC) $(GTK_FLAGS) $(C_FLAGS) -c detect.c + + # The rules for subdirectories +-graph/: FORCE +- cd graph; make all ++graph: ++ +make -C $@ + +-postscript/: FORCE +- cd postscript; make all ++postscript: ++ +make -C $@ + +-po/: FORCE +- cd po; make all ++po: ++ +make -C $@ + + # This is used to force an update + FORCE: ++ ++.PHONY: graph postscript po diff --git a/sci-chemistry/easychem/metadata.xml b/sci-chemistry/easychem/metadata.xml new file mode 100644 index 000000000000..f55348bea1a8 --- /dev/null +++ b/sci-chemistry/easychem/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> + EasyChem is a program designed to draw chemical molecules, written under + Linux using Gtk+ 2.4. It is implemented with a strong focus on producing + press quality molecules. Easychem can be a little more difficult to learn to + use, but when mastered it can be very fast and powerful. It can draw + ornaments easily, and exports to EPS with LaTeX fonts among other things. + </longdescription> + <upstream> + <remote-id type="sourceforge">easychem</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/eden/Manifest b/sci-chemistry/eden/Manifest new file mode 100644 index 000000000000..6bd4d732fd44 --- /dev/null +++ b/sci-chemistry/eden/Manifest @@ -0,0 +1,9 @@ +AUX 5.3-makefile-fixes.patch 1647 SHA256 63af22242c70e5b3b9890d3e6214aa4b41346b1a91b0e4f1c692749f0715bda5 SHA512 3ec4f8ba8d3b600b729bfb32cef3fb1f82a1f51a485ebab143e01052ea1487a78c3395c902079fe0e5d5c3df8a2a83b2ce4d37d823e1d89426087874ec47391d WHIRLPOOL 916baab24c34f94bd03b5a647161cd1b17f86b122847b192b85879c15ed362a15390316da6790452f1d6e745bb6503eab471e703065e6b45487845b0b1c0c29d +AUX eden-5.3-format-security.patch 3202 SHA256 098c6fdd0dc433a2a2f3c18df7f9e8307e9a2d1bf21366e75a14343e38fcbff6 SHA512 01e100fe5481a73de2efa6652fe38c19337eae0dc13557ef0ad3e3a4f186becbfb8831aece0a619c08541e1a667e999c47b28438ec431f056c44f12849662c12 WHIRLPOOL 89eaad2e0025c7552642cc6441ad6a3ae9f6563f2f5f00dd5a06756d02a3aa961d622b1b4bc7439947b1f15b836d64781f9ed7057faffb207fe7f87d4ee08bc7 +AUX eden-5.3-impl-dec.patch 899 SHA256 b1760b8deab3bc01661a586a0a8c536449ea6f1f201e9c40fccccfdce07be10e SHA512 e89f1e0c028099e305a79befa558a86bc47d050c1e30394178999c7a1568bae9c3e525953bf152888690e0e1607dd72c522d2995f45b1eccfb9f7bf75e7866c2 WHIRLPOOL 0a2a50d0819346861e899ae17e65746936caf23454cd4e7fe0477b0d1aff0e958ce2c8f6f3179f676ab7a94d1c446d32c7acd0182f3cc2f5103c3485829b9dd0 +AUX makefile-fixes.patch 837 SHA256 6f7612404cccd9e40de19df3f86eb86be9a17fa105eac21e615c0d464f92cc31 SHA512 818fe1d23fa940cb533afcb9e84bdc5c719651005136304ca66d368fc21cf4d7a1facb0a383c9689ab1658632cec30969322fdffccadae941a754900542237e7 WHIRLPOOL adf204b3f1a361dfa426249b6e1ab89b1565d8c9852b03fbe770c429e098ece80b5528464d6c4c1a680960f1cb2d3dc6c7826799b41688dfffd33ebd1e4a96c4 +DIST eden_V5.3.tar.gz 1139981 SHA256 249447f507ace3e188ce0d76796c6e307c043592405db1f6c24f3e90917ec524 SHA512 c59d08004bdb72ef39fe205aef546fbcff9c57ee42942c0391052de9c501c7793ed3bd280569020c2b9ec6133a87362d184a2012b61c6be18b5f6ba9b59716c5 WHIRLPOOL f0329805ab1d3b75febcc07c87583ee30f2ca44d5b5ae5c3512d4891a8763bf45ab7dc94abed831c0326cdbc35502f4bc3904ccb7447b090100b2f7d52b1156b +EBUILD eden-5.3-r2.ebuild 1845 SHA256 4130ee8fb2d23b7d951da8bccd3fd8cf4585d79dd678c0a1a925cc6d17a63cef SHA512 5de7c7da62d7819ee74c8983ba5f222853995d9fae865a7a0802c7ee583f3406d6dbbdc335b3ad60c138d5642d6eb3df683c7a6f26ab91afd39707b63b1579a0 WHIRLPOOL 9184db6ede5b2c9526e68b8ee3aa0becf740b09723566ef7d89b3682a4ab71cda33c096555671e2ef9f9730d28cf278bc3d3286a5002846e7634abb73a4a15d4 +MISC ChangeLog 2560 SHA256 dab00a887a063445f2c835898509daca160d4f860c90da595b3504eb5ae49511 SHA512 bc4969b2ef58a9c65a138b9ee5daa19da922fd2b58f2d2885fb066b73808789f98ee6f8ab56d4de69fdecba13eda03503a10ae2db277761fa91a00f99647880b WHIRLPOOL 03ec9a20119fccb452b2986f96db1695cdd4c035dbbf4b8d93f2652b906f46d8cec556b01cf34b7932ce16b29a8ddaca136f7419b6a7bb199413a47ff48d2e45 +MISC ChangeLog-2015 3378 SHA256 c631c4ccbbcad0726cfb6dbbb20904680f8d8e1dd42d88a4f2bb62abf29031a6 SHA512 693e40d0be56df97e081bcb2bb1532f69b8cfa5efdfd7a805a5bb9e6973dad3fb3bf87e4e17f53da405ea579941bf800652c8ea0b086025a106cb7008649170b WHIRLPOOL b60b0e6df65dc091c5fafb25c3fee62d93baa1bfdcf50b87b1c2501e508105ca66b512f22b28a33d1d94e757181ef4f1df337f787054c706d958085b3efa5b49 +MISC metadata.xml 383 SHA256 d05b3ed09ac4e1d1ec83875570e0090f7bbec36a6fcd678baa9dfb58365734f3 SHA512 e23cc36f53622230ac9c70cb886cd9812e4bfefba8c0912059b3f072e063c235ba52cce893ea3b49ba05dda047097ba505c4ce5c53248d5acf720f16e123be84 WHIRLPOOL 86b3e99bea59d1846041b82b80283eb5e9156209495a0c081d7403a21dd8589cfd4e7b885ad6723ff2bbfcfa1d197850265126223a987b048d35fe98642af65f diff --git a/sci-chemistry/eden/eden-5.3-r2.ebuild b/sci-chemistry/eden/eden-5.3-r2.ebuild new file mode 100644 index 000000000000..8bf667224ba8 --- /dev/null +++ b/sci-chemistry/eden/eden-5.3-r2.ebuild @@ -0,0 +1,88 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils multilib python-r1 toolchain-funcs + +MY_P="${PN}_V${PV}" + +DESCRIPTION="A crystallographic real-space electron-density refinement & optimization program" +HOMEPAGE="http://www.gromacs.org/pipermail/eden-users/" +SRC_URI="mirror://gentoo/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="double-precision" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + sci-libs/fftw:2.1 + sci-libs/gsl + ${PYTHON_DEPS}" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${PN}" + +SRC="${S}/source" + +pkg_setup() { + export EDENHOME="${EPREFIX}/usr/$(get_libdir)/${PN}" +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-makefile-fixes.patch \ + "${FILESDIR}"/${P}-impl-dec.patch \ + "${FILESDIR}"/${P}-format-security.patch + + sed -i \ + -e "s:^\(FFTW.*=\).*:\1 ${EPREFIX}/usr:g" \ + -e "s:^\(LIB.*=.*\$(FFTW)/\).*:\1$(get_libdir):g" \ + -e "s:^\(BIN.*=\).*:\1 ${D}usr/bin:g" \ + -e "s:^\(CFLAGS.*=\).*:\1 ${CFLAGS}:g" \ + -e "s:-lgsl -lgslcblas:$($(tc-getPKG_CONFIG) --libs gsl):g" \ + ${SRC}/Makefile || die + + if ! use double-precision; then + sed -i -e "s:^\(DOUBLESWITCH.*=\).*:\1 OFF:g" ${SRC}/Makefile || die + EDEN_EXE="s${PN}" + else + EDEN_EXE="d${PN}" + fi +} + +src_compile() { + emake CC=$(tc-getCC) -C ${SRC} +} + +src_install() { + emake -C ${SRC} install + + python_foreach_impl python_newscript python/${PN}.py i${PN} + python_foreach_impl python_domodule python/FileListDialog.py + + rm python/*py || die + insinto ${EDENHOME}/python + doins python/* + + insinto ${EDENHOME}/help + doins help/* + + insinto ${EDENHOME}/tools + doins tools/* + + dodoc manual/UserManual.pdf + + cat >> "${T}"/60${PN} <<- EOF + EDENHOME="${EDENHOME}" + EOF + + doenvd "${T}"/60${PN} + + dosym ${EDEN_EXE} /usr/bin/${PN} +} diff --git a/sci-chemistry/eden/files/5.3-makefile-fixes.patch b/sci-chemistry/eden/files/5.3-makefile-fixes.patch new file mode 100644 index 000000000000..632358341784 --- /dev/null +++ b/sci-chemistry/eden/files/5.3-makefile-fixes.patch @@ -0,0 +1,60 @@ + source/Makefile | 17 ++++++++++------- + 1 files changed, 10 insertions(+), 7 deletions(-) + +diff --git a/source/Makefile b/source/Makefile +index 46d89cc..aa751c7 100644 +--- a/source/Makefile ++++ b/source/Makefile +@@ -78,8 +78,10 @@ CFLAGS = -Wall -pipe -g3 + #CFLAGS = -Wall -pipe -marchi686 -pedantic -gdwarf-2 -g3 + #CFLAGS = -Wall -O3 -march=i686 + ifneq ($(FFTW),/usr/local) ++ifneq ($(FFTW),/usr) + CFLAGS += -I$(INC) + endif ++endif + + # NOTE: + # DOUBLESWITCH = ON for double precision; +@@ -91,15 +93,15 @@ endif + DOUBLESWITCH = ON + + ifeq ($(DOUBLESWITCH),ON) +-LDFLAGS = -L$(LIB) -ldfftw -lm ++LIBS = -L$(LIB) -ldfftw -lm + CFLAGS += -DDOUBLE + TARGET = deden + else +-LDFLAGS = -L$(LIB) -lsfftw -lm ++LIBS = -L$(LIB) -lsfftw -lm + TARGET = seden + endif + +-LDFLAGS += -g -lgsl -lgslcblas ++LIBS += -lgsl -lgslcblas + + # GSL_PREFIX:= /sw/lib + # LDFLAGS += -l$(GSL_PREFIX)/libgsl.a -l$(GSL_PREFIX)/libgslcblas.a +@@ -120,17 +122,18 @@ OBJ = addmaps.o apodfc.o apodfo.o back.o cadhkl.o \ + all: eden fbyteswap + + eden: eden.o $(OBJ) +- $(CC) $^ $(LDFLAGS) -o $@ ++ $(CC) $(LDFLAGS) -o $@ $^ $(LIBS) + + fbyteswap: fbyteswap.c +- $(CC) -o $@ $^ ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) + + install: all ++ mkdir -p $(BIN) + mv fbyteswap $(BIN) + mv eden $(BIN)/$(TARGET) + chmod 751 $(BIN)/$(TARGET) +- chmod +x mkeden.csh +- ./mkeden.csh $(BIN) $(BIN)/$(TARGET) ++# chmod +x mkeden.csh ++# ./mkeden.csh $(BIN) $(BIN)/$(TARGET) + + dist: clean + cd ../..; tar -cvf eden_$(VERSION).tar --exclude CVS --exclude \#\*\# --exclude \*~ --exclude Misc --exclude .\* eden; gzip -f eden_$(VERSION).tar diff --git a/sci-chemistry/eden/files/eden-5.3-format-security.patch b/sci-chemistry/eden/files/eden-5.3-format-security.patch new file mode 100644 index 000000000000..04b5ecfddebb --- /dev/null +++ b/sci-chemistry/eden/files/eden-5.3-format-security.patch @@ -0,0 +1,96 @@ + source/back.c | 2 +- + source/concosts.c | 4 ++-- + source/count.c | 4 ++-- + source/eden.c | 2 +- + source/util.c | 4 ++-- + 5 files changed, 8 insertions(+), 8 deletions(-) + +diff --git a/source/back.c b/source/back.c +index fd517b9..185a02b 100644 +--- a/source/back.c ++++ b/source/back.c +@@ -112,7 +112,7 @@ void back_main(int argc, char *argv[]) + ballpark(caller) ; + + if (argc > optind+2) +- sprintf(sf_filename, argv[optind+2]) ; ++ sprintf(sf_filename, "%s", argv[optind+2]) ; + + /********************************************* + Pull off prefix defining whereabouts of input +diff --git a/source/concosts.c b/source/concosts.c +index d62d2e3..590f073 100644 +--- a/source/concosts.c ++++ b/source/concosts.c +@@ -452,7 +452,7 @@ void prepare_singlets(char *filename) + sprintf(message, + "s=%d, p=%d, n=%d, phase=%g, old phase=%g, delta=%g\n", + s, p, n, phase, *(checks+n), phase-*(checks+n)) ; +- fprintf(fp_log, message) ; ++ fprintf(fp_log, "%s", message) ; + } + } + /*********************************************** +@@ -556,7 +556,7 @@ void prepare_triplets(char *filename) + sprintf(message, + "Triplet (%d %d %d) from input (%d %d %d) corresponds to point w/o fobs info!\n", + newh, newk, newl, t_h[q], t_k[q], t_l[q]) ; +- fprintf(fp_log, message) ; ++ fprintf(fp_log, "%s", message) ; + legal_triplet = FALSE ; + } + } +diff --git a/source/count.c b/source/count.c +index c3bc390..ca13008 100644 +--- a/source/count.c ++++ b/source/count.c +@@ -460,12 +460,12 @@ void print_el_count(char *filename, + } + + sprintf(message, "\nTotal no. of electrons is %g\n", totnump*volvox) ; +- fprintf(fp, message) ; ++ fprintf(fp, "%s", message) ; + printTwice(message) ; + + sprintf(message, "Count of all remaining electrons: %g %g %g\n", + remainder0*volvox, remainder1*volvox, remainder2*volvox) ; +- fprintf(fp, message) ; ++ fprintf(fp, "%s", message) ; + printTwice(message) ; + + fclose(fp) ; +diff --git a/source/eden.c b/source/eden.c +index dea3246..5a9b389 100644 +--- a/source/eden.c ++++ b/source/eden.c +@@ -319,7 +319,7 @@ int main(int argc, char *argv[]) + + get_unique_logname() ; + +- sprintf(command_line, argv[0]) ; ++ sprintf(command_line, "%s", argv[0]) ; + + for (k = 1; k < argc; k++) { + strcat(command_line, " ") ; +diff --git a/source/util.c b/source/util.c +index 6fff179..41c624c 100644 +--- a/source/util.c ++++ b/source/util.c +@@ -266,7 +266,7 @@ void printTwice(char *mess) /* send info to terminal (stdout) and to log */ + + void prompt(char *mess) /* Send message to user, await reply */ + { +- fprintf(stdout, mess) ; ++ fprintf(stdout, "%s", mess) ; + + while (fgets(terminp, MAXSTRING, stdin) != NULL) { + if ((int)strlen(terminp) > 0) +@@ -722,7 +722,7 @@ void start_record() + int k ; + + rec_length = k = sprintf(record, "\n") ; +- rec_length += sprintf(record+k, timestamp()) ; ++ rec_length += sprintf(record+k, "%s", timestamp()) ; + k = rec_length ; + + if ((cwd = getcwd(NULL, 120)) == NULL) diff --git a/sci-chemistry/eden/files/eden-5.3-impl-dec.patch b/sci-chemistry/eden/files/eden-5.3-impl-dec.patch new file mode 100644 index 000000000000..af67508d090e --- /dev/null +++ b/sci-chemistry/eden/files/eden-5.3-impl-dec.patch @@ -0,0 +1,28 @@ + source/fbyteswap.c | 1 + + source/util.c | 1 + + 2 files changed, 2 insertions(+), 0 deletions(-) + +diff --git a/source/fbyteswap.c b/source/fbyteswap.c +index 83015b9..c9033c3 100644 +--- a/source/fbyteswap.c ++++ b/source/fbyteswap.c +@@ -39,6 +39,7 @@ and shall not be used for advertising or product endorsement purposes. + + #include <stdio.h> + #include <fcntl.h> ++#include <unistd.h> + #include <sys/stat.h> + #include <sys/types.h> + void byteswap(); +diff --git a/source/util.c b/source/util.c +index 6fff179..ca7a957 100644 +--- a/source/util.c ++++ b/source/util.c +@@ -89,6 +89,7 @@ and shall not be used for advertising or product endorsement purposes. + + *******************************************************************************/ + #include <sys/time.h> /* ... for picking up date & time */ ++#include <time.h> + #include <signal.h> /* ... for capturing kill */ + #include "util.h" + diff --git a/sci-chemistry/eden/files/makefile-fixes.patch b/sci-chemistry/eden/files/makefile-fixes.patch new file mode 100644 index 000000000000..4cfff3f515df --- /dev/null +++ b/sci-chemistry/eden/files/makefile-fixes.patch @@ -0,0 +1,25 @@ +diff -ur eden.orig/source/Makefile eden/source/Makefile +--- eden.orig/source/Makefile 2004-10-18 10:40:03.000000000 -0700 ++++ eden/source/Makefile 2005-12-15 22:32:45.000000000 -0800 +@@ -78,8 +78,10 @@ + #CFLAGS = -Wall -pipe -marchi686 -pedantic -gdwarf-2 -g3 + #CFLAGS = -Wall -O3 -march=i686 + ifneq ($(FFTW),/usr/local) ++ifneq ($(FFTW),/usr) + CFLAGS += -I$(INC) + endif ++endif + + # NOTE: + # DOUBLESWITCH = ON for double precision; +@@ -129,8 +131,8 @@ + mv fbyteswap $(BIN) + mv eden $(BIN)/$(TARGET) + chmod 751 $(BIN)/$(TARGET) +- chmod +x mkeden.csh +- ./mkeden.csh $(BIN) $(BIN)/$(TARGET) ++# chmod +x mkeden.csh ++# ./mkeden.csh $(BIN) $(BIN)/$(TARGET) + + dist: clean + cd ../..; tar -cvf eden_$(VERSION).tar --exclude CVS --exclude \#\*\# --exclude \*~ --exclude Misc --exclude .\* eden; gzip -f eden_$(VERSION).tar diff --git a/sci-chemistry/eden/metadata.xml b/sci-chemistry/eden/metadata.xml new file mode 100644 index 000000000000..6113635247f3 --- /dev/null +++ b/sci-chemistry/eden/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="double-precision">More precise calculations at the expense of + speed</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/elem/Manifest b/sci-chemistry/elem/Manifest new file mode 100644 index 000000000000..78239f288908 --- /dev/null +++ b/sci-chemistry/elem/Manifest @@ -0,0 +1,6 @@ +DIST elem-src-1.0.3-Linux.tgz 58364 SHA256 a570736165b939841a9dbf273110a6c01ddfd77559e5b020574aad8e3f5af296 SHA512 24b163c5cc3019c1beb677ce7b432b21289352f7cdbad686ab9161c628d3aadbb90d8abf9bef49f1c7d077b706bbd4ea6b381f356cc85adf907f3c15a4f4893c WHIRLPOOL 8713731938e78450b1c3ab2046405b7740ec7c9f14c33f3a0ee21924da0a774d8828673cb5b7bdf2436bb55e446b7e16a502f6b39428ea27e48b2eb95a316855 +EBUILD elem-1.0.3-r1.ebuild 668 SHA256 c5e155390a3435acc10103b97aa6a374bb60e0a8774409999e494e6e657bb606 SHA512 b83e43f0cc8198e19276e6b85e3f48c045c9c5f569718507c93bec4215cdd9dbb5e29575f204db23269a6a4e016071fa3e0778e60f9a858424188f3fe4fe3e6c WHIRLPOOL ac32eb53f2baa2545d8229f9fea1ac230ffcbef5ad0b072991b60bad5d4000a33fef4d8309d5fbb5e520d5c51aa154510c6581e3d8e33dd0305e2556920cd7c4 +EBUILD elem-1.0.3-r2.ebuild 801 SHA256 741b689d033d343ecd4ef297597826087650cba806cf8d04c9614574dbf68f4a SHA512 4a13dd36dd4c09ab9a4af15a6d1f0f4b6f07421a2a41e5a5fddce083448635a64ded03011f393b868c720691e184332541628bc7ad62f48e1bd7e9c3e28d1e5b WHIRLPOOL 745a5f6c0379927ff116a9db0fcd0572ca1537b0f81435999f2fa62c31db0833a01681b9b05481ebce197cc750a4f024153cdc1df059b0f0d7cd7a0c7ee26c62 +MISC ChangeLog 2481 SHA256 0c634240055d04b7ce3de014f72af9d94e5076f1d793e62e20f1a706995673ee SHA512 8593e7452a04dd4083824d3f41ce303b52d7ae56a9b635c27e044ac075e115cd987b198adb5cf342842a46a9857e56e6b59aeede6a70300fc2d5ca3f4f7b7453 WHIRLPOOL d98cd493ef0f6ce36665b460f0a40e593a83f164cab2e835afd2749ac306c62b04b9de15b32e5bfc4303c030d3031587f96bf590f60e310338f176261e0150ad +MISC ChangeLog-2015 2390 SHA256 cdc2dcd029202a5a329866d6b2dd3d8da602ba7e10d3a1968baea006dda32f1b SHA512 6d64f72c349c2faa3b2f7bab5ff8a8438767a93e2e0ffce2d94dff9fc3d9f2cd73a6081f3483f74ead3bfd842b0e865acbccd808e2a6c81581ad960fe0447102 WHIRLPOOL b049282bd0379f857172f3635a0ed166437cba1c1663f986ed6dfcb70600f85ab96d47f6236e30dab9eae0ab08ee3b21ec70f5e982b818970229504428cbfaa5 +MISC metadata.xml 339 SHA256 07664a2e4073fda2d395da132b56bd09058018bc2ac9980b7736ae075ba2cc9e SHA512 daecddff7728e2a0b00d5e16bb4fc1c88bd316783f8921705dc76b41f427a8918ead92e663fa202ff57508242daa454cae2c04057c8bf9cf767b95d59e43c177 WHIRLPOOL 07127d2390215614938e8efb00856b9e259587301534ed5c64fd7549509688f43f298018a7a322943ecd26c86d4e4a7fcb715411ec351828f2cecbf11037e33d diff --git a/sci-chemistry/elem/elem-1.0.3-r1.ebuild b/sci-chemistry/elem/elem-1.0.3-r1.ebuild new file mode 100644 index 000000000000..eafbb9c4c0b7 --- /dev/null +++ b/sci-chemistry/elem/elem-1.0.3-r1.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +inherit toolchain-funcs + +DESCRIPTION="periodic table of the elements" +HOMEPAGE="http://elem.sourceforge.net/" +SRC_URI="mirror://sourceforge/elem/${PN}-src-${PV}-Linux.tgz" +LICENSE="GPL-2" +KEYWORDS="amd64 sparc x86" +SLOT="0" +IUSE="" + +DEPEND="x11-libs/xforms" +RDEPEND="${DEPEND}" + +src_unpack() { + unpack ${A} + cd "${S}" + sed -e 's:\(^LIBS = .*\):\1 -lXpm:' -i Makefile || die "sed failed" +} + +src_compile () { + emake COMPILER="$(tc-getCC)" FLAGS="${CFLAGS}" all || die "Build failed." +} + +src_install () { + into /usr + dobin elem elem-de elem-en + dohtml -r doc/* +} diff --git a/sci-chemistry/elem/elem-1.0.3-r2.ebuild b/sci-chemistry/elem/elem-1.0.3-r2.ebuild new file mode 100644 index 000000000000..5a9a8c132cf3 --- /dev/null +++ b/sci-chemistry/elem/elem-1.0.3-r2.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +inherit toolchain-funcs + +DESCRIPTION="periodic table of the elements" +HOMEPAGE="http://elem.sourceforge.net/" +SRC_URI="mirror://sourceforge/elem/${PN}-src-${PV}-Linux.tgz" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~sparc ~x86" +SLOT="0" +IUSE="" + +DEPEND="x11-libs/xforms" +RDEPEND="${DEPEND}" + +src_unpack() { + unpack ${A} + cd "${S}" + sed -e 's:\(^LIBS = .*\):\1 -lXpm:' \ + -e "s:\${FLAGS} -o elem:\$(LDFLAGS) &:" \ + -i Makefile || die #336190 + sed -e "/string.h/ i #include <stdlib.h>" \ + -i elem_cb.c || die #implicit exit() +} + +src_compile () { + emake COMPILER="$(tc-getCC)" FLAGS="${CFLAGS}" all || die "Build failed." +} + +src_install () { + dobin elem elem-de elem-en || die + dohtml -r doc/* || die +} diff --git a/sci-chemistry/elem/metadata.xml b/sci-chemistry/elem/metadata.xml new file mode 100644 index 000000000000..ca4cdc816a9f --- /dev/null +++ b/sci-chemistry/elem/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">elem</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/freeon/Manifest b/sci-chemistry/freeon/Manifest new file mode 100644 index 000000000000..fed9df94b32c --- /dev/null +++ b/sci-chemistry/freeon/Manifest @@ -0,0 +1,9 @@ +AUX freeon-1.0.10-stop.patch 970 SHA256 3629c408c0923553ce763b50b178150d00300c135b72a1639b1f27a7911c0cf6 SHA512 b0ba7adaf23a7b91650790cad77e0f06e75a42183c0443dbb5c8f569c77fda2dae2702729236275bc148759247675be5bef4080bba4b9532c22e21160ea62ce7 WHIRLPOOL ed0ad8499f6a7b06f561ef1bcbefacda82b4f815973f59960ed9b80582ac5b9e0852c8da4c31b635f4d6c55d35bb7578b8a2d8745c33db7e3cb2fb86fa0a3c60 +AUX freeon-1.0.8-blas.patch 5076 SHA256 387b50d28afddce2a132b7b78c9cc9ac8ed75d5e9fb29b1c7057047c2e4435a6 SHA512 89012c6f8583a8736344a7bfa74a64bbe1af793443b7255ccb1fd73366d44527ed40c6dc3124caff1af02f4e662227c66aeced8d8526dbd26bb7a50e294b5da3 WHIRLPOOL 689f9f8d8c4137156da18320bb48be2f9954de39fe8de97c0ac9e4dbc495c49027ad60a5b923168845ff13ab0d2e551f7351ef296f25f70730070050fe8565d4 +DIST freeon-1.0.10.tar.bz2 5872019 SHA256 01f0086a53930afb3078a2794baa1fccdacdc4a23082725cb016068d5a10ec38 SHA512 5bae89d6421600792bf986f6fb7504d321d5d51782587237ecba35191e54c1ec6c5ea1fdc50ed2d339551c527e4efcc5421048ccce0404c4b06875cbd0800862 WHIRLPOOL 84fcf7ca4d62e5a2407f2920f9a13fd2a4930f2637d098954b3be81f540e4a10344d17053a1d05046c2743f317a8898886148439d51364ce10dc66a313eadb8b +DIST freeon-1.0.8.tar.bz2 5957707 SHA256 ae14c1b640e4dcd9f18d2807f2debf9fc005b7451401e3e5d7b9dc76919f381d SHA512 1227f670a73b4ea39beb26e4136ad535e126ad17d66171c31b3bd403a3886eee150cda865806a2d9dad85646ccb086a6be4f645455eab24603cb064fb725efbd WHIRLPOOL b41a3b1e4bb152309a12ac0c4fec07c932809bb465af4b08cb76f6e0bf089c4d91682e1428c47d1adb449d153a1338cd3d540e860ca22774a299e21da44a16c1 +EBUILD freeon-1.0.10.ebuild 653 SHA256 5c0b75da4022e7262c51208bd49f713c72c32e35ddd20a86799dd6e07b379d91 SHA512 2438b254eb1205f2403617154140db86e96e89d17ed5e620e37cf96c6ad98ce709a7b4efcba7370cc54547c0eb1973ae089c700e96bdc511f4bd7bd4b2d26b64 WHIRLPOOL e7dad93d59078fdaa8e71a54166a01637fc10795e3e8a78ca5bb007b2fc96cddef6d1280074e191fcd1c9a53d00319529a6fd91491d749d29fb39f83e1c374eb +EBUILD freeon-1.0.8-r1.ebuild 632 SHA256 5b96c81d1b1db6a3e04dd122bb7ab317d8a38f3577a8e2fdfba68c9e12c0c635 SHA512 5690b98cfb4d8e88c4b918104aa4d3a4007988a54ec8cbbfdae24e6b547bd4197cadd928767e31610d4ae48d5e178747562aa8f9bd1259dd9bc945e2bd8ab771 WHIRLPOOL 3c732bbdb5785607cfa2cc031bc17887a1e7b766519f5f3ee7b9a71d01f7f3c997a110c5346bb3674659c44d43f20ab3e59831b0ce7453b7bb7b246ea532dec3 +MISC ChangeLog 2675 SHA256 9c0ffe0d97c4d6af43b6aeaf2c8262a55f434bc1823cee221d6c19eacdb8f997 SHA512 4010149a791b0d1d1a7bb4dc14946faa4a9a1539992eb4e794b48e14e4c917d18397eaf4ac81196f04355b215b18ed09451ebd9b56d07c49e905b91485893ce7 WHIRLPOOL f64eba272ae9f33731c0112217443aba6e8a5a5fba4ff776956666c9474da9f3077fa5c8cd44ca3d66c483f70747a1982a5dc2741085137df6a0510c08f0e598 +MISC ChangeLog-2015 990 SHA256 499a8633ace571cab489a832b5247bf26a7ac97df11add601761d5140d5ff511 SHA512 290ecfe9ba4fe0b0e6747183402b3f9a02039d2454bc16d3dfe259dedace07a1150ddb10dea373c5689890515471ae0ce1c8ef3150e76b6a3effd598dea65ac0 WHIRLPOOL 11ee500554b252d1a7165a8b17629528a7527c476fb991dc8c7afbfb37275b57b2fe635b5ce9ad923175acef94356ae903142e4ec487ca1a8de92aeb05be40ff +MISC metadata.xml 528 SHA256 5b029938eb397ae1537d79c76f26bda312d9ba9a7a8d0cb8b63ee05cab63e687 SHA512 4eea3876d046b423706f565571cbe20dbe2ff724ecd8de7f92ba0103c83f78d9e1d28789d6c35e62a8f0527f13bdadf6303695c529b7b6622bc2e14cf57044da WHIRLPOOL 9f0dfbaf97eb7c70ce7e62c5263df9da19952a14801eddea3b8ad8337a0bd3eb3e5d5f6c2063b2d98789609cdc71289b61b28d7975ad8189e4a34b60f1fda8ee diff --git a/sci-chemistry/freeon/files/freeon-1.0.10-stop.patch b/sci-chemistry/freeon/files/freeon-1.0.10-stop.patch new file mode 100644 index 000000000000..a20d520e553c --- /dev/null +++ b/sci-chemistry/freeon/files/freeon-1.0.10-stop.patch @@ -0,0 +1,36 @@ +From 882b51fb718c2eed98ef3e8f3be0c5b7320024e1 Mon Sep 17 00:00:00 2001 +From: Justin Lecher <jlec@gentoo.org> +Date: Mon, 2 Jan 2017 07:56:11 +0000 +Subject: [PATCH] Add missing blank after STOP + +The STOP statement requires preceding blank. Newer gcc +will fail with + + CASE DEFAULT; STOP'Err:WghtMtrx' + 1 +Error: Blank required in STOP statement near (1) + +See: +https://bugs.gentoo.org/show_bug.cgi?id=604138 + +Signed-off-by: Justin Lecher <jlec@gentoo.org> +--- + FreeON/Optimizer.F90 | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/FreeON/Optimizer.F90 b/FreeON/Optimizer.F90 +index 0ef22269..0bbd9008 100644 +--- a/FreeON/Optimizer.F90 ++++ b/FreeON/Optimizer.F90 +@@ -3055,7 +3055,7 @@ CONTAINS + SELECT CASE(FromTo) + CASE('CToWC');IFromTo=0 + CASE('WCToC');IFromTo=1 +- CASE DEFAULT; STOP'Err:WghtMtrx' ++ CASE DEFAULT; STOP 'Err:WghtMtrx' + END SELECT + DO AtB=1,NAtoms + IF(IFromTo.EQ.0) THEN +-- +2.11.0 + diff --git a/sci-chemistry/freeon/files/freeon-1.0.8-blas.patch b/sci-chemistry/freeon/files/freeon-1.0.8-blas.patch new file mode 100644 index 000000000000..46fca7fa2a52 --- /dev/null +++ b/sci-chemistry/freeon/files/freeon-1.0.8-blas.patch @@ -0,0 +1,165 @@ + FreeON/Makefile.am | 2 +- + HiCu/Makefile.am | 2 +- + ONX/Makefile.am | 1 + + OneE/Makefile.am | 2 +- + QCTC/Makefile.am | 2 +- + SCFeqs/Makefile.am | 2 +- + configure.ac | 12 ++++++++---- + make.inc | 2 +- + tests/Makefile.am | 8 ++++---- + tools/Makefile.am | 2 +- + 10 files changed, 20 insertions(+), 15 deletions(-) + +diff --git a/FreeON/Makefile.am b/FreeON/Makefile.am +index 18e0283..12db056 100644 +--- a/FreeON/Makefile.am ++++ b/FreeON/Makefile.am +@@ -50,7 +50,7 @@ FreeON_DEPENDENCIES = $(LIBRARY_DEPENDENCY_FILES) + + SOURCES_DEPCHECK = $(FreeON_SOURCES) + +-FreeON_LDADD = $(LDADD_MODULES) ++FreeON_LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + AM_CPPFLAGS += \ + -DFREEON_BASISSETS=\"$(datadir)/$(PACKAGE)/BasisSets\" \ +diff --git a/HiCu/Makefile.am b/HiCu/Makefile.am +index 1847354..cc4ebef 100644 +--- a/HiCu/Makefile.am ++++ b/HiCu/Makefile.am +@@ -27,7 +27,7 @@ EXTRA_DIST = \ + MMA/CubeRules/RuleD.Inc \ + MMA/CubeRules/RuleE.Inc + +-LDADD = $(LDADD_MODULES) ++LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + EXTRA_INCLUDES = -I$(top_srcdir)/Modules/MMA/Functionals + AM_CPPFLAGS += -DRULE7 -DEXPLICIT_SOURCE +diff --git a/ONX/Makefile.am b/ONX/Makefile.am +index 4d25029..b27b149 100644 +--- a/ONX/Makefile.am ++++ b/ONX/Makefile.am +@@ -61,6 +61,7 @@ EXTRA_INCLUDES = \ + + LDADD = \ + $(LDADD_MODULES) \ ++ $(LAPACK_LIBS) \ + $(builddir)/../TwoE/libfreeonTwoE.la + + # In case we have ctags installed, make the necessary tags files. +diff --git a/OneE/Makefile.am b/OneE/Makefile.am +index 784bede..ea86ae7 100644 +--- a/OneE/Makefile.am ++++ b/OneE/Makefile.am +@@ -46,7 +46,7 @@ EXTRA_DIST = \ + MMA/QQuad32.Inc \ + MMA/QQuad64.Inc + +-LDADD = $(LDADD_MODULES) ++LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + EXTRA_INCLUDES = -I$(srcdir)/MMA + +diff --git a/QCTC/Makefile.am b/QCTC/Makefile.am +index 3ec39f0..53c358c 100644 +--- a/QCTC/Makefile.am ++++ b/QCTC/Makefile.am +@@ -105,7 +105,7 @@ EXTRA_DIST = \ + PBCTensor/Majik_Kubic_WS2.Inc + + EXTRA_INCLUDES = -I$(top_builddir)/OneE -I$(top_srcdir)/Modules/MMA/LookUpTables_800_6x +-LDADD = $(LDADD_MODULES) libktrax.la ++LDADD = $(LDADD_MODULES) libktrax.la $(LAPACK_LIBS) + + # In case we have ctags installed, make the necessary tags files. + .PHONY : tags +diff --git a/SCFeqs/Makefile.am b/SCFeqs/Makefile.am +index 2ee640f..709f220 100644 +--- a/SCFeqs/Makefile.am ++++ b/SCFeqs/Makefile.am +@@ -57,7 +57,7 @@ SOURCES_DEPCHECK = \ + $(P2Use_SOURCES) \ + $(DIIS_SOURCES) + +-LDADD = $(LDADD_MODULES) ++LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + # In case we have ctags installed, make the necessary tags files. + .PHONY : tags +diff --git a/configure.ac b/configure.ac +index e0c6a77..726c880 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -784,12 +784,16 @@ END PROGRAM test_compiler + you use a version >= 4.2.0])]) + + # Check for BLAS. +-AC_SEARCH_LIBS([dgemm], [blas], [], +- [AC_MSG_FAILURE([specify the location of dgemm()])]) ++PKG_CHECK_MODULES([BLAS],[blas],[], ++ AC_SEARCH_LIBS([dgemm], [blas], [], ++ [AC_MSG_FAILURE([specify the location of dgemm()])]) ++ ) + + # Check for LAPACK. +-AC_SEARCH_LIBS([dsyev], [lapack], [], +- [AC_MSG_FAILURE([specify the library that contains dsyev()])]) ++PKG_CHECK_MODULES([LAPACK],[lapack],[], ++ AC_SEARCH_LIBS([dsyev], [lapack], [], ++ [AC_MSG_FAILURE([specify the library that contains dsyev()])]) ++ ) + + AC_ARG_VAR([H5CC], [h5cc compiler wrapper command]) + +diff --git a/make.inc b/make.inc +index cf35e40..5766ff9 100644 +--- a/make.inc ++++ b/make.inc +@@ -9,7 +9,7 @@ AM_CPPFLAGS = @AM_CPPFLAGS@ + # Fix for bug in autoconf-2.59 + builddir = . + +-LDADD_MODULES = $(top_builddir)/Modules/libfreeonmodules.la ++LDADD_MODULES = $(top_builddir)/Modules/libfreeonmodules.la $(LAPACK_MODULES) + + # On filesystems which are case-insensitive (which really means HFS+ on OS X) + # we can not preprocess into a filename that differs by the case only, i.e. .C +diff --git a/tests/Makefile.am b/tests/Makefile.am +index 6bd89f2..ae9da60 100644 +--- a/tests/Makefile.am ++++ b/tests/Makefile.am +@@ -7,16 +7,16 @@ noinst_PROGRAMS = \ + sendReceive_HGRho + + sleeper_SOURCES = sleeper.F90 +-sleeper_LDADD = $(LDADD_MODULES) ++sleeper_LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + lock_SOURCES = lock.F90 +-lock_LDADD = $(LDADD_MODULES) ++lock_LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + sendReceive_DBL_RNK2_SOURCES = sendReceive_DBL_RNK2.F90 +-sendReceive_DBL_RNK2_LDADD = $(LDADD_MODULES) ++sendReceive_DBL_RNK2_LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + sendReceive_HGRho_SOURCES = sendReceive_HGRho.F90 +-sendReceive_HGRho_LDADD = $(LDADD_MODULES) ++sendReceive_HGRho_LDADD = $(LDADD_MODULES) $(LAPACK_LIBS) + + if HAVE_MPIRUN + MPI_TESTS = locktest +diff --git a/tools/Makefile.am b/tools/Makefile.am +index e0baaff..a6b18b2 100644 +--- a/tools/Makefile.am ++++ b/tools/Makefile.am +@@ -19,7 +19,7 @@ python_PYTHON = \ + bin_PROGRAMS = printBCSR convertBCSR + + printBCSR_SOURCES = printBCSR.F90 +-printBCSR_LDADD = $(top_builddir)/Modules/libfreeonmodules.la ++printBCSR_LDADD = $(top_builddir)/Modules/libfreeonmodules.la $(LAPACK_LIBS) + + convertBCSR_SOURCES = \ + convertBCSR.cc \ diff --git a/sci-chemistry/freeon/freeon-1.0.10.ebuild b/sci-chemistry/freeon/freeon-1.0.10.ebuild new file mode 100644 index 000000000000..f6ce62de1925 --- /dev/null +++ b/sci-chemistry/freeon/freeon-1.0.10.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_STANDARD=90 +PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} ) + +inherit autotools fortran-2 python-any-r1 + +DESCRIPTION="An experimental suite of programs for linear scaling quantum chemistry" +HOMEPAGE="http://www.freeon.org" +SRC_URI="http://download.savannah.gnu.org/releases/${PN}/${PN}-${PV}.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + sci-libs/hdf5 + virtual/blas + virtual/lapack" +DEPEND="${RDEPEND} + ${PYTHON_DEPS}" + +PATCHES=( + "${FILESDIR}"/${P}-stop.patch +) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-chemistry/freeon/freeon-1.0.8-r1.ebuild b/sci-chemistry/freeon/freeon-1.0.8-r1.ebuild new file mode 100644 index 000000000000..41acb419c4f2 --- /dev/null +++ b/sci-chemistry/freeon/freeon-1.0.8-r1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=1 +FORTRAN_STANDARD=90 +PYTHON_COMPAT=( python{2_7,3_4} ) + +inherit autotools-utils fortran-2 python-any-r1 + +DESCRIPTION="An experimental suite of programs for linear scaling quantum chemistry" +HOMEPAGE="http://www.freeon.org" +SRC_URI="http://download.savannah.gnu.org/releases/${PN}/${PN}-${PV}.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + sci-libs/hdf5 + virtual/blas + virtual/lapack" +DEPEND="${RDEPEND} + ${PYTHON_DEPS}" + +PATCHES=( "${FILESDIR}"/${P}-blas.patch ) diff --git a/sci-chemistry/freeon/metadata.xml b/sci-chemistry/freeon/metadata.xml new file mode 100644 index 000000000000..8f4e98e7e5bf --- /dev/null +++ b/sci-chemistry/freeon/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <longdescription lang="en"> + FreeON is an experimental, open source (GPL) suite of programs for linear scaling quantum chemistry. + </longdescription> + <maintainer type="person"> + <email>nicolasbock@gentoo.org</email> + <name>Nicolas Bock</name> + </maintainer> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/gabedit/Manifest b/sci-chemistry/gabedit/Manifest new file mode 100644 index 000000000000..0cdbface949b --- /dev/null +++ b/sci-chemistry/gabedit/Manifest @@ -0,0 +1,10 @@ +AUX CONFIG.Gentoo 349 SHA256 9ecf7149934fee3f91024cb13b4431808b62febb2a4e77b1191734e446396b8f SHA512 bb028864b3810183add9d26607ae2fb59cc391de9254e5a3593dc1db0efa609a4a02309336816fa9111489b6463a9f448b7dd3040afc40c3eb3bda4a6b095eb7 WHIRLPOOL 641a6993b95877c4242f7a2dc572e4c6465e371c60d50acd8f29dd2c822b4e8821401ca788e0f94790f9c51fa8e562cfef1f3c3cbc63a8b98f819f461f606251 +DIST GabeditSrc246.tar.gz 1964406 SHA256 3881df1f2d4788d4b3660e7d8af0f7318223dd50194fd9ed0072dd58a6beaa12 SHA512 fbd92ff532ce21e97dcc2d012927fb0d19f4634956e88122a8e9a41e9484592ede455c3a88670cbd1c6387a4d0916425f897d2ade1957ebf4b25b89c7365a076 WHIRLPOOL 12be8d5299e6adcb63e4c989542f2fae02136a18bf515ded7ce8f7b3ab4e69f9fb085778be0bd5589b9ae42b7fd80c5ea7fa451a24377e5feedeb09ddff7a6b7 +DIST GabeditSrc247.tar.gz 1990187 SHA256 e9f84aae6751146f72e5cd8d3f33ec68f057f720edc68e3a89d53c5a2c3c9020 SHA512 a562dd650f9dc90a3c28a6d6b45212dc1d945548c9021f84e25a96022e67f95309030ded30bc20c052526783d0613f328830c640955822237828fcbac6d91b95 WHIRLPOOL f6a69e8e6a60fb48ef23849538a8718f507abc4e09de97abe10016ecf7b4ae101c09135f2762d7db7d764c4a66f9a268bd194ece9f05d6162b94a70b36ccec7a +DIST GabeditSrc248.tar.gz 1992373 SHA256 38d6437a18280387b46fd136f2201a73b33e45abde13fa802c64806b6b64e4d3 SHA512 d06b54693c4887e3cecb6bb20b98307db8aeb7f32ff87b85af536a4034f2d6af04f30809c04e29ed6fb4744e6290dcd276c9f85b2940daa71a595f6bd5f154da WHIRLPOOL c47cf238b7080dbeddb3992162e6bb31f17a33623299a0bc4608aa86d2d4ff71f18159f3ca952d71251b039ace9bca0d3736a56af3e1dc8305200395c2a422e3 +EBUILD gabedit-2.4.6.ebuild 1347 SHA256 3396947402b4d644ad6e73fe5c4d8d361705510ffb6543bdcd16a53c64c99e22 SHA512 e31ac44e026dae879c27bd318f4a7002616588d22cde029af80faf8ece841c13698d6152d6d0ca970089a609a4232a9772737c177af8a453ad251614a98e53b1 WHIRLPOOL ed8e9c00b87ef9478a98539e91f3b4f3eab6052100147be7320f791528189add46b3e6cbe2238c269b55526e30517b75d2d1bcb0125fe7fbfed5db954e7cf31a +EBUILD gabedit-2.4.7.ebuild 1349 SHA256 5c8d2b9b25ad7b6a98345ad91ecb02c6ba7f7c6211b2dd8a8bc7154b72c5a66b SHA512 9a481026b8395bf7c2d743b129e03d2e9a21e048becd2da93fa41b35fcb85574334486ab80118a042b7bbe8d818370dcef3e9f6c5eb25933cc7317f82ec97d1c WHIRLPOOL efe5118e1d219dac9801c92fff95a904b60a58d8d28b3863c2d359a0cca0adc0edc87c23246841b6372b87f52bdeba16e8d8aabb00a409810b563993360c7a9b +EBUILD gabedit-2.4.8.ebuild 1349 SHA256 d329b2cf5f0286ef0ef6f0d63349d4886002020b2397fdfbe1d48ddcee6dee8c SHA512 a34c323240c2b8bbdd6dcd64bc65c0f5084a9a18fed42016e6082752bb376f635e6d2477488cb8616c74e760a3956dfd8dab78241df9c24e93720ebbcbd08955 WHIRLPOOL 68d0df3d9987551d07ae47a69c2941aa84ba7d1ee454418a59872caa3f25b00af113736e79ae046d08036565180c172faa6cc7805c00f1d4627518e3a39ebde6 +MISC ChangeLog 2733 SHA256 9f5a5594d06b7dc9c8d1f8118c219b8d2e83f2a58debc55f4a976a52725b5d74 SHA512 79436f0fe8233cbbad2dcc0daca0cdac3692995e616bb299fbc3fdfbd091dcb9119429ef4b0375be2fc9e7207fb706536771a6e4305bf973beb26459c79c6d69 WHIRLPOOL 7a41f0775bcb1784ddbe24508bf6532bfebb7f4f0238bec1af47cc15bbc8625219b390b76857cb3efb869e90d1013c6d2e882fb59c47204ec9dd3764fb025616 +MISC ChangeLog-2015 4008 SHA256 43b7305e118802cfd3bc8f35312febf6c7c005eeabc55d51d00c939053830d59 SHA512 f2f6284219f4a09c00d6f7796a95ecbfcb9bdc4817853674bcbe4a8bf54e2ea64ca410a883a0a85195cb090a23362493a761707dcf018ad9b6a86295ac3451f4 WHIRLPOOL d8a3a7e9ca9e21d1f647523ac5f8511e061f775706ee67de12fe15e15437c5ab8183d2fc213b53ae419794ddfc679eb36720c4555461210bb4ae3f1da3e8256a +MISC metadata.xml 352 SHA256 ebfde317ab9841e0e605a8f6c93550d259675f8c5d7b6279a942c26833894b65 SHA512 d4d34b084d7aeffa74d5d19e75fda4048af684fdebcf8ee1f336238c40ca514fa1cf35802edcb4c718b310f710353fd8264e3caf78fa6bcf1d9d43f2035fd381 WHIRLPOOL 31dada7bcbf5a4a918217e2973afba51ca8a843daa37839830b1e1aed8cb02a8543aa62c61a44788bbd2e47b5f0e5d391160913d33357d1a5d3a93b24963b3d0 diff --git a/sci-chemistry/gabedit/files/CONFIG.Gentoo b/sci-chemistry/gabedit/files/CONFIG.Gentoo new file mode 100644 index 000000000000..9cf387c752eb --- /dev/null +++ b/sci-chemistry/gabedit/files/CONFIG.Gentoo @@ -0,0 +1,14 @@ +GTKLIB = `pkg-config --libs gtk+-2.0 gtkglext-1.0` +GTKCFLAGS = `pkg-config --cflags gtk+-2.0 gtkglext-1.0` +OGLLIB = `pkg-config --libs glu` +OGLCFLAGS = `pkg-config --cflags glu` +X11LIB = `pkg-config --libs x11` +LIBPTHREAD = -lpthread +RM = rm -f +MAKE = make +MKDIR = mkdir -p +WIN32LIB = + +#DRAWGEOMGL= +DRAWGEOMGL=-DDRAWGEOMGL + diff --git a/sci-chemistry/gabedit/gabedit-2.4.6.ebuild b/sci-chemistry/gabedit/gabedit-2.4.6.ebuild new file mode 100644 index 000000000000..59be69442ad2 --- /dev/null +++ b/sci-chemistry/gabedit/gabedit-2.4.6.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs versionator + +MY_PN=${PN/g/G} +MY_PV=$(delete_all_version_separators) +MY_P="${MY_PN}Src${MY_PV}" + +DESCRIPTION="GUI for computational chemistry packages" +HOMEPAGE="http://gabedit.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="openmp" + +RDEPEND=" + dev-libs/glib:2 + x11-libs/cairo + x11-libs/gdk-pixbuf:2 + x11-libs/gtk+:2 + x11-libs/gtkglext + x11-libs/gl2ps + x11-libs/pango + virtual/opengl + virtual/glu" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + sed -i "/rmdir tmp/d" "${S}"/Makefile || die + sed \ + -e "/GTK_DISABLE_DEPRECATED/s:define:undef:g" \ + -i "${S}/Config.h" || die + sed -e 's:-g::g' -i Makefile || die + cp "${FILESDIR}"/CONFIG.Gentoo "${S}"/CONFIG + + if use openmp && tc-has-openmp; then + cat <<- EOF >> "${S}/CONFIG" + OMPLIB=-fopenmp + OMPCFLAGS=-DENABLE_OMP -fopenmp + EOF + fi + echo "COMMONCFLAGS = ${CFLAGS} -DENABLE_DEPRECATED \$(OMPCFLAGS) \$(DRAWGEOMGL)" >> CONFIG + + tc-export CC +} + +src_compile() { + emake clean + emake external_gl2ps=1 +} + +src_install() { + local size + dobin ${PN} + dodoc ChangeLog + for size in 16 24 32 48; do + doicon -s ${size} icons/Gabedit${size}.* + done +} diff --git a/sci-chemistry/gabedit/gabedit-2.4.7.ebuild b/sci-chemistry/gabedit/gabedit-2.4.7.ebuild new file mode 100644 index 000000000000..755e1928327a --- /dev/null +++ b/sci-chemistry/gabedit/gabedit-2.4.7.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs versionator + +MY_PN=${PN/g/G} +MY_PV=$(delete_all_version_separators) +MY_P="${MY_PN}Src${MY_PV}" + +DESCRIPTION="GUI for computational chemistry packages" +HOMEPAGE="http://gabedit.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="openmp" + +RDEPEND=" + dev-libs/glib:2 + x11-libs/cairo + x11-libs/gdk-pixbuf:2 + x11-libs/gtk+:2 + x11-libs/gtkglext + x11-libs/gl2ps + x11-libs/pango + virtual/opengl + virtual/glu" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + sed -i "/rmdir tmp/d" "${S}"/Makefile || die + sed \ + -e "/GTK_DISABLE_DEPRECATED/s:define:undef:g" \ + -i "${S}/Config.h" || die + sed -e 's:-g::g' -i Makefile || die + cp "${FILESDIR}"/CONFIG.Gentoo "${S}"/CONFIG + + if use openmp && tc-has-openmp; then + cat <<- EOF >> "${S}/CONFIG" + OMPLIB=-fopenmp + OMPCFLAGS=-DENABLE_OMP -fopenmp + EOF + fi + echo "COMMONCFLAGS = ${CFLAGS} -DENABLE_DEPRECATED \$(OMPCFLAGS) \$(DRAWGEOMGL)" >> CONFIG + + tc-export CC +} + +src_compile() { + emake clean + emake external_gl2ps=1 +} + +src_install() { + local size + dobin ${PN} + dodoc ChangeLog + for size in 16 24 32 48; do + doicon -s ${size} icons/Gabedit${size}.* + done +} diff --git a/sci-chemistry/gabedit/gabedit-2.4.8.ebuild b/sci-chemistry/gabedit/gabedit-2.4.8.ebuild new file mode 100644 index 000000000000..54436b2cabba --- /dev/null +++ b/sci-chemistry/gabedit/gabedit-2.4.8.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs versionator + +MY_PN=${PN/g/G} +MY_PV=$(delete_all_version_separators) +MY_P="${MY_PN}Src${MY_PV}" + +DESCRIPTION="GUI for computational chemistry packages" +HOMEPAGE="http://gabedit.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="openmp" + +RDEPEND=" + dev-libs/glib:2 + x11-libs/cairo + x11-libs/gdk-pixbuf:2 + x11-libs/gtk+:2 + x11-libs/gtkglext + x11-libs/gl2ps + x11-libs/pango + virtual/opengl + virtual/glu" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + sed -i "/rmdir tmp/d" "${S}"/Makefile || die + sed \ + -e "/GTK_DISABLE_DEPRECATED/s:define:undef:g" \ + -i "${S}/Config.h" || die + sed -e 's:-g::g' -i Makefile || die + cp "${FILESDIR}"/CONFIG.Gentoo "${S}"/CONFIG + + if use openmp && tc-has-openmp; then + cat <<- EOF >> "${S}/CONFIG" + OMPLIB=-fopenmp + OMPCFLAGS=-DENABLE_OMP -fopenmp + EOF + fi + echo "COMMONCFLAGS = ${CFLAGS} -DENABLE_DEPRECATED \$(OMPCFLAGS) \$(DRAWGEOMGL)" >> CONFIG + + tc-export CC +} + +src_compile() { + emake clean + emake external_gl2ps=1 +} + +src_install() { + local size + dobin ${PN} + dodoc ChangeLog + for size in 16 24 32 48; do + doicon -s ${size} icons/Gabedit${size}.* + done +} diff --git a/sci-chemistry/gabedit/metadata.xml b/sci-chemistry/gabedit/metadata.xml new file mode 100644 index 000000000000..958aa61e8b1c --- /dev/null +++ b/sci-chemistry/gabedit/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">gabedit</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/gelemental/Manifest b/sci-chemistry/gelemental/Manifest new file mode 100644 index 000000000000..ddd27fc6e636 --- /dev/null +++ b/sci-chemistry/gelemental/Manifest @@ -0,0 +1,10 @@ +AUX gelemental-1.2.0-doxygen.patch 1281 SHA256 687fa06347030ba1f2f6acb211664c4e945ab67e6d85cac6dc19064169173b6a SHA512 f5d7c49ef6a0a7d8570dcb20d9651af31eb07fbf8f75685c83c8d5e9f44cc07ea0945af6d04cf45694aeb9a2471382c348532717700059dbdd562d1838b4f52f WHIRLPOOL d08cf1c33f4d894af15ddc31d8d0546636273a238ea2ea190c3067d2d0472bf2af7cb9c3a1dba21ee2fe56a7fbb8df6d5d85889b49d3e117c28a2ca048fb4ca3 +AUX gelemental-1.2.0-fix-c++14.patch 399 SHA256 57b8bf85586c9e1f20e99deea4294ad6aa5d1431e2b2cc360ae069f2fdcee4e9 SHA512 9d134a3fe3dfb5a0238cc2f88803eb449cc596b5e4cd7c565c63dcc6cc11f7ed9ea605a075d75585d205fd4b502301dce9ed91725d81dffaca5cdbec95ce9d0c WHIRLPOOL a84cf8db49e21cb6211686210eec91ea4fc9b48e9c0ad6fac790bf0a5a6dc0db6c1738cd044347bda061ba7c0da11de8c1cb85248ba13e58597bde82b22a473f +AUX gelemental-1.2.0-gcc4.3.patch 387 SHA256 0747ec32d6ee9f6ff75bbf2271f24018b547b6d71b98660d16fac450519c5918 SHA512 d7b103a533dd3edda30d349b0205b241cd5e23c97a562912cc28bd7fb210c3e6f5c33ce2a3321817fe3748812f655b1295d23058aefd35ae2b2746bee99c35e3 WHIRLPOOL 9bf3603af284d8a27d19e4aee212234ce115e1ddf2b24234233040bf8e37192fb784915dd598c007140b670a389f84d829d64a2fd7ac19af1c65b546c55db66b +AUX gelemental-1.2.0-glib-2.32.patch 1235 SHA256 630d4fcbdc6ccd3313c43324052bfd42a575cccf5e61a39c513369e003326c34 SHA512 2e414b8d4f57a6edcdb4322b0bf39b6d89c7be0c67086f2bd2d468aaff36f9f98339f14cb2fe11444113b5395b8b4742ea82461df84094c8c1e4ca7f21ebb1c9 WHIRLPOOL a9ca2c49a365aaa7fbbba59c4481b134d996a489249ab52a323b97ab5d3480bdea41273d091d0ecca7b4943331e9e2d1bfff09e313111fb3e590d1a81faf0855 +DIST gelemental-1.2.0.tar.bz2 460757 SHA256 4f2797200af98d74c71db0065506f99a97820392f39f67cf3ef42de6dca3859b SHA512 2e6ef2c22b389cff69728b01e1eb397578974362356f5132098f29a9e01a64be228a24686738bd84ea575cee5aef068d9ab3d6c20233f995ccc5f1a1cb5d5673 WHIRLPOOL 6814ce64ad66a872073af31460e9938f2ac385500af9a94a60d3ce28c85bad467ef09ce9a2596e0b3e508121959b662e77cba685a6d3359a5d840a9af9fa34bb +DIST gelemental_1.2.0-8.debian.tar.gz 29877 SHA256 b03ddad5587fdfb279d570388105ea5fb3b16eebbb2626f1f293ff283456869e SHA512 83c236e3b91af304c96f28c0f12577821ee2f47c9e01fb1f3664228afb002dc19b1a71e6dcd6040d09ea991d131b147ea5b36283d8ead290d50014c15e69878c WHIRLPOOL 16bc07c03b88e7a0c161677302d2a9d2cdb74aa6baf702b0d6d2c2a6f2ec8fe21d626cc58ecb34850da8369bccb36b889f5391c013e0861c338bd68c1f38e3ca +EBUILD gelemental-1.2.0-r1.ebuild 1842 SHA256 249818a53f999c99dedd0778b3d3f622d323e7a5ef459741fe9a9b4aa5c21569 SHA512 e34da62f56231fcf5c93040397c2af02b689ee630afbdf658e3bcdcddca3822b216c669b7a247714504dcc925572f60054c2684fca5bc299a4a76c8c87895dde WHIRLPOOL 9948b24e97be7dbcdb9ce0ea7fb236412efb15bd7846ec9bd2da5c5e644389bbefa9e78b111fb72f58afc4a2ddd892428f7c5b500d16d8704532654be5817eae +MISC ChangeLog 3833 SHA256 438d17223bc8f357c930b6ec1c3f192b8c2c38b67923b51211ced83523fc7cff SHA512 6d84f9e273b0e0710fa643d4dce0a5af32555178882b56a2fd26d1cddcc230d638b1d8c3c11eba925de2f00ac0f97e50c19ea2f138e59db14ee024513f4e5489 WHIRLPOOL dc6fb75b689029c170abe4318ee61dde122601a27d81c3f9c9cfe6e352746a83f5f052366cff2dabe6279beb047a619ba28d8483fc8679d86c5dd983eb975b36 +MISC ChangeLog-2015 1775 SHA256 4fc11b57e1703162c90267ebd0c346a3e8270f9e2d3e1324ac73f42aea8342e0 SHA512 4257dbeb65053037529524c8175a596eda433fc6fcbf8ffada651594eade5c03e1c6b2a7597fd1c5d0d8359b4e7ba5ba882c043474826a6f5c23502b31cdc6c9 WHIRLPOOL 924b91493e4ac7206bb3e26a132df21793de0b3d5f50ba1c6f45ae7c159dd3d27e077ad401afd8f6bdf402b9bbe26c8eb170169727d3eebd3a2ac9aec0f18f11 +MISC metadata.xml 342 SHA256 63ec4810674345dd1e70a4516cbce043bbea134e70bf2289bd1fd2fc03e08981 SHA512 bb9f0244e85513e0c85bcd55d4f9466ae8a9ab09bebac17713b192ee1b346a31c476bc67e54cdb650a234e696f0783dc493e54df63de379f3fecac00e2ecbc3b WHIRLPOOL 92387e60dc7b0a0efcf196b4f93c075c9baa0ba2abfca6c1da61eff9fb45950c6c5b7633cdaa1a228f4a39078edb06feea3fbc068933b8818e85251c611a1a35 diff --git a/sci-chemistry/gelemental/files/gelemental-1.2.0-doxygen.patch b/sci-chemistry/gelemental/files/gelemental-1.2.0-doxygen.patch new file mode 100644 index 000000000000..8c904e844586 --- /dev/null +++ b/sci-chemistry/gelemental/files/gelemental-1.2.0-doxygen.patch @@ -0,0 +1,30 @@ +Author: Joachim Reichel <reichel@debian.org> +Description: Skip installing (no longer generated) .dot and .gif files +Origin: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=590382#15 +Bug-Debian: http://bugs.debian.org/590382 +Reviewed-By: Michael Banck <mbanck@debian.org> +Forwarded: no +Last-Update: 2010-09-22 + +--- a/docs/api/Makefile.am ++++ b/docs/api/Makefile.am +@@ -12,7 +12,7 @@ + install-api: $(srcdir)/html/index.html + @$(NORMAL_INSTALL) + $(mkinstalldirs) $(DESTDIR)/$(apidir) +- @dir='$(<D)'; for p in $$dir/*.html $$dir/*.css $$dir/*.png $$dir/*.gif $$dir/*.dot ; do \ ++ @dir='$(<D)'; for p in $$dir/*.html $$dir/*.css $$dir/*.png ; do \ + f="`echo $$p | sed -e 's|^.*/||'`"; \ + echo " $(INSTALL_DATA) $$p $(DESTDIR)$(apidir)/$$f"; \ + $(INSTALL_DATA) $$p $(DESTDIR)$(apidir)/$$f; \ +--- a/docs/api/Makefile.in ++++ b/docs/api/Makefile.in +@@ -393,7 +393,7 @@ + install-api: $(srcdir)/html/index.html + @$(NORMAL_INSTALL) + $(mkinstalldirs) $(DESTDIR)/$(apidir) +- @dir='$(<D)'; for p in $$dir/*.html $$dir/*.css $$dir/*.png $$dir/*.gif $$dir/*.dot ; do \ ++ @dir='$(<D)'; for p in $$dir/*.html $$dir/*.css $$dir/*.png ; do \ + f="`echo $$p | sed -e 's|^.*/||'`"; \ + echo " $(INSTALL_DATA) $$p $(DESTDIR)$(apidir)/$$f"; \ + $(INSTALL_DATA) $$p $(DESTDIR)$(apidir)/$$f; \ diff --git a/sci-chemistry/gelemental/files/gelemental-1.2.0-fix-c++14.patch b/sci-chemistry/gelemental/files/gelemental-1.2.0-fix-c++14.patch new file mode 100644 index 000000000000..0965fe15b43e --- /dev/null +++ b/sci-chemistry/gelemental/files/gelemental-1.2.0-fix-c++14.patch @@ -0,0 +1,14 @@ +Fix building with C++14, which errors out due to bool -> T* conversions +See also: https://bugs.gentoo.org/show_bug.cgi?id=593994 + +--- a/src/dialogs.cc ++++ b/src/dialogs.cc +@@ -255,7 +255,7 @@ + const Gtk::TreePath& tpath, bool) + { + Gtk::TreeIter iter = store->get_iter (tpath); +- return iter ? iter->get_value (cols.property) : false; ++ return iter ? iter->get_value (cols.property) : NULL; + } + + diff --git a/sci-chemistry/gelemental/files/gelemental-1.2.0-gcc4.3.patch b/sci-chemistry/gelemental/files/gelemental-1.2.0-gcc4.3.patch new file mode 100644 index 000000000000..8e69e98a5437 --- /dev/null +++ b/sci-chemistry/gelemental/files/gelemental-1.2.0-gcc4.3.patch @@ -0,0 +1,12 @@ +diff -Naru gelemental-1.2.0/libelemental/value.tcc gelemental-1.2.0.new/libelemental/value.tcc +--- gelemental-1.2.0/libelemental/value.tcc 2007-09-25 01:10:16.000000000 -0400 ++++ gelemental-1.2.0.new/libelemental/value.tcc 2008-10-19 10:08:35.000000000 -0400 +@@ -26,6 +26,8 @@ + #error "value.tcc must be included from value.hh." + #endif + ++#include <limits> ++ + namespace Elemental { + + diff --git a/sci-chemistry/gelemental/files/gelemental-1.2.0-glib-2.32.patch b/sci-chemistry/gelemental/files/gelemental-1.2.0-glib-2.32.patch new file mode 100644 index 000000000000..eab2ad1f194e --- /dev/null +++ b/sci-chemistry/gelemental/files/gelemental-1.2.0-glib-2.32.patch @@ -0,0 +1,46 @@ + libelemental/misc/extras.cc | 2 +- + libelemental/misc/widgets.cc | 2 +- + src/main.cc | 4 ++-- + 3 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/libelemental/misc/extras.cc b/libelemental/misc/extras.cc +index a8e5720..c042604 100644 +--- a/libelemental/misc/extras.cc ++++ b/libelemental/misc/extras.cc +@@ -21,7 +21,7 @@ + + #include <algorithm> + #include <stdexcept> +-#include <glib/gmem.h> ++#include <glib.h> + #include <glibmm/utility.h> + + namespace misc { +diff --git a/libelemental/misc/widgets.cc b/libelemental/misc/widgets.cc +index 002310c..941d881 100644 +--- a/libelemental/misc/widgets.cc ++++ b/libelemental/misc/widgets.cc +@@ -20,7 +20,7 @@ + #include "macros.hh" + #include "widgets.hh" + +-#include <glib/gmessages.h> ++#include <glib.h> + #include <gtkmm/alignment.h> + #include <gtkmm/image.h> + #include <gtkmm/label.h> +diff --git a/src/main.cc b/src/main.cc +index 41cfe03..68bbb4c 100644 +--- a/src/main.cc ++++ b/src/main.cc +@@ -26,8 +26,8 @@ + #include <clocale> + #include <iostream> + #include <locale> +-#include <glib/goption.h> +-#include <glib/gutils.h> ++#include <glib.h> ++#include <glib.h> + #include <glibmm/optionentry.h> + #include <gtk/gtkaboutdialog.h> + #include <gtk/gtkversion.h> diff --git a/sci-chemistry/gelemental/gelemental-1.2.0-r1.ebuild b/sci-chemistry/gelemental/gelemental-1.2.0-r1.ebuild new file mode 100644 index 000000000000..3aa417510233 --- /dev/null +++ b/sci-chemistry/gelemental/gelemental-1.2.0-r1.ebuild @@ -0,0 +1,65 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils fdo-mime flag-o-matic gnome2-utils eutils + +DESCRIPTION="Periodic table viewer with detailed information on the chemical elements" +HOMEPAGE="http://freecode.com/projects/gelemental/" +SRC_URI=" + http://www.kdau.com/files/${P}.tar.bz2 + mirror://debian/pool/main/g/${PN}/${PN}_${PV}-8.debian.tar.gz" + +LICENSE="GPL-3 MIT" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="doc static-libs" + +RDEPEND=" + dev-cpp/gtkmm:2.4 + dev-cpp/glibmm:2" +DEPEND="${RDEPEND} + virtual/pkgconfig + sys-devel/gettext + dev-util/intltool + doc? ( app-doc/doxygen )" + +PATCHES=( + "${FILESDIR}"/${P}-gcc4.3.patch + "${FILESDIR}"/${P}-glib-2.32.patch + "${FILESDIR}"/${P}-doxygen.patch + "${WORKDIR}"/debian/patches/579183_adjust_size_middle_button.patch + "${WORKDIR}"/debian/patches/604612_fix_menu_category.patch + "${WORKDIR}"/debian/patches/604618_scrollable_properties_dialog.patch + "${WORKDIR}"/debian/patches/656372_element_renames.patch + "${WORKDIR}"/debian/patches/add_new_wave_theme.patch + "${WORKDIR}"/debian/patches/czech_translation_559028.patch + "${WORKDIR}"/debian/patches/fix_gtkmm_2.18.patch + "${WORKDIR}"/debian/patches/fix_zinc_german_translation.patch + "${WORKDIR}"/debian/patches/ftbfs_missing_limits.patch + "${WORKDIR}"/debian/patches/lp673285_link_in_about.patch + "${FILESDIR}"/${PN}-1.2.0-fix-c++14.patch + ) + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +src_configure() { + append-cxxflags -std=c++11 #566450 + local myeconfargs=( $(use_enable doc api-docs) ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install apidir="/usr/share/doc/${PF}/html" +} + +pkg_postinst() { + gnome2_icon_cache_update + fdo-mime_desktop_database_update +} + +pkg_postrm() { + gnome2_icon_cache_update + fdo-mime_desktop_database_update +} diff --git a/sci-chemistry/gelemental/metadata.xml b/sci-chemistry/gelemental/metadata.xml new file mode 100644 index 000000000000..eb677830c9f8 --- /dev/null +++ b/sci-chemistry/gelemental/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="freecode">gelemental</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/ghemical/Manifest b/sci-chemistry/ghemical/Manifest new file mode 100644 index 000000000000..4b39c6b5f18c --- /dev/null +++ b/sci-chemistry/ghemical/Manifest @@ -0,0 +1,6 @@ +AUX 2.99.2-docs.patch 785 SHA256 f24ab5181a6a03eb1f6b86fec835d2253eb9cba3e0b6519248e59b917678a4e7 SHA512 0d8754b31eeec184a0d3becb75d3c69c2e922abbe00c175c8cb23d7ea96838896db2da90de45653a7612a041975975f062d289d7d362f6f1abae1d916dbc4b89 WHIRLPOOL 0eb22670870a2b9bfcedf8863d95cd7eeec414aeede617429f2df2bfdd24b5e27615071c31630237aaccef3adb8cac6db0556a24ed2e661edbdc4fe7a975bed9 +DIST ghemical-3.0.0.tar.gz 2196716 SHA256 babb2bda93cf0c20f234452eeb7d19d1d8c0e4c4d611734f110f8de066a1bcb2 SHA512 d4dd0b063a4dea33fa7430e77a2da253c74079fd8b5f21e8c2b5da1383f3689b93305417e1bf0d4908b87c91afb33c3266dd6bd6fbcd768cc98614a3f730ee94 WHIRLPOOL 80dcc426bbd17d57a346d6703d2b5366c7489666f33bb9ec2a1f36cf0e133e2b6c944a5f328cd3882241812b0856c59b3b3cd1648d59498ca80467ea65fe7971 +EBUILD ghemical-3.0.0.ebuild 1348 SHA256 26e232cd2f4a0e4e9a0801d6d4d99225b80c041f2a14acd878e8864010b32397 SHA512 a6c018a4b4e49d46eef4b004ebb3c55db9dff66c05390c465a51903af62c03f0bea15a8d33a1d27ca8123207ad8214295bb0dc8888385d200f8268d8aab05fb4 WHIRLPOOL 82fa02dd28b2032730c5876c34e5df5d15752a0158383f58b31ee26ecc682206948e3e8aa711484e0098eeb8f6f8ca9839e66eeabba610de79b0726ea4c52e5b +MISC ChangeLog 2947 SHA256 f2337342c758a4496326a43af16c88cf25878069a971f0813ee391a691e2696b SHA512 099ff855768ba3ce59222cbebc85984d28cde6185ca9a666aa2c073ec3f0dccecc61083b7a8eec7faab687f5d76e57a70b30570841d3af0f1064370aebf2b904 WHIRLPOOL 97c25d15e96f50eab39b89d1272c5992181556f1dd9d82236c3fdea38fe9c298259e45422f505ea0eade0d8b9a2a0f5c03122bf6b5298b2553c4d5e0077c6661 +MISC ChangeLog-2015 7090 SHA256 6b8ab0e1effbf5062d272bb6ef58a7ed768d988b9ef97fd257db58e828d00622 SHA512 6598ac90c58c566430aa13e50e649a25cff4bb519e2700aefed8a3922391fe9149d322dab7727c419e44c1e70ade8953bb285dd3683bbef788c659cab5b61bab WHIRLPOOL 4b2d282b6b9d084ef2a89b4db56560c2e47f818ee12397e2e14566ecf22ebb90dc9e38a93d000ea2d4e4889bec9a735f8bb734659dc3a4d7af3bce196333c0bd +MISC metadata.xml 775 SHA256 9a440ba6236e2b3edb1fe28ba0d41c7e84313d77fd9b3888b0e56f59a6b2f64a SHA512 59e27f59b90d5f7436855509a6de0c0b296cd9ae1ccaec02570a5055482e033c12df040430f466a1ba2c004b555fdd89617ad65b608590a40fe27790888940fe WHIRLPOOL 93478eebcc9c573a4101a5ffe1ffecdc97bf9e23d0689b865114d887239a54cf2582356e6a86149fcc8d1bfa8cbed503c368f703d3eb5c6d484ebf6747775cc8 diff --git a/sci-chemistry/ghemical/files/2.99.2-docs.patch b/sci-chemistry/ghemical/files/2.99.2-docs.patch new file mode 100644 index 000000000000..85f31dfd729f --- /dev/null +++ b/sci-chemistry/ghemical/files/2.99.2-docs.patch @@ -0,0 +1,22 @@ +diff --git a/docs/user-docs/Makefile.am b/docs/user-docs/Makefile.am +index 030f67c..dcb207b 100644 +--- a/docs/user-docs/Makefile.am ++++ b/docs/user-docs/Makefile.am +@@ -1,6 +1,6 @@ + SUBDIRS = images + +-helpfilesdir = $(datadir)/ghemical/@APPVERSION@/user-docs ++helpfilesdir = $(datadir)/doc/ghemical-@APPVERSION@/html + helpfiles_DATA = *.css *.html + + EXTRA_DIST = $(helpfiles_DATA) +diff --git a/docs/user-docs/images/Makefile.am b/docs/user-docs/images/Makefile.am +index fae0ffd..a569151 100644 +--- a/docs/user-docs/images/Makefile.am ++++ b/docs/user-docs/images/Makefile.am +@@ -1,4 +1,4 @@ +-helpimagesdir = $(datadir)/ghemical/@APPVERSION@/user-docs/images ++helpimagesdir = $(datadir)/doc/ghemical-@APPVERSION@/html/images + helpimages_DATA = *.png + + EXTRA_DIST = $(helpimages_DATA) diff --git a/sci-chemistry/ghemical/ghemical-3.0.0.ebuild b/sci-chemistry/ghemical/ghemical-3.0.0.ebuild new file mode 100644 index 000000000000..ed816b7a5491 --- /dev/null +++ b/sci-chemistry/ghemical/ghemical-3.0.0.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools eutils + +DESCRIPTION="Chemical quantum mechanics and molecular mechanics" +HOMEPAGE="http://bioinformatics.org/ghemical/" +SRC_URI="http://bioinformatics.org/ghemical/download/current/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="openbabel seamonkey threads" + +RDEPEND=" + dev-libs/glib:2 + gnome-base/libglade:2.0 + sci-chemistry/mpqc + >=sci-libs/libghemical-3.0.0 + >=x11-libs/liboglappth-1.0.0 + virtual/opengl + x11-libs/pango + x11-libs/gtk+:2 + x11-libs/gtkglext + openbabel? ( sci-chemistry/openbabel )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( "${FILESDIR}"/2.99.2-docs.patch ) + +src_prepare() { + default + eautoreconf +} + +src_configure() { +# With amd64, if you want gamess I recommend adding gamess and gtk-gamess to package.provided for now. + +# Change the built-in help browser. + if use seamonkey ; then + sed -i -e 's|mozilla|seamonkey|g' src/gtk_app.cpp || die "sed failed for seamonkey!" + else + sed -i -e 's|mozilla|firefox|g' src/gtk_app.cpp || die "sed failed for firefox!" + fi + + econf \ + $(use_enable openbabel) \ + $(use_enable threads) +} + +src_install() { + emake DESTDIR="${D}" install + make_desktop_entry /usr/bin/ghemical Ghemical /usr/share/ghemical/${PV}/pixmaps/ghemical.png +} diff --git a/sci-chemistry/ghemical/metadata.xml b/sci-chemistry/ghemical/metadata.xml new file mode 100644 index 000000000000..05b56d91546f --- /dev/null +++ b/sci-chemistry/ghemical/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +Ghemical supports both quantum-mechanics (semi-empirical and ab initio) models +and molecular mechanics models (there is an experimental Tripos 5.2-like force +field for organic molecules). Also a tool for reduced protein models is +included. Geometry optimization, molecular dynamics and a large set of +visualization tools are currently available. +</longdescription> + <use> + <flag name="openbabel">Use <pkg>sci-chemistry/openbabel</pkg> for file + conversions</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/gperiodic/Manifest b/sci-chemistry/gperiodic/Manifest new file mode 100644 index 000000000000..84eeabdd7fcb --- /dev/null +++ b/sci-chemistry/gperiodic/Manifest @@ -0,0 +1,11 @@ +AUX gperiodic-2.0.10-makefile.patch 2266 SHA256 e9a0d0e041e442baeedd8bf6dbba5f1e0054685bd2b2b9dabd1388f07f64a8f0 SHA512 f2e8369e7ad35e546f70191a18e07961f5000c354f0624ca5bd0a7bf77f6a8fb5e3fa299688ffccba8fbd1c7e0e28de9e214a030f5a6d2909c72f26772ac2b73 WHIRLPOOL 6cf663b6365bd31cc7be3d32dcf8ca635230aeaafd4890ca6d223fac1a3f0983eb2dbf59cf78f40793fbb0dd6552496739d5014ad4ff6a0edee4ba19c702a82d +AUX gperiodic-2.0.10-nls.patch 508 SHA256 61d66f8d376f39eaf185ba728d6057987f4ce1851315b62a6641b83f8cefccb0 SHA512 1c5a6f067ac9e6f9b1073bc97c3f5ae133f7f1f84e54ee30a9898cb658b31db20c4c483cc9557bd43db3eec2ce9a82df49611fb4d692e5b004b08461cb149a43 WHIRLPOOL 56da48d0d7c99fc6a14e762bbba4a062d2e83d54cdf1dc3451cbf9014e6fc322d2a35605be9d3e6a2181e020c37fa4b3af545cd2363e6642047a4a1bf65e7571 +AUX gperiodic-3.0.1-makefile.patch 3196 SHA256 661b0c978db44c189a22268f08256a06453422d5b3c0fbbef7d6ed0275b0d9a4 SHA512 fd2f17a2f83c32387769ecf5d42599a41fd2c5775cefe5fcf5c9f3fcc0f3d5e077c524bcb1467c0fe6176304f78a4ba7ff377da9d92cbd57e576f5aceb5d13e4 WHIRLPOOL ec94cd1c046f20e23ef7273d4f2cb3671e99d4398336850834f9357bb44b298f6d67f397e4b1425476f1f6c53eedf59dc2b239ad4c5320823b4dd2acadea8dbc +AUX gperiodic-3.0.1-nls.patch 488 SHA256 674816ad43963021719b53477e5f05b0e4b686f061e7b90c4d41ef5dc9ddf684 SHA512 acd270f4c8e4cd271f2d48ea48e716195cb39e14ea09a41dc48787756f4f5806fea3bb3cf5072aac49f897c610a36fcbe89de433efefab845f7462d4693a5eef WHIRLPOOL 25593bb7fcc4e751d0929dd1f971cbe95e0c32a05bbb3ff0808787dc96da7ad35aca8cf352a7d94e4e6bda46451f70ee6d2764aa53901da456a7a5c6c67953ec +DIST gperiodic-2.0.10.tar.gz 131213 SHA256 78d72870c51c39e4a35c804c05b8ef5e39f88d42eced52b2934e21d74fb8d096 SHA512 23d0074ad5b0f9e25e8eee63f8c375e2448b1ee7c00f89e965b7dd8ce3f60f20251d7699a2f7a767228316144b946a5ac204a3e478c395767133f7fc801b51ba WHIRLPOOL b758b622bfb980aad45b0bb6e2850579408959c3bf700f4dbb21d4bc64168d2a589a9ed5974f75b5eaf7f6c9d593c69dbc9b470957b01457caa30eb356850f14 +DIST gperiodic-3.0.1.tar.gz 375347 SHA256 d023e6f3b8aef773331c5f87d1de17f5fa120e67f7b6da1439ca7861a2df0905 SHA512 3bf47359dda1a029f3528ea04d28cd75909bceb535f6e1dc6c90f5a17b668e0dd98900ddd83633649383ff4e2fc588265275e0e4a27897ecc4ac6db4e93befc1 WHIRLPOOL 8700f0ad254d7ece507b4c01d54ce510121b266d3b533d6035d17ef236d6310008ba2bd80900e92697bbc42c985632421c2be87a2f4bea43903c0207df231198 +EBUILD gperiodic-2.0.10-r2.ebuild 983 SHA256 e5836482ed953516a10cb76e3eb476d6d84f4e3a8920f530b13cf373e1423d47 SHA512 98a0ae652b27414758ce0c58ba04f1ec83d48a467522c0cda190627721833e57b39092c2dabe2fd56523f4c766ed30e98830eff5ef4930897d81261365897a8f WHIRLPOOL fa92014cadd331ee23407eb20d4d39dd54ebc015c70e7c618f25bb9ec575212169f7d8e5d749f65e1dce5febad6dc75634746f579efa065352dccd2318963d18 +EBUILD gperiodic-3.0.1.ebuild 1295 SHA256 7f738c1a41ec2954c7448eb04d1614a24bd93fac80013dbed469677786924060 SHA512 03ea47fd92351d360ab97a50824d3a4976aace5b5f8c5f1dc4606d09cc5f0ddc3038dffd589030bd458dfbe11d5b3421d29f643d8905a8b403d511f15eeb84f7 WHIRLPOOL c4773b2c471965d276d70ab4a5928c4528275407d89ba14701175eeb8492816daad69edb0c4a5bd47a2af859733d237cbf6abead82ac292dcbc7d7bfb9b3e075 +MISC ChangeLog 4015 SHA256 98a57e50f4b219795e21ea810d4c93104b10d9eeb0b9eb89434023e33c8727b5 SHA512 a993c0faf74c72ba1d03dd15a65b1a3d5523435dd6d49cf4cfaaa293c823f9c76c7d63478214febbfe1b050dc37efb45121f46a77e72411d61e12a286f98989b WHIRLPOOL 9933f2c0fe03727c537ba7284f41815d3dd6fef73baf3c24260f785bc1e1441495c4c0b6fb264e0b1a1d34956adf6696284f1ae6f48c57c965fb68c034e4cf1d +MISC ChangeLog-2015 4395 SHA256 9096b1a982181ea6bb04f0120f430c53f96ad956d2d01a3a35d809467d61ed81 SHA512 514efe3a790500ca26421338cb2c0c8b587eeece02307dd73b55d6939b7d4c44775e36dc36f0067e31219aa52d5b0cac78a1bebc1d3b523bd93ce1f5f18badb2 WHIRLPOOL eb6e2babe13920062dff6c24262971acc37b3016579a5fbe5b0a84d8b6d93fecd4d5d95ed3ad70c06b5850b2e2637fcbb9b0048a2be8c647173e40f7730b4671 +MISC metadata.xml 556 SHA256 bbc0a62437a897ae88e71e02d04c2118e79ddf39e934b5b073743fe48af04812 SHA512 d765609bc38fc5e5855863130053520d23b2dd36c8f2934feeedb6a8f1f62786460c69a6f95b474c7442cefb3560edff8daaf6388c84014241560d4f1b13bdfb WHIRLPOOL 900db836a4a4cabe5f035937024f8efca6fc8c51acd5ce5b0d7f3d83a1cc9f8acf587aa3ed8b9204a42d0413b1501fde4e441d946a53f2cd844b1369084fa011 diff --git a/sci-chemistry/gperiodic/files/gperiodic-2.0.10-makefile.patch b/sci-chemistry/gperiodic/files/gperiodic-2.0.10-makefile.patch new file mode 100644 index 000000000000..abdb5caae4f2 --- /dev/null +++ b/sci-chemistry/gperiodic/files/gperiodic-2.0.10-makefile.patch @@ -0,0 +1,64 @@ +Respect CC, CFLAGS, LDFLAGS +Fix install paths +Fix parallel build +Drop DEPRECATED flags, bug #391099 + +--- Makefile ++++ Makefile +@@ -1,6 +1,5 @@ +-CC := gcc +-CFLAGS := `pkg-config --cflags gtk+-2.0` -I. -DG_DISABLE_DEPRECATED -DGDK_DISABLE_DEPRECATED -DGDK_PIXBUF_DISABLE_DEPRECATED -DGTK_DISABLE_DEPRECATED +-LIBS :=`pkg-config --libs gtk+-2.0` ++CFLAGS += `pkg-config --cflags gtk+-2.0` -I. ++LIBS +=`pkg-config --libs gtk+-2.0` + bindir ?= /usr/bin + datadir ?= /usr/share + enable_nls ?= 1 +@@ -8,12 +7,11 @@ + .c.o: + $(CC) -c $(CFLAGS) $(CPPFLAGS) $< + +-all: +- make gperiodic +- make -C po/ all enable_nls=$(enable_nls) ++all: gperiodic ++ $(MAKE) -C po/ all enable_nls=$(enable_nls) + + gperiodic: gperiodic.o +- $(CC) $(CFLAGS) -o gperiodic gperiodic.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o gperiodic gperiodic.o $(LIBS) + ifeq ($(strip),1) + strip gperiodic + endif +@@ -23,24 +21,21 @@ + gperiodic.o: gperiodic.c gperiodic.h table_data.h + + install: +- mkdir -p $(DESTDIR)$(bindir) +- install -m 755 gperiodic $(DESTDIR)$(bindir) +- mkdir -p $(DESTDIR)$(datadir)/applications +- install -m 644 gperiodic.desktop $(DESTDIR)$(datadir)/applications +- mkdir -p $(DESTDIR)$(datadir)/pixmaps +- install -m 644 gperiodic.png $(DESTDIR)$(datadir)/pixmaps +- install -m 644 gperiodic-crystal.png $(DESTDIR)$(datadir)/pixmaps +- make -C po/ install enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR) ++ install -D -m 755 gperiodic $(DESTDIR)$(bindir)/gperiodic ++ install -D -m 644 gperiodic.desktop $(DESTDIR)$(datadir)/applications/gperiodic.desktop ++ install -D -m 644 gperiodic.png $(DESTDIR)$(datadir)/pixmaps/gperiodic.png ++ install -m 644 gperiodic-crystal.png $(DESTDIR)$(datadir)/pixmaps/gperiodic-crystal.png ++ $(MAKE) -C po/ install enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR) + + uninstall: + rm -f $(bindir)/gperiodic \ + $(datadir)/applications/gperiodic.desktop + $(datadir)/pixmaps/gperiodic.png \ + $(datadir)/pixmaps/gperiodic-crystal.png +- make -C po/ uninstall enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR) ++ $(MAKE) -C po/ uninstall enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR) + + clean: + rm -f *.o gperiodic +- make -C po/ clean ++ $(MAKE) -C po/ clean + + .PHONY: install uninstall clean diff --git a/sci-chemistry/gperiodic/files/gperiodic-2.0.10-nls.patch b/sci-chemistry/gperiodic/files/gperiodic-2.0.10-nls.patch new file mode 100644 index 000000000000..de0bea04dc14 --- /dev/null +++ b/sci-chemistry/gperiodic/files/gperiodic-2.0.10-nls.patch @@ -0,0 +1,20 @@ + po/Makefile | 2 ++ + 1 files changed, 2 insertions(+), 0 deletions(-) + +diff --git a/po/Makefile b/po/Makefile +index d7d7d78..179dad6 100644 +--- a/po/Makefile ++++ b/po/Makefile +@@ -26,10 +26,12 @@ endif + + install: + $(MAKE) all ++ifeq ($(enable_nls),1) + for f in $(FILES_MO) ; do \ + mkdir -p $(DESTDIR)$(LOCALEDIR)/`basename $$f .mo`/LC_MESSAGES ; \ + install -m 644 $$f $(DESTDIR)$(LOCALEDIR)/`basename $$f .mo`/LC_MESSAGES/$(PACKAGE).mo ; \ + done ++endif + + uninstall: + for f in $(FILES_MO) ; do \ diff --git a/sci-chemistry/gperiodic/files/gperiodic-3.0.1-makefile.patch b/sci-chemistry/gperiodic/files/gperiodic-3.0.1-makefile.patch new file mode 100644 index 000000000000..a7a402a1a781 --- /dev/null +++ b/sci-chemistry/gperiodic/files/gperiodic-3.0.1-makefile.patch @@ -0,0 +1,66 @@ + Makefile | 36 ++++++++++++++---------------------- + 1 file changed, 14 insertions(+), 22 deletions(-) + +diff --git a/Makefile b/Makefile +index 7e86dc4..9bd4fe8 100644 +--- a/Makefile ++++ b/Makefile +@@ -14,8 +14,8 @@ enable_nls ?= 1 + $(CC) -c $(CFLAGS) $(CPPFLAGS) $< + + all: +- make gperiodic +- make -C po/ all enable_nls=$(enable_nls) ++ $(MAKE) gperiodic ++ $(MAKE) -C po/ all enable_nls=$(enable_nls) + intltool-merge -d po gperiodic.desktop.in gperiodic.desktop + + gperiodic: gperiodic.o +@@ -29,24 +29,16 @@ gpdata.o: gpdata.c gperiodic.h + gperiodic.o: gperiodic.c gperiodic.h table_data.h + + install: +- mkdir -p $(DESTDIR)$(bindir) +- install -m 755 gperiodic $(DESTDIR)$(bindir) +- mkdir -p $(DESTDIR)$(datadir)/applications +- install -m 644 gperiodic.desktop $(DESTDIR)$(datadir)/applications +- mkdir -p $(DESTDIR)$(datadir)/pixmaps +- install -m 644 icons/gperiodic.png $(DESTDIR)$(datadir)/pixmaps +- install -m 644 icons/gperiodic.xpm $(DESTDIR)$(datadir)/pixmaps +- mkdir -p $(DESTDIR)$(mandir) +- install -m 644 gperiodic.1 $(DESTDIR)$(mandir) +- mkdir -p $(DESTDIR)$(iconsdir)/hicolor/16x16/apps +- mkdir -p $(DESTDIR)$(iconsdir)/hicolor/32x32/apps +- mkdir -p $(DESTDIR)$(iconsdir)/hicolor/48x48/apps +- mkdir -p $(DESTDIR)$(iconsdir)/hicolor/64x64/apps +- install -m 644 icons/hicolor/16x16/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/16x16/apps +- install -m 644 icons/hicolor/32x32/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/32x32/apps +- install -m 644 icons/hicolor/48x48/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/48x48/apps +- install -m 644 icons/hicolor/64x64/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/64x64/apps +- make -C po/ install enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR) ++ install -D -m 755 gperiodic $(DESTDIR)$(bindir)/gperiodic ++ install -D -m 644 gperiodic.desktop $(DESTDIR)$(datadir)/applications/gperiodic.desktop ++ install -D -m 644 icons/gperiodic.png $(DESTDIR)$(datadir)/pixmaps/gperiodic.png ++ install -D -m 644 icons/gperiodic.xpm $(DESTDIR)$(datadir)/pixmaps/gperiodic.xpm ++ install -D -m 644 gperiodic.1 $(DESTDIR)$(mandir)/gperiodic.1 ++ install -D -m 644 icons/hicolor/16x16/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/16x16/apps/gperiodic.png ++ install -D -m 644 icons/hicolor/32x32/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/32x32/apps/gperiodic.png ++ install -D -m 644 icons/hicolor/48x48/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/48x48/apps/gperiodic.png ++ install -D -m 644 icons/hicolor/64x64/apps/gperiodic.png $(DESTDIR)$(iconsdir)/hicolor/64x64/apps/gperiodic.png ++ $(MAKE) -C po/ install enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR) + + uninstall: + rm -f $(bindir)/gperiodic \ +@@ -58,10 +50,10 @@ uninstall: + $(iconsdir)/hicolor/32x32/apps/gperiodic.png \ + $(iconsdir)/hicolor/48x48/apps/gperiodic.png \ + $(iconsdir)/hicolor/64x64/apps/gperiodic.png +- make -C po/ uninstall enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR) ++ $(MAKE) -C po/ uninstall enable_nls=$(enable_nls) datadir=$(datadir) DESTDIR=$(DESTDIR) + + clean: + rm -f *.o gperiodic gperiodic.desktop +- make -C po/ clean ++ $(MAKE) -C po/ clean + + .PHONY: install uninstall clean diff --git a/sci-chemistry/gperiodic/files/gperiodic-3.0.1-nls.patch b/sci-chemistry/gperiodic/files/gperiodic-3.0.1-nls.patch new file mode 100644 index 000000000000..4420ca68e585 --- /dev/null +++ b/sci-chemistry/gperiodic/files/gperiodic-3.0.1-nls.patch @@ -0,0 +1,20 @@ + po/Makefile | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/po/Makefile b/po/Makefile +index d7d7d78..c596e5b 100644 +--- a/po/Makefile ++++ b/po/Makefile +@@ -26,10 +26,12 @@ endif + + install: + $(MAKE) all ++ifeq ($(enable_nls),1) + for f in $(FILES_MO) ; do \ + mkdir -p $(DESTDIR)$(LOCALEDIR)/`basename $$f .mo`/LC_MESSAGES ; \ + install -m 644 $$f $(DESTDIR)$(LOCALEDIR)/`basename $$f .mo`/LC_MESSAGES/$(PACKAGE).mo ; \ + done ++endif + + uninstall: + for f in $(FILES_MO) ; do \ diff --git a/sci-chemistry/gperiodic/gperiodic-2.0.10-r2.ebuild b/sci-chemistry/gperiodic/gperiodic-2.0.10-r2.ebuild new file mode 100644 index 000000000000..d13194b76ff0 --- /dev/null +++ b/sci-chemistry/gperiodic/gperiodic-2.0.10-r2.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Periodic table application for Linux" +HOMEPAGE="http://www.frantz.fi/software/gperiodic.php" +SRC_URI="http://www.frantz.fi/software/${P}.tar.gz" + +KEYWORDS="amd64 x86" +SLOT="0" +LICENSE="GPL-2" +IUSE="nls" + +RDEPEND=" + sys-libs/ncurses:0 + x11-libs/gtk+:2 + x11-libs/cairo[X] + nls? ( sys-devel/gettext )" + +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-makefile.patch \ + "${FILESDIR}"/${P}-nls.patch + sed \ + -e '/Encoding/d' \ + -i ${PN}.desktop || die +} + +src_compile() { + local myopts + use nls && myopts="enable_nls=1" || myopts="enable_nls=0" + emake CC=$(tc-getCC) ${myopts} +} + +src_install() { + local myopts + use nls && myopts="enable_nls=1" || myopts="enable_nls=0" + emake DESTDIR="${D}" ${myopts} install + dodoc AUTHORS ChangeLog README NEWS + newdoc po/README README.translation +} diff --git a/sci-chemistry/gperiodic/gperiodic-3.0.1.ebuild b/sci-chemistry/gperiodic/gperiodic-3.0.1.ebuild new file mode 100644 index 000000000000..5e16fff43ec1 --- /dev/null +++ b/sci-chemistry/gperiodic/gperiodic-3.0.1.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Periodic table application for Linux" +HOMEPAGE="http://www.frantz.fi/software/gperiodic.php" +SRC_URI="http://downloads.sourceforge.net/project/${PN}/${P}.tar.gz" + +KEYWORDS="~amd64 ~x86" +SLOT="0" +LICENSE="GPL-2" +IUSE="nls" +MY_AVAILABLE_LINGUAS=" be bg cs da de es fi fr gl id is it lt ms nl pl pt_BR pt ru sv tr uk" +IUSE="${IUSE} ${MY_AVAILABLE_LINGUAS// / linguas_}" + +RDEPEND=" + sys-libs/ncurses:0 + x11-libs/gtk+:2 + x11-libs/cairo[X] + nls? ( sys-devel/gettext )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-makefile.patch \ + "${FILESDIR}"/${P}-nls.patch + for lang in ${MY_AVAILABLE_LINGUAS}; do + if ! use linguas_${lang}; then + einfo "Cleaning translation for ${lang}" + rm po/${lang}.po || die + fi + done +} + +src_compile() { + local myopts + use nls && myopts="enable_nls=1" || myopts="enable_nls=0" + emake \ + CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + CC=$(tc-getCC) ${myopts} +} + +src_install() { + local myopts + use nls && myopts="enable_nls=1" || myopts="enable_nls=0" + emake DESTDIR="${D}" ${myopts} install + dodoc AUTHORS ChangeLog README + newdoc po/README README.translation +} diff --git a/sci-chemistry/gperiodic/metadata.xml b/sci-chemistry/gperiodic/metadata.xml new file mode 100644 index 000000000000..fdfc090a816f --- /dev/null +++ b/sci-chemistry/gperiodic/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> + GPeriodic is a program for looking up various data about elements from the + periodic table, based on the GTK2 toolkit. It also features a command line + interface. + </longdescription> + <upstream> + <remote-id type="sourceforge">downloads</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest new file mode 100644 index 000000000000..9a2f81836bc6 --- /dev/null +++ b/sci-chemistry/gromacs/Manifest @@ -0,0 +1,29 @@ +DIST gromacs-2016.1.tar.gz 27336258 SHA256 9e7d2892a903777b982bc9ab4306de969d92cb45b51a562f523ec5fe58db41e3 SHA512 d30a4ad5faa6e12c95b8e94acaabc387d9aab3780490f5442c48ccac2f86bef6dca60df5bb6097dbc68ab28e6f1a15e234e1244606afdf12a841b88ece65c97b WHIRLPOOL 4be9c84d99286889dda23d9f1e2dd7b2d87a70740fb686bd58e59155771e897471d0920b02c5ec529a01a4b01428ebb2ca5b27e4d8df9034d2d3b33c5ab1a1ca +DIST gromacs-2016.2.tar.gz 27339623 SHA256 b6ac3632b848ab0c19f8f319dd5b58fcd09b8e2005ee7509478606613e5409a5 SHA512 f5e74bb8c126823c90d205ac0f0835e61fdd13a4550bc15aa9c972ee9b187f6451cdc90877c17276d2f889d61abb5eaa5ea1b54f7cbf3da67074146c749c1aa6 WHIRLPOOL 698c4d4e67266483be4f1047eb947b243b5c8caa3c5e30bdab6b5f0dd302bb51ac5aa6e3a3357beab567cf71c1b8ecc1f9684a89754d18f963dd6f5fc90a33f4 +DIST gromacs-2016.3.tar.gz 27342692 SHA256 7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27 SHA512 16593df0a52620766fb86cfeb16328793503f860cb07cdbbd503ba7f41e6430efb4848389b7179ca3907b57311162666d05224b454e1afb1b74b220f38498d86 WHIRLPOOL dfe31f212545ae2baf7373fde31f715a8df203d098d3ace915d4269b7bf16d06a1f91ead33ccbf8a17e9e0091b593818d0ce2eff151ce532238a8c27f5e20cda +DIST gromacs-2016.4.tar.gz 27368706 SHA256 4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264 SHA512 69661d2a7a8a5259be277de35e2baa4b688d1f7bef225fc7d733a9b00c6ee135dcbad517c7c9f751121647c2fbd085f2c9cdf22dbd941c7ebc5d3b09e7e08f1f WHIRLPOOL c1586377d2a27f0b529370efb63e09ecca64cdb3d418fe9bc4f3ea1ff82ff5293d159834f4ed5d0136d801095d6f4085722e0d91bce873776fa4549853497ff7 +DIST gromacs-2016.tar.gz 27321561 SHA256 aa0a27cd13050a4b70aacfbd169ddce2fe507c7e668f460ecf6cf32afcac5771 SHA512 756771baaa85a1d16e7d5b8e4c96bbd1c04c7acdc536a253886cff186316330f06d60d206a0159efb15f47f161c779d3757dc5dbceab8c097241c1382d376201 WHIRLPOOL 1cc3d3797e1aaf93e1e0cb2e71173896e33fee2bb03f4e97e06be3ab85842e6da3feaf8701425358f1d701e00159ff6ce3b24fa1488d5e8ef70a1acbb914361c +DIST gromacs-5.0.4.tar.gz 26342095 SHA256 78068eeccc0b950018ddb45c41280e53c8bedae4639dca48e17c940f8896b23b SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee WHIRLPOOL d8458d3d563e015e830622ae0c924e896765a6329ffe4cb1a31c7aef3c804f392d29e3f1db5617051e85058403422f7d69a160a6c7cc810564696d88f9d50bd4 +DIST gromacs-5.1.3.tar.gz 27095702 SHA256 c962d9446939a9ba9905e7ca440c9306fd310f08600da3b744806bfd0eacccde SHA512 9ab26e1b2268f8d567b89b2d99d0b75b937b28edceaec56d17ca3243c76faa31255ffc0c45d762c7c693fe500b00e36ad43b80572d1d7f92dc87f9d2d98c0ba6 WHIRLPOOL bdd9c63ceb5e61963c4edd0af815cc34a3f237d8dee410c834b9b55bb82374de65b437828390a668282e50428b9907b887cd5265caf2a2007fc7673e7ab23733 +DIST regressiontests-2016.1.tar.gz 67094518 SHA256 10c9f50ff3cb32cf629aa35e35d957965dcfce4af84a6569e6d65a16c4e09eb7 SHA512 fc01c802d81400373a147171881f3b7b9309402e8ffb08287ba393aefbb701ba93bbe0b9549ff6fa264a8befbba445c2d2c7450633063a724f78ec8ca81ae8c9 WHIRLPOOL e8c54164558fcbaa1e65e9280e438882c96bbbaa6c9389a2ee5aed37d70b83b6b36e95dd5141b4e64b303e3799411ee01cf04aa919f25014d172011e49714126 +DIST regressiontests-2016.2.tar.gz 67095329 SHA256 53fa9ad062cc3e269fc6186db1ccbb64a93d36c2fa1cafd6433564ba2583c112 SHA512 e0aceb56d1f38a7e6ab9fdaac5063fd20c5b3a162ffb6eddd0e6dc7dff9b724bfe31363493a9437e9f9d5421a534b375960fcb31e903a4901a0fa94ed8511294 WHIRLPOOL 408741abf781ecf880f8f1337590ed81196cabcf25a49d2cd97bbe0596c8495ea866d6aa64a944c6ee0eb209110883dff204f0f52f6aa6e6dd52f50bcbbade66 +DIST regressiontests-2016.3.tar.gz 67093968 SHA256 a3d1b09acfc61820dddd765a381f706190b4657606488f1e676becb859ea7ecc SHA512 ee87df9f339954da0e1f1b4c8b8d4deb574f3b73d174010a295a7a0e8bc462ead7691090ea7cf8ac3d984a6cd70f1cd22c3592fa161b2967061ae5ba2796286b WHIRLPOOL 2e986136f7faf6db108bc79e6fb6db9fe81d05f5af8bc27037b80cd25869f7cd4162d5cabc03994b36c71945910be79a217ff27f61463d1548cbdff6acd99f56 +DIST regressiontests-2016.4.tar.gz 67643648 SHA256 d58d1a2a53c22c06e2dc03bd98ae1eea0a0d51696a1f20f635dfc394fa3da957 SHA512 367438b897a05e1cc0dcd1d3872fb6a0e9ff6b1146e9448d941d6517dce789f0c478d20cf0a4f3565070f132dc88872441aadb8b499f59efa0e1e4a6dd6a7135 WHIRLPOOL 695a3b7f81915247a90e95c0a83823c0297fba6ae6266195e86c61ec540ca58afd8d01ba236c5ddb3f44b41fb9301ba6a836b15cad1875bae42ba6276670daff +DIST regressiontests-2016.tar.gz 66908712 SHA256 30a72362f011fd9e3a8d33004018126f938536c13fcb70f590afc74beaec5406 SHA512 59902c1973c33ea8f003f21a737dc7cc64da3258112322eedc9834b53628134a6817d5ee5b3950c9bfd97a3a0580aef88ddef0609ef2c58693c96c7575651e01 WHIRLPOOL 9d210aed00ddfa57df47733169997ef04dec84c524eb5a9c5c6dd9b05ad9ec2d7f3c8a5a43f2ade9be166d80f35a260c04b1a48ac092f5969a213475bb63ae20 +DIST regressiontests-5.0.4.tar.gz 65193251 SHA256 89ad9bc067035ac8f340319b538c446983d937b910067e871911d7afe2ecb3f0 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65 WHIRLPOOL e15ccab0a0beefac41aeff11e2e596e971167f1590eed159ff82c4a8e3aec1d234287be597026951904ecfe6099f30ef3bcd48f2098b9f5201bde62e15fbc4f9 +DIST regressiontests-5.1.3.tar.gz 66994083 SHA256 fd5797dcfd29f7ae70857a438dcd4200a8006fce222f297892c8e90123993ebc SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022 WHIRLPOOL 6ddb76859ee8fa3aba4d995e397970e6fd270acbdd6cc07ab77de0aebb0bfdbd2bd1107ae39d4410e750641047ae4b75c703eafad95a57ff42deb3bf1c742d08 +EBUILD gromacs-2016.1.ebuild 7987 SHA256 b08ac9aeebcb1be657f0c5158a7ffe4000b4b8006aad0180d800dd813cd867ad SHA512 ce2b0d2730e87831a517468033cada7097ba431d8a60dcef77a04c9e05bf4cfacb6eb500a5196e378f4c69e5020f8e9f871eac6e61dd2776834aee006ecb167f WHIRLPOOL 48c75e1f34974d01cbe418bef84da7d5f11b901abba4f5e690297b703bacd47823a5e29cd502092ddfa7c37460269ac4f45d825d6c1567db2249aa5e8aeab3b2 +EBUILD gromacs-2016.2.ebuild 7971 SHA256 d31a9442cf6a8006a28c9e865d3eadebe456bc74a16eb99e3ff21dc3276025b1 SHA512 7a85084cc29da0d3da6c9aabf65320edb38cd682146cc1b739120b728c6704c3e20941b9022c846b84a111e3ca88f29ca21cdbcdf4c5b7204989ac194bf15725 WHIRLPOOL bb33ab24491d76672c5b90d5257f9f8551a9f5ab1b6ff03e01710876df08175aeefda8af1dc241d05f3e7212ff91adf53e1a8dea25ea753e40f7433d385a0180 +EBUILD gromacs-2016.3.ebuild 7974 SHA256 aa24c46b8980a9e24dc4ef179c74248731f5589f6ce45e1c4a088fc319e70e3b SHA512 9a3415f66fdd5832abf764b6adfe5deccb62b3f233ccd9156e1caac61907835c13623a3772673c43c9a3e9dbe544e83b2f20953a09d9b598c6af0120cfed558d WHIRLPOOL 4c25b8fa669bfd0f9c95f8e55df5c84481a187f7886fcd1b6b1b41a15cf33568b2bda517ca8a49355a6c7c74c084ce5b2f99f4b5e1a79dc21f3fdb676dc57673 +EBUILD gromacs-2016.4.ebuild 7987 SHA256 b08ac9aeebcb1be657f0c5158a7ffe4000b4b8006aad0180d800dd813cd867ad SHA512 ce2b0d2730e87831a517468033cada7097ba431d8a60dcef77a04c9e05bf4cfacb6eb500a5196e378f4c69e5020f8e9f871eac6e61dd2776834aee006ecb167f WHIRLPOOL 48c75e1f34974d01cbe418bef84da7d5f11b901abba4f5e690297b703bacd47823a5e29cd502092ddfa7c37460269ac4f45d825d6c1567db2249aa5e8aeab3b2 +EBUILD gromacs-2016.9999.ebuild 7987 SHA256 b08ac9aeebcb1be657f0c5158a7ffe4000b4b8006aad0180d800dd813cd867ad SHA512 ce2b0d2730e87831a517468033cada7097ba431d8a60dcef77a04c9e05bf4cfacb6eb500a5196e378f4c69e5020f8e9f871eac6e61dd2776834aee006ecb167f WHIRLPOOL 48c75e1f34974d01cbe418bef84da7d5f11b901abba4f5e690297b703bacd47823a5e29cd502092ddfa7c37460269ac4f45d825d6c1567db2249aa5e8aeab3b2 +EBUILD gromacs-2016.ebuild 7968 SHA256 a63d5dccbcb7b6e990376fe76598445eca85d7f3721771b575aab1c1ba9ebb69 SHA512 3ca5d4ae9b01a106b279bc828e42366a017b9517a450b773b944c6d12dce64199e3a80d280e4c475c637c70009a1a0fd1ca74f99b03f08067a10d9e9ad450d8f WHIRLPOOL 8c6fc59a53161b049f92d6920eebc89fda1d1d6b1fc36770dfa5cfcfc83aad476e7fa58345df078984b6457ca2f0d0e273587ee4f271fcc676ab98e37fe310e0 +EBUILD gromacs-4.6.9999.ebuild 8110 SHA256 96cbde0c96f098c536ef0c1f0d21c59e3a36aef5e479ab24167bd47927f4cb4a SHA512 2206e257f0b29b6f3a90c5d7739079b9add3e04f2a3acbd58c814811b389b5d51b3594815a94529d1de43deb380504029c302d18fc16d63a81c92727254e863e WHIRLPOOL e56c938308d7280c6a7ae70a91deae9108c61e8d74542d1c67d061e69fa5b8d65b3477b459737bb87137cbe9c377885024b250189d04ba5cd90acddae55c6114 +EBUILD gromacs-5.0.4.ebuild 8429 SHA256 58a81cb292694c9aeabc0c9c6f16fae3eca51c31b398f32d2976993680e23cbb SHA512 d1e91cc25c5f90bd0fbad15060cae9c8bf1235ca45a2b72521b3a4f5f091bdd7d32ec2e6ff2bb22cd3fe165092f11a24ea148ae8000b8517f0b8671f6c2af6f2 WHIRLPOOL 513f5bcfb5b0a9396334eb38dc6d016b752814b7f459114b38e3c7bed8eadedb12a74697855b578786e6dbee1edcf1efc600fc2882e58ebbb4f7e2ee20b0f4e3 +EBUILD gromacs-5.0.9999.ebuild 8439 SHA256 6076d6c33242030628b75f79c3ac0168768efc000f8acbff271e6c435f3032d3 SHA512 6756116cdeae9c21b094f74ea1b1d9f41617467dc736878cdcff27fed9f53b338830a608e23e87238d0756884799fbc5d62f02685774ea86c239ecc3e8804814 WHIRLPOOL 356da8a8bea3b28d52acb9fb4391615667241530452d78493ed76697c88be05cb5161995268c52e3f51ff9d3c009b7694204102b9d7fe993770f75f559cfc891 +EBUILD gromacs-5.1.3.ebuild 7783 SHA256 dbdef1d04a48534a458562fd9b57ee80884cd79bcfa330c6a73617582c3af557 SHA512 8cf9573ec5dfa09e283b1d50513863214ca216007ad76cce15bc54caa2f1e55de8c992db8bd4b2e4fa95bc3f5d50eef32fce78ca61bc09cae2fe37e35a4cee68 WHIRLPOOL f052b72e7d98b650fd4b5e98c22ab638434cef8d7b980f3d5b3ef8f2f25dbb4829233f4a1d3b55043edf239190c49b093b2a66b9ed2e1da1f02745084243d104 +EBUILD gromacs-5.1.9999.ebuild 7783 SHA256 dbdef1d04a48534a458562fd9b57ee80884cd79bcfa330c6a73617582c3af557 SHA512 8cf9573ec5dfa09e283b1d50513863214ca216007ad76cce15bc54caa2f1e55de8c992db8bd4b2e4fa95bc3f5d50eef32fce78ca61bc09cae2fe37e35a4cee68 WHIRLPOOL f052b72e7d98b650fd4b5e98c22ab638434cef8d7b980f3d5b3ef8f2f25dbb4829233f4a1d3b55043edf239190c49b093b2a66b9ed2e1da1f02745084243d104 +EBUILD gromacs-9999.ebuild 7710 SHA256 abaf042bb97763484fa218d866bd1e5b3d8f6412adc1812474433400ddfe1703 SHA512 a3cb96cf8ada5f278b4b932fafac93659ca2c65ab530337567bf87be53ddea7123e2e03c0c3fefd2faca8bc3ce9494ebf960f1fdf9cff000b548790b5e0c9d81 WHIRLPOOL ffd2dc5f13c0925fe70ae99b318a17400e53d5cf963f803f5a38be4e92eeed0876af4b2443530a1fdaa5240abc652cbc18edc88e321e5dccd993ee3c92ecb594 +MISC ChangeLog 5897 SHA256 f9aa37d4f0d3e91213ecc14abde6a5964e078116d3738d5a6e8d4c6fc8caba9d SHA512 851d8c285829d064faa97aa4dfb754246da26f324f82f86c12d85817b4f21df6da4d4450286d92e589d6248557a5477ae283e627412f93f23b1149051bff304c WHIRLPOOL af9519b2218526a1173e71880c17657353dfa5a9d045f0b5c7d0714e294a808e41b1c0bf26afe30a053ff67c46f49dfb28b3a093e5194a9f86cc2d84cf52becc +MISC ChangeLog-2015 25428 SHA256 53aac500e5e16707be8e785a6dc56446b68432df865673ec8d2888d1f1af7c09 SHA512 a593fca6785df3966a28fb52c7f4dec13d52a081a26a5df58e43504503b5dbc6ce33e8ede0aa76a63e80a8b4eb38254d7b620be9cbb3698d0dd735392ec9b810 WHIRLPOOL 0e441b5c8555d8c48398fe61e19da0fd3120ed386402729edd72799ab57743cf61091438088923624caf5b709ab94ac4d5967033f06c252610972893dd8785d2 +MISC metadata.xml 1221 SHA256 e97c67c09ba23439f9ca347b568ba4dfb127f646d1b6dfe81c3d0361e1a0466a SHA512 97190ed07204e0c32df368070cf16103f0fb7f263d6e49d5a00294f5c5ae9e25e5280caf9d2931f77cb72e104424c8abe1c13fda839825b5eea21834bd200f42 WHIRLPOOL 482e708eb59ef67664cf865aad5394c243daed6af93839bd997593c00d5fe007fb653869052910c0bff8cd643cbbef07f8cc9add1dc3e033b4cac0631128488e diff --git a/sci-chemistry/gromacs/gromacs-2016.1.ebuild b/sci-chemistry/gromacs/gromacs-2016.1.ebuild new file mode 100644 index 000000000000..7e426ddfdf5a --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2016.1.ebuild @@ -0,0 +1,276 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + https://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + ) + dev-libs/tinyxml2 + " +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + xdg_environment_reset #591952 + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl && has_version "<sci-libs/mkl-11.3"; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/linux/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/linux/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DBUILD_TESTING=OFF + -DGMX_BUILD_UNITTESTS=OFF + -DGMX_EXTERNAL_TINYXML2=ON + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + "${cuda[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + for x in "${ED}"usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-2016.2.ebuild b/sci-chemistry/gromacs/gromacs-2016.2.ebuild new file mode 100644 index 000000000000..3b371d273088 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2016.2.ebuild @@ -0,0 +1,275 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + https://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + ) + dev-libs/tinyxml2 + " +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + xdg_environment_reset #591952 + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl && has_version "<sci-libs/mkl-11.3"; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/linux/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/linux/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DBUILD_TESTING=OFF + -DGMX_BUILD_UNITTESTS=OFF + -DGMX_EXTERNAL_TINYXML2=ON + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + "${cuda[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + for x in "${ED}"usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-2016.3.ebuild b/sci-chemistry/gromacs/gromacs-2016.3.ebuild new file mode 100644 index 000000000000..b361f69c44f4 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2016.3.ebuild @@ -0,0 +1,275 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + https://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + ) + dev-libs/tinyxml2 + " +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + xdg_environment_reset #591952 + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl && has_version "<sci-libs/mkl-11.3"; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/linux/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/linux/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DBUILD_TESTING=OFF + -DGMX_BUILD_UNITTESTS=OFF + -DGMX_EXTERNAL_TINYXML2=ON + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + "${cuda[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + for x in "${ED}"usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-2016.4.ebuild b/sci-chemistry/gromacs/gromacs-2016.4.ebuild new file mode 100644 index 000000000000..7e426ddfdf5a --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2016.4.ebuild @@ -0,0 +1,276 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + https://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + ) + dev-libs/tinyxml2 + " +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + xdg_environment_reset #591952 + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl && has_version "<sci-libs/mkl-11.3"; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/linux/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/linux/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DBUILD_TESTING=OFF + -DGMX_BUILD_UNITTESTS=OFF + -DGMX_EXTERNAL_TINYXML2=ON + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + "${cuda[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + for x in "${ED}"usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild new file mode 100644 index 000000000000..7e426ddfdf5a --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild @@ -0,0 +1,276 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + https://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + ) + dev-libs/tinyxml2 + " +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + xdg_environment_reset #591952 + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl && has_version "<sci-libs/mkl-11.3"; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/linux/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/linux/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DBUILD_TESTING=OFF + -DGMX_BUILD_UNITTESTS=OFF + -DGMX_EXTERNAL_TINYXML2=ON + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + "${cuda[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + for x in "${ED}"usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-2016.ebuild b/sci-chemistry/gromacs/gromacs-2016.ebuild new file mode 100644 index 000000000000..84f5c56a6aae --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2016.ebuild @@ -0,0 +1,273 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + https://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}" + inherit git-r3 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + xdg_environment_reset #591952 + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl && has_version "<sci-libs/mkl-11.3"; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/linux/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/linux/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DBUILD_TESTING=OFF + -DGMX_BUILD_UNITTESTS=OFF + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + "${cuda[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + for x in "${ED}"usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild new file mode 100644 index 000000000000..082685525590 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild @@ -0,0 +1,262 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +TEST_PV="4.6.6" +MANUAL_PV="4.6.6" + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + https://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + EGIT_BRANCH="release-4-6" + inherit git-r3 + LIVE_DEPEND="doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + sys-apps/coreutils + )" + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz + doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf ) + test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )" + LIVE_DEPEND="" + KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + gsl? ( sci-libs/gsl ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi )" +DEPEND="${CDEPEND} + virtual/pkgconfig + ${LIVE_DEPEND} + doc? ( app-doc/doxygen )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) +HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ ) + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use doc; then + EGIT_REPO_URI="git://git.gromacs.org/manual.git" \ + EGIT_BRANCH="release-4-6" EGIT_COMMIT="release-4-6" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/manual"\ + git-r3_src_unpack + fi + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="release-4-6" EGIT_COMMIT="release-4-6" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_GSL=$(usex gsl) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_ACCELERATION="$acce" + -DGMXLIB="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DGMX_PREFIX_LIBMD=ON + -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF + -DGMX_USE_GCC44_BUG_WORKAROUND=OFF + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) "${cuda[@]}" -DGMX_OPENMM=OFF + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile mdrun + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + #manual can only be build after gromacs was installed once in image + if use doc && [[ $PV = *9999* && ! -d ${WORKDIR}/manual_build ]]; then + mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" ) + BUILD_DIR="${WORKDIR}"/manual_build \ + CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure + [[ ${CHOST} = *-darwin* ]] && \ + export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)" + BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make + [[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)" + newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + DESTDIR="${D}" cmake-utils_src_make install-mdrun + done + + use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf" + newbashcomp "${ED}"/usr/bin/completion.bash ${PN} + if use zsh-completion ; then + insinto /usr/share/zsh/site-functions + newins "${ED}"/usr/bin/completion.zsh _${PN} + fi + rm -f "${ED}"usr/bin/completion.* + rm -rf "${ED}"usr/share/gromacs/html + rm -f "${ED}"usr/bin/g_options* + rm -f "${ED}"usr/bin/GMXRC* + + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + if use offensive; then + einfo + einfo $(g_luck) + einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc" + fi + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-5.0.4.ebuild b/sci-chemistry/gromacs/gromacs-5.0.4.ebuild new file mode 100644 index 000000000000..ac93b9770c1e --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-5.0.4.ebuild @@ -0,0 +1,278 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + https://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + EGIT_BRANCH="release-5-0" + inherit git-r3 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" + KEYWORDS="~alpha amd64 arm ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + boost? ( >=dev-libs/boost-1.55 ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="master" EGIT_COMMIT="master" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + $(cmake-utils_use X GMX_X11) + $(cmake-utils_use blas GMX_EXTERNAL_BLAS) + $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) + $(cmake-utils_use openmp GMX_OPENMP) + $(cmake-utils_use offensive GMX_COOL_QUOTES) + $(cmake-utils_use boost GMX_EXTERNAL_BOOST) + $(cmake-utils_use tng GMX_USE_TNG) + $(cmake-utils_use doc GMX_BUILD_MANUAL) + $(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF + -DGMX_USE_GCC44_BUG_WORKAROUND=OFF + -DBUILD_TESTING=OFF + -DGMX_BUILD_UNITTESTS=OFF + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + $(cmake-utils_use threads GMX_THREAD_MPI) + "${cuda[@]}" + -DGMX_OPENMM=OFF + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # generate bash completion, not 100% necessary for + # rel ebuilds as bundled + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile completion + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + #release ebuild does this automatically + if [[ $PV = *9999* ]]; then + cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die + echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + #concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs) + #little hacckery as some gmx-completion* newlines ,so cat won't work + for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do + echo $(<${x}) + done > "${T}"/gmx-bashcomp || die + newbashcomp "${T}"/gmx-bashcomp gmx + bashcomp_alias gmx mdrun + rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die + if use double-precision && use single-precision; then + bashcomp_alias gmx gmx_d + bashcomp_alias gmx mdrun_d + fi + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild new file mode 100644 index 000000000000..d417af1167a2 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild @@ -0,0 +1,283 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + https://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + EGIT_BRANCH="release-5-0" + inherit git-r3 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" + KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + boost? ( >=dev-libs/boost-1.55 ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="master" EGIT_COMMIT="master" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_EXTERNAL_BOOST=$(usex boost) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_SYMLINK_OLD_BINARY_NAMES=$(usex make-symlinks) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF + -DGMX_USE_GCC44_BUG_WORKAROUND=OFF + -DBUILD_TESTING=OFF + -DGMX_BUILD_UNITTESTS=OFF + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + "${cuda[@]}" + -DGMX_OPENMM=OFF + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # generate bash completion, not 100% necessary for + # rel ebuilds as bundled + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile completion + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + #release ebuild does this automatically + if [[ $PV = *9999* ]]; then + cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die + echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + #concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs) + #little hacckery as some gmx-completion* newlines ,so cat won't work + for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do + echo $(<${x}) + done > "${T}"/gmx-bashcomp || die + newbashcomp "${T}"/gmx-bashcomp gmx + bashcomp_alias gmx mdrun + rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die + if use double-precision && use single-precision; then + bashcomp_alias gmx gmx_d + bashcomp_alias gmx mdrun_d + fi + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-5.1.3.ebuild b/sci-chemistry/gromacs/gromacs-5.1.3.ebuild new file mode 100644 index 000000000000..b08ea7c3af7f --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-5.1.3.ebuild @@ -0,0 +1,268 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + https://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}" + inherit git-r3 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" + KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + boost? ( >=dev-libs/boost-1.55 ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_EXTERNAL_BOOST=$(usex boost) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF + -DGMX_USE_GCC44_BUG_WORKAROUND=OFF + -DBUILD_TESTING=$(usex test) + -DGMX_BUILD_UNITTESTS=$(usex test) + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + "${cuda[@]}" + -DGMX_OPENMM=OFF + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + for x in "${ED}"usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild new file mode 100644 index 000000000000..b08ea7c3af7f --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild @@ -0,0 +1,268 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + https://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}" + inherit git-r3 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" + KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + boost? ( >=dev-libs/boost-1.55 ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_EXTERNAL_BOOST=$(usex boost) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF + -DGMX_USE_GCC44_BUG_WORKAROUND=OFF + -DBUILD_TESTING=$(usex test) + -DGMX_BUILD_UNITTESTS=$(usex test) + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + "${cuda[@]}" + -DGMX_OPENMM=OFF + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + for x in "${ED}"usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild new file mode 100644 index 000000000000..b38e62cc3e58 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -0,0 +1,267 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ $PV = *9999* ]]; then + EGIT_REPO_URI="git://git.gromacs.org/gromacs.git + https://gerrit.gromacs.org/gromacs.git + https://github.com/gromacs/gromacs.git + http://repo.or.cz/r/gromacs.git" + [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 + KEYWORDS="" +else + SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz + test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +fi + +ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="http://www.gromacs.org/" + +# see COPYING for details +# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING +# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib +LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" +SLOT="0/${PV}" +IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + X? ( + x11-libs/libX11 + x11-libs/libSM + x11-libs/libICE + ) + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) + fftw? ( sci-libs/fftw:3.0 ) + hwloc? ( sys-apps/hwloc ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi ) + " +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + media-gfx/imagemagick + )" +RDEPEND="${CDEPEND}" + +REQUIRED_USE=" + || ( single-precision double-precision ) + cuda? ( single-precision ) + mkl? ( !blas !fftw !lapack )" + +DOCS=( AUTHORS README ) + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" + use openmp && ! tc-has-openmp && \ + die "Please switch to an openmp compatible compiler" +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + xdg_environment_reset #591952 + + cmake-utils_src_prepare + + use cuda && cuda_src_prepare + + GMX_DIRS="" + use single-precision && GMX_DIRS+=" float" + use double-precision && GMX_DIRS+=" double" + + if use test; then + for x in ${GMX_DIRS}; do + mkdir -p "${WORKDIR}/${P}_${x}" || die + cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die + done + fi + + DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + + #go from slowest to fastest acceleration + local acce="None" + use cpu_flags_x86_sse2 && acce="SSE2" + use cpu_flags_x86_sse4_1 && acce="SSE4.1" + use cpu_flags_x86_fma4 && acce="AVX_128_FMA" + use cpu_flags_x86_avx && acce="AVX_256" + use cpu_flags_x86_avx2 && acce="AVX2_256" + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl && has_version "=sci-libs/mkl-10*"; then + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="${MKLROOT}/include" + -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" + ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + -DGMX_X11=$(usex X) + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex doc) + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_SIMD="$acce" + -DGMX_LIB_INSTALL_DIR="$(get_libdir)" + -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" + -DBUILD_TESTING=$(usex test) + -DGMX_BUILD_UNITTESTS=$(usex test) + ${extra} + ) + + for x in ${GMX_DIRS}; do + einfo "Configuring for ${x} precision" + local suffix="" + #if we build single and double - double is suffixed + use double-precision && use single-precision && \ + [[ ${x} = "double" ]] && suffix="_d" + local p + [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" + local cuda=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && \ + cuda=( -DGMX_GPU=ON ) + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=OFF + -DGMX_THREAD_MPI=$(usex threads) + "${cuda[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + use mpi || continue + einfo "Configuring for ${x} precision with mpi" + mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_THREAD_MPI=OFF + -DGMX_MPI=ON ${cuda} + -DGMX_OPENMM=OFF + -DGMX_BUILD_MDRUN_ONLY=ON + -DBUILD_SHARED_LIBS=OFF + -DGMX_BUILD_MANUAL=OFF + -DGMX_BINARY_SUFFIX="_mpi${suffix}" + -DGMX_LIBS_SUFFIX="_mpi${suffix}" + ) + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile + # not 100% necessary for rel ebuilds as available from website + if use doc; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile manual + fi + use mpi || continue + einfo "Compiling for ${x} precision with mpi" + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ + cmake-utils_src_compile + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_make check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install + if use doc; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + use mpi || continue + BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ + cmake-utils_src_install + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${ED}"usr/bin/GMXRC* || die + for x in "${ED}"usr/bin/gmx-completion-*.bash ; do + local n=${x##*/gmx-completion-} + n="${n%.bash}" + cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + newbashcomp "${T}"/"${n}" "${n}" + done + rm "${ED}"usr/bin/gmx-completion*.bash || die + readme.gentoo_create_doc +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " + einfo "https://dx.doi.org/10.1021/ct700301q" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml new file mode 100644 index 000000000000..b8361e7073ce --- /dev/null +++ b/sci-chemistry/gromacs/metadata.xml @@ -0,0 +1,28 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>junghans@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <maintainer type="person"> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="cuda">Enable cuda non-bonded kernels</flag> + <flag name="double-precision">More precise calculations at the expense of speed</flag> + <flag name="single-precision">Single precision version of gromacs (default)</flag> + <flag name="boost">Enable external boost library</flag> + <flag name="hwloc">Enable HWLoc lib support</flag> + <flag name="tng">Enable new trajectory format - tng</flag> + <flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag> + <!-- acceleration optimization flags --> + <flag name="offensive">Enable gromacs partly offensive quotes</flag> + <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/gsim/Manifest b/sci-chemistry/gsim/Manifest new file mode 100644 index 000000000000..f0fc16777525 --- /dev/null +++ b/sci-chemistry/gsim/Manifest @@ -0,0 +1,7 @@ +AUX gsim-21.3-build.conf.patch 1897 SHA256 565b9db57e8525ad4b3bc7e9d445cd54d282500d5f7e1beb0cef31db2da1bacb SHA512 d1bd0fb6ce8279edfa5aff48ce9d7174825c17531b6d71b5fa872b744160d9c836f80c751e184b34308b05e1f7a817c4fd6b9071bab7e874ca2d59280adc8312 WHIRLPOOL dd9ff16c359e9f7a2d88b9f193c0d646a6be1e724d310e903b0d8188f0c4f935f77335b03dfcaccaf66ab2dee4e4d98f06c358c46c266770e7615aa59b430d30 +DIST gsim-21.3.tar.gz 4100589 SHA256 d3dd161078862fa990b40ff5df988bb82c8469e17dda8e81eda5f1419742de47 SHA512 0a65ec416a11893fe9f249126ed8e7b9f7991dc8f02d6b62b01962de6dfabda805acdc3d7fc6939b609ff018f16cefff616f37ee906776712209460374bb225d WHIRLPOOL d8dde220a52608b5dc48e494fb1b0bad49f13f770e132641b9671cd544c951cdd03a4578bf983492dfb0b74567e51ef716ecbb828ba40b2a3385d26788b83bea +EBUILD gsim-21.3-r1.ebuild 1794 SHA256 c18bfdd909e7a50fa57eae5a834adfecf7bff564e804e18adc2e20bc8d0edf78 SHA512 7222acbf7145886e3f4e1b6758ffba1d656edbf536e6f3caa25989812df67dbfd9794e77578394fb0a51879db8512d7be5ed119f08327ca465ad37cf5c0f786f WHIRLPOOL de7436b5317a35024816f9a4c94e5c6812efb75642a7e4bae53dde8c229a0c61b040e81d1e5847f7d5eb56144bec3801a51e22e56a5daf2558252c6149c25bc6 +EBUILD gsim-21.3.ebuild 1584 SHA256 4b82507ee74c14d650bf25d98b06b306aa22b0ddcb6bada085ff6cbfde60369d SHA512 44b321797c196099c93ccf07747aed4c1d023da78edf44e3deb87a17905cf11adc15b4c20eba649337734634e80bb170bc89142e592f16e1d9d5cf4a5c78c57a WHIRLPOOL 959f3738974c35243adc64702accd0aa2d47bc5d01f390fc91be2668f27b55b5c58d9a27ea90ad1f8c95ab01056a9af2ab5979258ed0240f7a7ca3c007cc9f47 +MISC ChangeLog 3196 SHA256 95fba6bbd01106bc4e2bf872ed8cba4da1e2234b4424ec65bf2fbee1fc4073b3 SHA512 60b9723227d723f18f5dc9610cdc37a4053aae2d6d8ce60b95e5655f46ee7c20f600fe543597a3d27bf7bd03c2c50ac49f209c2c9a00d9e4f698a08f353a212b WHIRLPOOL 03cc6c697e305373dfd330845e2de5b612694fe47a13cdd298a4eeef5c0f682a9e6752ec49ba0ec5f6bcf78e44f08bd9e985cef550ef787a29ed074b40fc6d41 +MISC ChangeLog-2015 1847 SHA256 8c38512d6a95c21f235691f7c424211588df06f9ee72c5aa81ecc4d8bda8a9dc SHA512 f0271aee3dd5744a2f9ba6774ba18a91a378fea4f511b7ff38da84dc8045436c55cab7612850bdb786cdc934661af6e2088db1870b666f65bb2d37e67e89b958 WHIRLPOOL 379b05d646e20673ad2dc0d0d4e51494aaafd0801a9869d5b1034c468e836270cb8abfb2e164b98f4d79711e992d6e18151f9cf91de363d3f4f80ea5e5ff40c2 +MISC metadata.xml 418 SHA256 b33b23ee4b8bc935dca4d48f930d3222e9e10a5770ccba79aa84b0b008c9a545 SHA512 d7ff66672b3e97b217dae26956f7cb56deeded4893eee1f27ad35c203917c2ab2e820b5eed5748fc63378cc7987cb45d699e05aab9fd80c4baa5a17a472f3ff8 WHIRLPOOL 9712b9168c668db5f9cf1142637128e194c036d069f6b8649ccf54e1d559eff1e9baff0aff5f6c4591382654e7f6fc9a4dc6553ef09aa0bc351bec779384af79 diff --git a/sci-chemistry/gsim/files/gsim-21.3-build.conf.patch b/sci-chemistry/gsim/files/gsim-21.3-build.conf.patch new file mode 100644 index 000000000000..da7d7b7b4457 --- /dev/null +++ b/sci-chemistry/gsim/files/gsim-21.3-build.conf.patch @@ -0,0 +1,49 @@ + gsim.pro | 23 ++++++++++++++---------
+ 1 file changed, 14 insertions(+), 9 deletions(-)
+
+diff --git a/gsim.pro b/gsim.pro
+index f88dc8a..579a91c 100755
+--- a/gsim.pro
++++ b/gsim.pro
+@@ -10,27 +10,32 @@
+
+ #Uncomment next line if you want to use EMF output
+ #EMF output requires libEMF or Wine on X11 systems and MAC(?)
+-CONFIG+=use_emf
++#CONFIG+=use_emf
+
+ #DO NOT UNCOMMENT NEXT LINE. The scripting possibilty won't work at the moment
+ #CONFIG+=use_script
+
+ # Change directories locations for libcmatrix, MinUIT and muParser libraries
+-unix:INCLUDEPATH += /home/dch0ph/libcmatrixR3nosse/include \
+- /home/dch1vz/Minuit2/include \
+- /home/dch1vz/muparser/include
++#unix:INCLUDEPATH += /home/dch0ph/libcmatrixR3nosse/include \
++# /home/dch1vz/Minuit2/include \
++# /home/dch1vz/muparser/include
+
+ win32:INCLUDEPATH += "C:\gsim\libcmatrixR3_qt4\include" "C:\gsim\Minuit2_qt4\include" "C:\gsim\muparser_qt4\include"
+
+-unix:LIBS += -lcmatrix -L/home/dch0ph/libcmatrixR3nosse/lib -lMinuit2Base -L/home/dch1vz/Minuit2/lib -L/home/dch1vz/muparser/lib -lmuparser
++#unix:LIBS += -lcmatrix -L/home/dch0ph/libcmatrixR3nosse/lib -lMinuit2Base -L/home/dch1vz/Minuit2/lib -L/home/dch1vz/muparser/lib -lmuparser
+
+ win32:LIBS += -lcmatrix -L"C:\gsim\libcmatrixR3_qt4\lib" -lMinuit2 -L"C:\gsim\Minuit2_qt4\lib" -L"C:\gsim\muparser_qt4\lib" -lmuparser
+
+ #Change directories location for libEMF (if used)
+-use_emf {
+- DEFINES+=USE_EMF_OUTPUT
+- unix:LIBS +=-lEMF -L/usr/include/libEmf
+- win32:LIBS +=-lgdi32
++#use_emf {
++# DEFINES+=USE_EMF_OUTPUT
++# unix:LIBS +=-lEMF -L/usr/include/libEmf
++# win32:LIBS +=-lgdi32
++#}
++
++GSIM_ROOT = .
++!include( $$GSIM_ROOT/build.conf ) {
++ message( "You need a build.conf file with local settings!" )
+ }
+
+ #################################################################################################
diff --git a/sci-chemistry/gsim/gsim-21.3-r1.ebuild b/sci-chemistry/gsim/gsim-21.3-r1.ebuild new file mode 100644 index 000000000000..ea74adc598c7 --- /dev/null +++ b/sci-chemistry/gsim/gsim-21.3-r1.ebuild @@ -0,0 +1,79 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic qmake-utils toolchain-funcs + +DESCRIPTION="Visualisation and processing of experimental and simulated NMR spectra" +HOMEPAGE="https://sourceforge.net/projects/gsim/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cpu_flags_x86_sse3 emf opengl" +REQUIRED_USE="cpu_flags_x86_sse3" + +RDEPEND=" + dev-cpp/muParser + media-libs/freetype + sci-libs/libcmatrix + sci-libs/minuit + virtual/blas + dev-qt/qtsvg:4 + emf? ( media-libs/libemf ) + opengl? ( dev-qt/qtopengl:4 )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( + "${FILESDIR}/${P}-build.conf.patch" +) +DOCS="release.txt README_GSIM.* quickstart.* changes.log programming.*" + +src_prepare() { + edos2unix ${PN}.pro + + default + + # C{,XX}FLAGS need to explicitly enable SSE3 support + # bug #555972 + filter-flags -mno-sse3 + append-cflags -msse3 + append-cxxflags -msse3 + + cat >> build.conf <<- EOF + INCLUDEPATH += "${EPREFIX}/usr/include/libcmatrixR3/" \ + "${EPREFIX}/usr/include/Minuit2" \ + "${EPREFIX}/usr/include" + LIBS += -lcmatrix -lMinuit2 -lmuparser $($(tc-getPKG_CONFIG) --libs cblas) + EOF + + use opengl && echo "CONFIG+=use_opengl" >> build.conf + + if use emf; then + cat >> build.conf <<- EOF + CONFIG+=use_emf + DEFINES+=USE_EMF_OUTPUT + LIBS += -L\"${EPREFIX}/usr/include/libEMF\" -lEMF + EOF + fi + sed \ + -e "s:quickstart.pdf:../share/doc/${PF}/quickstart.pdf:g" \ + -e "s:README_GSIM.pdf:../share/doc/${PF}/README_GSIM.pdf:g" \ + -i mainform.h || die +} + +src_configure() { + eqmake4 ${PN}.pro +} + +src_install() { + default + dobin ${PN} + insinto /usr/share/${PN} + doins -r images ${PN}.ico + insinto /usr/share/${PN}/ui + doins *.ui +} diff --git a/sci-chemistry/gsim/gsim-21.3.ebuild b/sci-chemistry/gsim/gsim-21.3.ebuild new file mode 100644 index 000000000000..332b51b655e0 --- /dev/null +++ b/sci-chemistry/gsim/gsim-21.3.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils qt4-r2 toolchain-funcs + +DESCRIPTION="Programm for visualisation and processing of experimental and simulated NMR spectra" +HOMEPAGE="https://sourceforge.net/projects/gsim/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="emf opengl" + +RDEPEND=" + dev-cpp/muParser + media-libs/freetype + sci-libs/libcmatrix + sci-libs/minuit + virtual/blas + dev-qt/qtsvg:4 + emf? ( media-libs/libemf ) + opengl? ( dev-qt/qtopengl:4 )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( "${FILESDIR}"/${P}-build.conf.patch ) +DOCS="release.txt README_GSIM.* quickstart.* changes.log programming.*" + +src_prepare() { + edos2unix ${PN}.pro + + qt4-r2_src_prepare + + cat >> build.conf <<- EOF + INCLUDEPATH += "${EPREFIX}/usr/include/libcmatrixR3/" \ + "${EPREFIX}/usr/include/Minuit2" \ + "${EPREFIX}/usr/include" + LIBS += -lcmatrix -lMinuit2 -lmuparser $($(tc-getPKG_CONFIG) --libs cblas) + EOF + + use opengl && echo "CONFIG+=use_opengl" >> build.conf + + if use emf; then + cat >> build.conf <<- EOF + CONFIG+=use_emf + DEFINES+=USE_EMF_OUTPUT + LIBS += -L\"${EPREFIX}/usr/include/libEMF\" -lEMF + EOF + fi + sed \ + -e "s:quickstart.pdf:../share/doc/${PF}/quickstart.pdf:g" \ + -e "s:README_GSIM.pdf:../share/doc/${PF}/README_GSIM.pdf:g" \ + -i mainform.h || die +} + +src_install() { + qt4-r2_src_install + dobin ${PN} + insinto /usr/share/${PN} + doins -r images ${PN}.ico + insinto /usr/share/${PN}/ui + doins *.ui +} diff --git a/sci-chemistry/gsim/metadata.xml b/sci-chemistry/gsim/metadata.xml new file mode 100644 index 000000000000..43fbb821ad19 --- /dev/null +++ b/sci-chemistry/gsim/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="emf">Support for .emf export</flag> + </use> + <upstream> + <remote-id type="sourceforge">gsim</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/hollow/Manifest b/sci-chemistry/hollow/Manifest new file mode 100644 index 000000000000..6cc0e4d4acff --- /dev/null +++ b/sci-chemistry/hollow/Manifest @@ -0,0 +1,5 @@ +DIST hollow-1.2.zip 62554 SHA256 9a2d97ad95fc102c1fd537e4fba3c1041ca0ba28d7d2dc0ddc8968b9d1b8722e SHA512 e253680cc0fae286ec697b2dac822b9e165d509cc7eefb27bbcafae6ab2617c3edc8cd9c8beefcc9ef2eb920c9d839fd0bc25f79d22160d857b1705cefbc05ca WHIRLPOOL 83d5d811defe43f91b3516dec873793d9aa6a6a93b2850289c1dd560d53b48a900c8064a16a33692edadb74d1c95b453c2c6fb3ff589a364b7393342e55f6587 +EBUILD hollow-1.2-r1.ebuild 832 SHA256 3c1eaac8dd1109f1835b59f81d8a5f7a348ccdd4cf72c28dfa09760f86804171 SHA512 bf29299b040db8f4f4cb3614671103c5d7ab927c8785538b06aacf72f0df36f39343308271db4ee54b9a87ad82895827e9bde1e151ca1eb17a2f11eb928821f9 WHIRLPOOL 325713d9e5d41b109324e792c1bb5224833b1c4da023498ee0f01eb48c2335a003d8f1f10a60f284433a0d1dad703ef99cda70ce87a859e714625b7a251640a0 +MISC ChangeLog 3117 SHA256 4d7b36cda31c3218850b31dc3a5e37345394cf3ed71881b54d238b1044183e43 SHA512 29eb805dc3983a06fb0b4546c2e66f68940392bfbb504c57b07d91f67724506658493db2bd341b02dc727cd40db980f6ab62f66aea42b6b73a5a79a05aac93e5 WHIRLPOOL 4ab24c22104993c89569bc891002e82e08e03254c411859e1b4511ca4f0a7725342660fc3da737893e91435e8112e5694f89db4b2f3995922200f018c72a7e30 +MISC ChangeLog-2015 750 SHA256 9921e7ead5aa842f47df7501f9b3570df00620fdfbd685f1df2213eafa89fa6e SHA512 2e42825740417aeb695ea69570bf421b90c14055d98bb946ac3c17d7bd99c20e24fff34062dda65f0d16037219bda40d218ba1cf80c39e05bf31b83c423ad61e WHIRLPOOL ac71c19fe3e0a561b99d0c7797b50bf022490d6f7133c8bf3ebc7d4188db2ffd292f267a8ef8d13fe1c7f36c2282fea4035f4f1ebfba7c84a84e387b3f6b6778 +MISC metadata.xml 351 SHA256 2b21d8fd7f37d0a6fe740b3b5190321df84651903520ac25b3abc4641d7da623 SHA512 977d69a6514595888b2a8c193a60dd2ae50ddde7bf9bbacc9051781aab58d50ff2543a911d270c1ed5e5bd152a23b8b2a3f03a186052c74d71c82939e30eeb27 WHIRLPOOL 797a91ab9269d98c25eb0a48432c5a6c4d2285d7bd364d1c42bbc15938fb8735c3d0d9098212272d02ee7fab38e1346e3ec07823c1282a80022a70b5548f19de diff --git a/sci-chemistry/hollow/hollow-1.2-r1.ebuild b/sci-chemistry/hollow/hollow-1.2-r1.ebuild new file mode 100644 index 000000000000..9c421e26b2bb --- /dev/null +++ b/sci-chemistry/hollow/hollow-1.2-r1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-r1 + +DESCRIPTION="Production of surface images of proteins" +HOMEPAGE="http://hollow.sourceforge.net/" +#SRC_URI="mirror://sourceforge/${P}.zip" +SRC_URI="http://hollow.sourceforge.net/${P}.zip" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-3" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + sci-chemistry/pymol[${PYTHON_USEDEP}]" +DEPEND="${PYTHON_DEPS} + app-arch/unzip" + +src_install() { + python_setup + esvn_clean + python_foreach_impl python_domodule pdbstruct + python_moduleinto ${PN} + python_foreach_impl python_domodule *.py hollow.txt + + python_foreach_impl python_newscript ${PN}.py ${PN} + + dodoc README + python_optimize +} diff --git a/sci-chemistry/hollow/metadata.xml b/sci-chemistry/hollow/metadata.xml new file mode 100644 index 000000000000..266ef9d56913 --- /dev/null +++ b/sci-chemistry/hollow/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">hollow</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/jmol/Manifest b/sci-chemistry/jmol/Manifest new file mode 100644 index 000000000000..b47b85f09a7c --- /dev/null +++ b/sci-chemistry/jmol/Manifest @@ -0,0 +1,15 @@ +AUX 12.0.45/jmol-manifest.patch 3726 SHA256 74cdf274352161ffdf155b34b8d9110dad9c4a15720467f73d301104005566bd SHA512 016e57a3c3e55d89fe2a72447160c0b6359affec305c6b4949892ddec3b4a648bad96b87ff0aa5cb0c5187f59e825b441cbbe60e6936a14df536ed0095f67112 WHIRLPOOL abb250bc77d15a5f3e0a441dd0ffd8809642d8959f896c1ae394b85695b74bd4578013ad99b38abca822ad5db514562b121ad6b2f0265090653d7e359ee85a2f +AUX 12.0.45/jmol-nointl.patch 13315 SHA256 6bbf13c59bc3633dc089346c1133ad2b3d0614463abdf364f5ec2e2ccd658df0 SHA512 deb54c7f94e3fd4b43a701d58c992edbc80f650397feea97594a8f00cdc14463a19e2314fa616fb3a0ca42af8b70770c0426b8eacfe1d81a30b53c566e6342c0 WHIRLPOOL 570e359517e1011ba76447161e6c03925db0e6533d262f11f13d9553f75989faa27a0ae5f39352dad19ec53e804e8e39e76bbc79f1b44b495fe948e7b8633472 +AUX caffeine.xyz 1116 SHA256 45a9afac0b247780595944a98f8e1076a7e7e0dbb3e02cb54cecb0764b1cb67f SHA512 863ee4a327b2d765ed042cf24055c708d3970a20c3c3b2ee45b46096390be11a7c02915faedb30ee6cb69101faa5942fcfb19fe2b530afb93460a2cd167c3688 WHIRLPOOL 18df972f5cbafc35be4bf20de29ad8049e7c6f921a668f0c80cd9aff2c3ede32b9b30e830f2629be2136923c554c3711b809915d45ea1bd1da854d8768d6e254 +AUX index.html 328 SHA256 8cba2c5eb7f25c0ecf23bc007eb61549a7d2177ac327db6c1e5f51f333ae2451 SHA512 e89c62ba91ecebb38d6f9c88cc1f257600bd7d6005df97713f2715036d3308dee53f7b838ca749c1acc810cc4701c384525f2763b96ac2f1d6802e639cd1961b WHIRLPOOL 0b407f950f4f2523d21c03b6e4f20f9ef4009e54d666ad3a222b87b0e49576816f3940e4fe076e55e9fda9832170c54f17ed543420333fe489f45f4d7296ee79 +AUX jmol-11.0.3-manifest.patch 3726 SHA256 74cdf274352161ffdf155b34b8d9110dad9c4a15720467f73d301104005566bd SHA512 016e57a3c3e55d89fe2a72447160c0b6359affec305c6b4949892ddec3b4a648bad96b87ff0aa5cb0c5187f59e825b441cbbe60e6936a14df536ed0095f67112 WHIRLPOOL abb250bc77d15a5f3e0a441dd0ffd8809642d8959f896c1ae394b85695b74bd4578013ad99b38abca822ad5db514562b121ad6b2f0265090653d7e359ee85a2f +AUX jmol-11.0.3-nointl.patch 11109 SHA256 56ad460779a0ecfb90ad61cf4cfae2fad9b017f9f78581a720241e4ea208b49a SHA512 0fe07fb53d989298f7395be39c6ee75f56ab59fc096e956d8481c38581706b17f799e745fcd5b6652c4f1115d4425e7ff9ebef454b606d8de7829e07e26b27e2 WHIRLPOOL daf992208b99fec51f5f0b26ca22d520ebd820a22d439c7baa2b84f2b4b3829ac7139d7d3c48076dd4681af1296fd5e61badd91332efa03cc97e58027b21697a +AUX jmol-12.2.27-nointl.patch 13821 SHA256 330a911405f00552d37a9c241c4a18b9d3e6812ce858933dbc4574df8248e345 SHA512 6ad196dfd6d38a086fad461f8170340f8ef3beb7ae69916e0285d8e30ce8a40efc278e461a3d0ae0da71611529f4a0e58c9a73336319764b1fef62d75336a8dc WHIRLPOOL 94be437d33ec73ed53c8461e78a7799c2aa34c9b606e309554da191ff74a465fe2243f4953a615aca790d3558e2b69b7edd122526f900475f5b05bb20d98d0fe +DIST Jmol-12.0.45-full.tar.gz 26501382 SHA256 f9a3fe242841f9b56a718f8da2efe4130e497afe2c12d77f2e68344c62d7f70e SHA512 b0e999335c039e5bde5e261c076f3eb75dd0c33a351445d5c086995d32b3fd03795b3a11dc57a06bf8ac39e74945f3c9f4547ecfbf18b56d827b9a42f5208c11 WHIRLPOOL d0bbae1fc5c96ddfb4dd29f6e09701e496a333a2f44ba266e2a24c60de2d36d73c2184bd9b8f6054b0955535d49856154d6101644ef0297b825c4f6745cfe3bb +DIST Jmol-12.2.27-full.tar.gz 29493780 SHA256 f2ca3b810ea16a488f6f57003d2a407c8ac040d610479a7ae6d95631157db801 SHA512 a8608e64dc06b6d3b0cb7e911f0a224456a65bdc15c51d6b420ee6abf8d82cdcec9f54f6b1a51cfe032e2e074f173f50a88bcff783311de19ce9b95ad990ebca WHIRLPOOL ae0826eab7eb364acb4f30eb77850450b871a24d8940eaabaf8fe9f3770efc39deb604e3c5f875a695c0d33b516ad47d523982c7a6460f2421f961f50a7680bf +DIST jmol-selfSignedCertificate.store.tar 10240 SHA256 416744934991ef4f1fa298c0afc8e855d43771de2f2278ed3fbc60f707ea46b2 SHA512 2c3e9d1183a0b174273346d0fba0729caa415ef53fe01629a4c47daa2393c9e18ca3f57984911e6340197429cf0ee581c64bb9b6072db902102976030d9f2c23 WHIRLPOOL 79dc2b2c95b304569f44bb986af3aa25150b0c5f8a9fc9b1698a979647800e60d0f20a7a4abbc89533a21f3d7f4b93a430840eed71bbe04b1cc0bdbcfae7fe63 +EBUILD jmol-12.0.45-r1.ebuild 2923 SHA256 6fb9b443fcfbe680b0e120d0233b0531116351a91bee3bf8d398a921480cfad9 SHA512 6336b5293150abcf0f8349ebd80088b26b4b6da3633f00ac53a9396569e65f1736f2fa14cd69f65ea16838e3507d0050734c71c23734311cefe41dc1bd3d0974 WHIRLPOOL c7890e2d7a8b8ebbf082d2fb65b18923ffad36c0f9ebc95bf00039f6f7b70cbe32bb3773b0e09c1f88146e8d1c19cb9c7099ccb97482c8e43b9f437571a5b07e +EBUILD jmol-12.2.27-r1.ebuild 2783 SHA256 41f0fbe61872ec8763ff3887f3f574bf9e3ed12751cd44fa7355968c78fea2fc SHA512 dd81a4edccc022a8f7aab66a8a8005feb68eec7e2e3a1a2278f9565c8b3bec364b5dcb0f994c1202a3fb97491ca31b11941ed41501e0a485d9238f233d9e0940 WHIRLPOOL 93d2ea57d5fec5229770ecc2f3e1df317ede5cb97eb4036e81bddd390311fa4df4e587254ae4627094eb323013626cf9a5084a9c884dc4e2ca8e16b50093894e +MISC ChangeLog 2878 SHA256 18b594c9d1d7ef41e2292dd65768c5847c18ed35c3bc4c65b83fef7f8326b075 SHA512 918cc2877676a207b037b56c1b2400b6b700c8bc367e2399fd4bf4f367ae81dddeaa7cfbbc3d9b73b1d3771ecff22b19e1031753e1ae579f2aeb3cba72c51a66 WHIRLPOOL cf0834fc982455bac386a8b1d9c8e05f2204a8a448579bc09f376a2eb14302c0d7bbc5864a47c8699e06d3b459c56273afb22feb7e96cf9ebe2bcfedd7b38ddb +MISC ChangeLog-2015 2982 SHA256 bf3153e33aa2d74e25570ecf4fec84e9bee42ad661c18791e1aacdb1e17e1f1a SHA512 fed110fe8de1074909ef53be8d8eb9f576946987e98cccb44540cedd990c37dd85dac54c2af67ba3c460b3a0c083582c883b621d8fe8c8a21b464eb3f3cdff10 WHIRLPOOL 6f7dc08ffcf2644bd452668f256f93f3fad41908fe5ae65cdc3230175fdaab984b82a25103e3181afa427a50ced58f278b2642439dbe3f894c6bbf268008e332 +MISC metadata.xml 458 SHA256 d1ff80e0cb82997846dd7daa0fb55428e4c29dd60645273cb29bd148c625d3e7 SHA512 2808cc38baa2aefa5fb873cab1f2f96d52125c41f969d37cf9405b19c16883aa0bec82895fc40001acc1eb9b7b02ceb5fb03b9a517b887e56ea13d3889dd9012 WHIRLPOOL a9e37b078f979bd05d2c86fa3d5b33b16ebb5f6c853001e95f3c3e26fb460427e20750241194b17709706263ccffbe8d85d5c8b3df793475a64cd43792942571 diff --git a/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch b/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch new file mode 100644 index 000000000000..3b43c219d94f --- /dev/null +++ b/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch @@ -0,0 +1,96 @@ +diff -aurN jmol-11.0.3-orig/manifest/applet0.txt jmol-11.0.3/manifest/applet0.txt +--- jmol-11.0.3-orig/manifest/applet0.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet0.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,6 @@ ++Main-Class: JmolApplet
++Sealed: true
++
++Name: org/jmol/api/
++Sealed: false
++
+diff -aurN jmol-11.0.3-orig/manifest/applet1.txt jmol-11.0.3/manifest/applet1.txt +--- jmol-11.0.3-orig/manifest/applet1.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet1.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,6 @@ ++Name: org/jmol/api/
++Sealed: false
++
++Name: org/jmol/applet/
++Sealed: true
++
+diff -aurN jmol-11.0.3-orig/manifest/applet2.txt jmol-11.0.3/manifest/applet2.txt +--- jmol-11.0.3-orig/manifest/applet2.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet2.txt 2007-05-16 01:56:19.000000000 -0500 +@@ -0,0 +1,3 @@ ++Name: javax/vecmath/ ++ ++ +diff -aurN jmol-11.0.3-orig/manifest/applet3.txt jmol-11.0.3/manifest/applet3.txt +--- jmol-11.0.3-orig/manifest/applet3.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet3.txt 2007-05-16 01:56:47.000000000 -0500 +@@ -0,0 +1,4 @@ ++ ++Name: org/jmol/g3d/ ++Sealed: true ++ +diff -aurN jmol-11.0.3-orig/manifest/applet4.txt jmol-11.0.3/manifest/applet4.txt +--- jmol-11.0.3-orig/manifest/applet4.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet4.txt 2007-05-16 01:57:05.000000000 -0500 +@@ -0,0 +1,4 @@ ++ ++Name: org/jmol/adapter/smarter/ ++Sealed: true ++ +diff -aurN jmol-11.0.3-orig/manifest/applet5.txt jmol-11.0.3/manifest/applet5.txt +--- jmol-11.0.3-orig/manifest/applet5.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet5.txt 2007-05-16 01:57:23.000000000 -0500 +@@ -0,0 +1,4 @@ ++Name: org/openscience/jmol/ui/ ++Sealed: true ++ ++ +diff -aurN jmol-11.0.3-orig/manifest/applet6.txt jmol-11.0.3/manifest/applet6.txt +--- jmol-11.0.3-orig/manifest/applet6.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet6.txt 2007-05-16 01:57:46.000000000 -0500 +@@ -0,0 +1,4 @@ ++ ++Name: org/jmol/viewer/ ++Sealed: true ++ +diff -aurN jmol-11.0.3-orig/manifest/appletMain.txt jmol-11.0.3/manifest/appletMain.txt +--- jmol-11.0.3-orig/manifest/appletMain.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/appletMain.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,5 @@ ++Manifest-Version: 1.0
++Sealed: true
++
++Name: org/jmol/api/
++Sealed: false
+diff -aurN jmol-11.0.3-orig/manifest/appletMonolithic.txt jmol-11.0.3/manifest/appletMonolithic.txt +--- jmol-11.0.3-orig/manifest/appletMonolithic.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/appletMonolithic.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,7 @@ ++Main-Class: JmolApplet
++Sealed: true
++
++Name: org/jmol/api/
++Sealed: false
++
++
+diff -aurN jmol-11.0.3-orig/manifest/applet.txt jmol-11.0.3/manifest/applet.txt +--- jmol-11.0.3-orig/manifest/applet.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,2 @@ ++Manifest-Version: 1.0
++Sealed: true
+\ No newline at end of file +diff -aurN jmol-11.0.3-orig/manifest/application.txt jmol-11.0.3/manifest/application.txt +--- jmol-11.0.3-orig/manifest/application.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/application.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1 @@ ++Main-Class: org.openscience.jmol.app.Jmol
+diff -aurN jmol-11.0.3-orig/manifest/jvxl.txt jmol-11.0.3/manifest/jvxl.txt +--- jmol-11.0.3-orig/manifest/jvxl.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/jvxl.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1 @@ ++Main-Class: org.openscience.jvxl.Jvxl
diff --git a/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch b/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch new file mode 100644 index 000000000000..c1b22e83c615 --- /dev/null +++ b/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch @@ -0,0 +1,313 @@ +--- build.xml 2011-02-25 12:59:43.000000000 -0600 ++++ build.xml.new 2011-02-27 12:16:02.398959959 -0600 +@@ -110,10 +110,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolGuide.docbook.xml, guide/*.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolUserGuide_fr/index.html">
+- <srcfiles dir="doc/source"
+- includes="JmolGuide_fr.docbook.xml, guide/*_fr.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -123,14 +119,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolHistory.xml,JmolHistoryToHtml.xsl,history/changes.xml" />
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolHistory_fr.xml,JmolHistoryToHtml.xsl,history/changes_fr.xml" />
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_nl.html">
+- <srcfiles dir="doc/source"
+- includes="JmolHistory_nl.xml,JmolHistoryToHtml.xsl,history/changes_nl.xml" />
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -140,14 +128,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolDevelopersGuide.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolDevelopersGuide_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolDevelopersGuide_fr.docbook.xml"/>
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolDevelopersGuide_de.html">
+- <srcfiles dir="doc/source"
+- includes="JmolDevelopersGuide_de.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -157,14 +137,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolAppletGuide.docbook.xml, applet/*.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolAppletGuide_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolAppletGuide_fr.docbook.xml, applet/*_fr.docbook.xml"/>
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolAppletGuide_de.html">
+- <srcfiles dir="doc/source"
+- includes="JmolAppletGuide_de.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -385,17 +357,12 @@ + </target>
+
+ <target name="jar" id="jar"
+- depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">
++ depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars">
+ <copy todir="${classes.dir}/org/openscience/jmol/Data/guide" >
+ <fileset dir="build/doc/JmolUserGuide">
+ <include name="**/*.html" />
+ </fileset>
+ </copy>
+- <copy todir="${classes.dir}/org/openscience/jmol/Data/guide_fr" >
+- <fileset dir="build/doc/JmolUserGuide_fr">
+- <include name="**/*.html" />
+- </fileset>
+- </copy>
+ <copy todir="${classes.dir}/org/openscience/jmol/Data" >
+ <fileset dir="build/doc/JmolHistory">
+ <include name="**/*.html" />
+@@ -587,18 +554,6 @@ + <fileset dir="${appletjars.dir}" includes="**/*"/>
+ </jar>
+
+- <for list="${all.JmolApplet.languages}" delimiter=","
+- param="current.Jmol.language">
+- <sequential>
+- <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+- manifest="manifest/applet_i18n.txt" >
+- <fileset dir="${applet.classes.dir}">
+- <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
+- </fileset>
+- </jar>
+- </sequential>
+- </for>
+-
+ <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
+ <fileset dir="${applet.classes.dir}">
+ <include name="org/jmol/minimize/**" />
+@@ -712,7 +667,6 @@ + <include name="org/jmol/bspt/**" />
+ <include name="org/jmol/g3d/**" />
+ <include name="org/jmol/geodesic/**" />
+- <include name="org/jmol/i18n/**" />
+ <include name="org/jmol/modelset/**" />
+ <include name="org/jmol/script/**" />
+ <include name="org/jmol/shape/**" />
+@@ -738,7 +692,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
+- <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
+ </indexjars>
+ </jar>
+ <!-- changes to this must be replicated below for the signed applet -->
+@@ -851,16 +804,6 @@ + keystore="selfSignedCertificate/selfSignedCertificate.store"
+ storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+
+- <for list="${all.JmolApplet.languages}" delimiter=","
+- param="current.Jmol.language">
+- <sequential>
+- <signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+- signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n_@{current.Jmol.language}.jar"
+- keystore="selfSignedCertificate/selfSignedCertificate.store"
+- storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+- </sequential>
+- </for>
+-
+ <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
+ <!-- this one must be treated specially because of jar indexing
+ we cannot simply rename the jar file, because the index has
+@@ -906,7 +849,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSurface.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Symmetry.jar" />
+- <fileset dir="${jmol.applet.build.dir}" includes="JmolAppletSigned0_i18n_*.jar" />
+ </indexjars>
+ </jar>
+ <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"
+@@ -944,18 +886,6 @@ + </fileset>
+ </jar>
+
+- <for list="${all.JmolApplet.languages}" delimiter=","
+- param="current.Jmol.language">
+- <sequential>
+- <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+- manifest="manifest/applet_i18n.txt" >
+- <fileset dir="${applet.classes.dir}">
+- <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
+- </fileset>
+- </jar>
+- </sequential>
+- </for>
+-
+ <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
+ <fileset dir="${applet.classes.dir}">
+ <include name="org/jmol/minimize/**" />
+@@ -1069,7 +999,6 @@ + <include name="org/jmol/bspt/**" />
+ <include name="org/jmol/g3d/**" />
+ <include name="org/jmol/geodesic/**" />
+- <include name="org/jmol/i18n/**" />
+ <include name="org/jmol/modelset/**" />
+ <include name="org/jmol/script/**" />
+ <include name="org/jmol/shape/**" />
+@@ -1095,7 +1024,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
+- <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
+ </indexjars>
+ </jar>
+ <!-- changes to this must be replicated below for the signed applet -->
+@@ -1104,7 +1032,7 @@ + </target>
+
+ <target name="dist" id="dist"
+- depends="doc,main-i18n,main,signed-applet">
++ depends="doc,main,signed-applet">
+ <!-- first build binary distribution -->
+ <delete dir="build/dist/jmol-${version}"/>
+ <mkdir dir="build/dist/jmol-${version}"/>
+@@ -1163,7 +1091,6 @@ + <fileset dir=".">
+ <include name="applet.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -1246,7 +1173,6 @@ + <fileset dir=".">
+ <include name="apisio.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -1342,7 +1268,7 @@ + <target name="xclean" id="xclean">
+ </target>
+
+- <target name="spotless" id="spotless" depends="clean,spotless-i18n">
++ <target name="spotless" id="spotless" depends="clean">
+ <delete dir="build"/>
+ <delete dir="${javadoc.dir}"/>
+ <delete dir="packaging/rpm/dist"/>
+@@ -1406,16 +1332,6 @@ + <arg value="../../../doc/source/JmolGuide.docbook.xml" />
+ <arg value="../../${docbook-xsl}/html/chunk.xsl" />
+ </java>
+- <echo message="Generating user's guide (fr)" />
+- <mkdir dir="build/doc/JmolUserGuide_fr" />
+- <java fork="true" dir="build/doc/JmolUserGuide_fr"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <jvmarg value="${proxyHost}" />
+- <jvmarg value="${proxyPort}" />
+- <arg value="../../../doc/source/JmolGuide_fr.docbook.xml" />
+- <arg value="../../${docbook-xsl}/html/chunk.xsl" />
+- </java>
+ </target>
+
+ <target name="jmolHistory" id="jmolHistory"
+@@ -1430,26 +1346,6 @@ + <arg value="../../../doc/source/JmolHistory.xml" />
+ <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+ </java>
+- <echo message="Generating history of changes (fr)" />
+- <java fork="true" dir="build/doc/JmolHistory"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="ChangeLog_fr.html" />
+- <arg value="../../../doc/source/JmolHistory_fr.xml" />
+- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+- <arg value="lang=fr" />
+- </java>
+- <echo message="Generating history of changes (nl)" />
+- <java fork="true" dir="build/doc/JmolHistory"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="ChangeLog_nl.html" />
+- <arg value="../../../doc/source/JmolHistory_nl.xml" />
+- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+- <arg value="lang=nl" />
+- </java>
+ </target>
+
+ <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"
+@@ -1463,24 +1359,6 @@ + <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />
+ <arg value="../${docbook-xsl}/html/docbook.xsl" />
+ </java>
+- <echo message="Generating developer's guide (fr)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolDevelopersGuide_fr.html" />
+- <arg value="../../doc/source/JmolDevelopersGuide_fr.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+- <echo message="Generating developer's guide (de)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolDevelopersGuide_de.html" />
+- <arg value="../../doc/source/JmolDevelopersGuide_de.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+ </target>
+
+ <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"
+@@ -1494,24 +1372,6 @@ + <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />
+ <arg value="../${docbook-xsl}/html/docbook.xsl" />
+ </java>
+- <echo message="Generating applet guide (fr)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolAppletGuide_fr.html" />
+- <arg value="../../doc/source/JmolAppletGuide_fr.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+- <echo message="Generating applet guide (de)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolAppletGuide_de.html" />
+- <arg value="../../doc/source/JmolAppletGuide_de.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+ </target>
+
+ <target name="test" id="test" depends="main,compile-tests">
+@@ -1543,12 +1403,4 @@ + <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />
+ </target>
+
+- <!-- i18n stuff -->
+- <target name="main-i18n" depends="classes">
+- <ant antfile="tools/build-i18n.xml" target="main-i18n"/>
+- </target>
+- <target name="spotless-i18n">
+- <ant antfile="tools/build-i18n.xml" target="spotless-i18n"/>
+- </target>
+-
+ </project>
diff --git a/sci-chemistry/jmol/files/caffeine.xyz b/sci-chemistry/jmol/files/caffeine.xyz new file mode 100644 index 000000000000..f0325b049f3c --- /dev/null +++ b/sci-chemistry/jmol/files/caffeine.xyz @@ -0,0 +1,26 @@ +24 +Caffeine +H -3.3804130 -1.1272367 0.5733036 +N 0.9668296 -1.0737425 -0.8198227 +C 0.0567293 0.8527195 0.3923156 +N -1.3751742 -1.0212243 -0.0570552 +C -1.2615018 0.2590713 0.5234135 +C -0.3068337 -1.6836331 -0.7169344 +C 1.1394235 0.1874122 -0.2700900 +N 0.5602627 2.0839095 0.8251589 +O -0.4926797 -2.8180554 -1.2094732 +C -2.6328073 -1.7303959 -0.0060953 +O -2.2301338 0.7988624 1.0899730 +H 2.5496990 2.9734977 0.6229590 +C 2.0527432 -1.7360887 -1.4931279 +H -2.4807715 -2.7269528 0.4882631 +H -3.0089039 -1.9025254 -1.0498023 +H 2.9176101 -1.8481516 -0.7857866 +H 2.3787863 -1.1211917 -2.3743655 +H 1.7189877 -2.7489920 -1.8439205 +C -0.1518450 3.0970046 1.5348347 +C 1.8934096 2.1181245 0.4193193 +N 2.2861252 0.9968439 -0.2440298 +H -0.1687028 4.0436553 0.9301094 +H 0.3535322 3.2979060 2.5177747 +H -1.2074498 2.7537592 1.7203047 diff --git a/sci-chemistry/jmol/files/index.html b/sci-chemistry/jmol/files/index.html new file mode 100644 index 000000000000..35a5d49217e2 --- /dev/null +++ b/sci-chemistry/jmol/files/index.html @@ -0,0 +1,14 @@ +<html> + <head> + <title>Jmol Test Page</title> + <div align="center"> <b>All the Sugar and Twice the Caffeine.</b> <br><br> + <script src="./Jmol.js"></script> + </head> + <body> + <script> + jmolInitialize("./"); // REQUIRED + jmolApplet(400, "load ./caffeine.xyz"); + </script></div> + </body> +</html> + diff --git a/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch b/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch new file mode 100644 index 000000000000..3b43c219d94f --- /dev/null +++ b/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch @@ -0,0 +1,96 @@ +diff -aurN jmol-11.0.3-orig/manifest/applet0.txt jmol-11.0.3/manifest/applet0.txt +--- jmol-11.0.3-orig/manifest/applet0.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet0.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,6 @@ ++Main-Class: JmolApplet
++Sealed: true
++
++Name: org/jmol/api/
++Sealed: false
++
+diff -aurN jmol-11.0.3-orig/manifest/applet1.txt jmol-11.0.3/manifest/applet1.txt +--- jmol-11.0.3-orig/manifest/applet1.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet1.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,6 @@ ++Name: org/jmol/api/
++Sealed: false
++
++Name: org/jmol/applet/
++Sealed: true
++
+diff -aurN jmol-11.0.3-orig/manifest/applet2.txt jmol-11.0.3/manifest/applet2.txt +--- jmol-11.0.3-orig/manifest/applet2.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet2.txt 2007-05-16 01:56:19.000000000 -0500 +@@ -0,0 +1,3 @@ ++Name: javax/vecmath/ ++ ++ +diff -aurN jmol-11.0.3-orig/manifest/applet3.txt jmol-11.0.3/manifest/applet3.txt +--- jmol-11.0.3-orig/manifest/applet3.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet3.txt 2007-05-16 01:56:47.000000000 -0500 +@@ -0,0 +1,4 @@ ++ ++Name: org/jmol/g3d/ ++Sealed: true ++ +diff -aurN jmol-11.0.3-orig/manifest/applet4.txt jmol-11.0.3/manifest/applet4.txt +--- jmol-11.0.3-orig/manifest/applet4.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet4.txt 2007-05-16 01:57:05.000000000 -0500 +@@ -0,0 +1,4 @@ ++ ++Name: org/jmol/adapter/smarter/ ++Sealed: true ++ +diff -aurN jmol-11.0.3-orig/manifest/applet5.txt jmol-11.0.3/manifest/applet5.txt +--- jmol-11.0.3-orig/manifest/applet5.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet5.txt 2007-05-16 01:57:23.000000000 -0500 +@@ -0,0 +1,4 @@ ++Name: org/openscience/jmol/ui/ ++Sealed: true ++ ++ +diff -aurN jmol-11.0.3-orig/manifest/applet6.txt jmol-11.0.3/manifest/applet6.txt +--- jmol-11.0.3-orig/manifest/applet6.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet6.txt 2007-05-16 01:57:46.000000000 -0500 +@@ -0,0 +1,4 @@ ++ ++Name: org/jmol/viewer/ ++Sealed: true ++ +diff -aurN jmol-11.0.3-orig/manifest/appletMain.txt jmol-11.0.3/manifest/appletMain.txt +--- jmol-11.0.3-orig/manifest/appletMain.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/appletMain.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,5 @@ ++Manifest-Version: 1.0
++Sealed: true
++
++Name: org/jmol/api/
++Sealed: false
+diff -aurN jmol-11.0.3-orig/manifest/appletMonolithic.txt jmol-11.0.3/manifest/appletMonolithic.txt +--- jmol-11.0.3-orig/manifest/appletMonolithic.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/appletMonolithic.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,7 @@ ++Main-Class: JmolApplet
++Sealed: true
++
++Name: org/jmol/api/
++Sealed: false
++
++
+diff -aurN jmol-11.0.3-orig/manifest/applet.txt jmol-11.0.3/manifest/applet.txt +--- jmol-11.0.3-orig/manifest/applet.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/applet.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1,2 @@ ++Manifest-Version: 1.0
++Sealed: true
+\ No newline at end of file +diff -aurN jmol-11.0.3-orig/manifest/application.txt jmol-11.0.3/manifest/application.txt +--- jmol-11.0.3-orig/manifest/application.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/application.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1 @@ ++Main-Class: org.openscience.jmol.app.Jmol
+diff -aurN jmol-11.0.3-orig/manifest/jvxl.txt jmol-11.0.3/manifest/jvxl.txt +--- jmol-11.0.3-orig/manifest/jvxl.txt 1969-12-31 18:00:00.000000000 -0600 ++++ jmol-11.0.3/manifest/jvxl.txt 2007-05-16 01:54:10.000000000 -0500 +@@ -0,0 +1 @@ ++Main-Class: org.openscience.jvxl.Jvxl
diff --git a/sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch b/sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch new file mode 100644 index 000000000000..25fd17e36c68 --- /dev/null +++ b/sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch @@ -0,0 +1,266 @@ +--- jmol-11.0.3-orig/build.xml 2007-05-17 09:35:04.000000000 -0500 ++++ jmol-11.0.3/build.xml 2007-05-17 09:40:21.000000000 -0500 +@@ -100,10 +100,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolGuide.docbook.xml, guide/*.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolUserGuide_fr/index.html">
+- <srcfiles dir="doc/source"
+- includes="JmolGuide_fr.docbook.xml, guide/*_fr.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -113,14 +109,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolHistory.xml,JmolHistoryToHtml.xsl,history/changes.xml" />
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolHistory_fr.xml,JmolHistoryToHtml.xsl,history/changes_fr.xml" />
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_nl.html">
+- <srcfiles dir="doc/source"
+- includes="JmolHistory_nl.xml,JmolHistoryToHtml.xsl,history/changes_nl.xml" />
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -130,14 +118,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolDevelopersGuide.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolDevelopersGuide_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolDevelopersGuide_fr.docbook.xml"/>
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolDevelopersGuide_de.html">
+- <srcfiles dir="doc/source"
+- includes="JmolDevelopersGuide_de.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -147,14 +127,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolAppletGuide.docbook.xml, applet/*.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolAppletGuide_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolAppletGuide_fr.docbook.xml, applet/*_fr.docbook.xml"/>
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolAppletGuide_de.html">
+- <srcfiles dir="doc/source"
+- includes="JmolAppletGuide_de.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -332,17 +304,12 @@ + </target>
+
+ <target name="jar" id="jar"
+- depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">
++ depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars">
+ <copy todir="${classes.dir}/org/openscience/jmol/Data/guide" >
+ <fileset dir="build/doc/JmolUserGuide">
+ <include name="**/*.html" />
+ </fileset>
+ </copy>
+- <copy todir="${classes.dir}/org/openscience/jmol/Data/guide_fr" >
+- <fileset dir="build/doc/JmolUserGuide_fr">
+- <include name="**/*.html" />
+- </fileset>
+- </copy>
+ <copy todir="${classes.dir}/org/openscience/jmol/Data" >
+ <fileset dir="build/doc/JmolHistory">
+ <include name="**/*.html" />
+@@ -462,7 +429,6 @@ + <!-- note that this class is included in JmolApplet0.jar -->
+ <exclude name="org/jmol/api/JmolAppletInterface.class" />
+ <include name="org/jmol/applet/**" />
+- <include name="org/jmol/i18n/**" />
+ <include name="org/jmol/popup/**" />
+ </fileset>
+ </jar>
+@@ -502,12 +468,6 @@ + </fileset>
+ </jar>
+
+- <jar destfile="${jmol.applet.build.dir}/JmolApplet_i18n.jar" manifest="manifest/applet_i18n.txt" >
+- <fileset dir="${applet.classes.dir}">
+- <include name="org/jmol/translation/**" />
+- </fileset>
+- </jar>
+-
+ <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
+ <!-- changes to this must be replicated below for the signed applet -->
+ <jar destfile="${jmol.applet.build.dir}/JmolApplet0.jar"
+@@ -527,7 +487,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolApplet4.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet5.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet6.jar" />
+- <pathelement path="${jmol.applet.build.dir}/JmolApplet_i18n.jar" />
+ </indexjars>
+ </jar>
+ <!-- changes to this must be replicated below for the signed applet -->
+@@ -564,10 +523,6 @@ + signedjar="${jmol.applet.build.dir}/JmolAppletSigned6.jar"
+ keystore="selfSignedCertificate/selfSignedCertificate.store"
+ storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+- <signjar jar="${jmol.applet.build.dir}/JmolApplet_i18n.jar"
+- signedjar="${jmol.applet.build.dir}/JmolAppletSigned_i18n.jar"
+- keystore="selfSignedCertificate/selfSignedCertificate.store"
+- storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+
+ <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
+ <!-- this one must be treated specially because of jar indexing
+@@ -589,7 +544,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned4.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned5.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned6.jar" />
+- <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned_i18n.jar" />
+ </indexjars>
+ </jar>
+ <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"
+@@ -599,7 +553,7 @@ + </target>
+
+ <target name="dist" id="dist"
+- depends="doc,main-i18n,main,signed-applet">
++ depends="doc,main,signed-applet">
+ <!-- first build binary distribution -->
+ <delete dir="build/dist/jmol-${version}"/>
+ <mkdir dir="build/dist/jmol-${version}"/>
+@@ -655,7 +609,6 @@ + <fileset dir=".">
+ <include name="applet.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -744,7 +697,6 @@ + <fileset dir=".">
+ <include name="apisio.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -839,7 +791,7 @@ + <target name="xclean" id="xclean">
+ </target>
+
+- <target name="spotless" id="spotless" depends="clean,spotless-i18n">
++ <target name="spotless" id="spotless" depends="clean">
+ <delete dir="build"/>
+ <delete dir="${javadoc.dir}"/>
+ <delete dir="packaging/rpm/dist"/>
+@@ -900,16 +852,6 @@ + <arg value="../../../doc/source/JmolGuide.docbook.xml" />
+ <arg value="../../${docbook-xsl}/html/chunk.xsl" />
+ </java>
+- <echo message="Generating user's guide (fr)" />
+- <mkdir dir="build/doc/JmolUserGuide_fr" />
+- <java fork="true" dir="build/doc/JmolUserGuide_fr"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <jvmarg value="${proxyHost}" />
+- <jvmarg value="${proxyPort}" />
+- <arg value="../../../doc/source/JmolGuide_fr.docbook.xml" />
+- <arg value="../../${docbook-xsl}/html/chunk.xsl" />
+- </java>
+ </target>
+
+ <target name="jmolHistory" id="jmolHistory"
+@@ -924,26 +866,6 @@ + <arg value="../../../doc/source/JmolHistory.xml" />
+ <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+ </java>
+- <echo message="Generating history of changes (fr)" />
+- <java fork="true" dir="build/doc/JmolHistory"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="ChangeLog_fr.html" />
+- <arg value="../../../doc/source/JmolHistory_fr.xml" />
+- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+- <arg value="lang=fr" />
+- </java>
+- <echo message="Generating history of changes (nl)" />
+- <java fork="true" dir="build/doc/JmolHistory"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="ChangeLog_nl.html" />
+- <arg value="../../../doc/source/JmolHistory_nl.xml" />
+- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+- <arg value="lang=nl" />
+- </java>
+ </target>
+
+ <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"
+@@ -957,24 +879,6 @@ + <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />
+ <arg value="../${docbook-xsl}/html/docbook.xsl" />
+ </java>
+- <echo message="Generating developer's guide (fr)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolDevelopersGuide_fr.html" />
+- <arg value="../../doc/source/JmolDevelopersGuide_fr.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+- <echo message="Generating developer's guide (de)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolDevelopersGuide_de.html" />
+- <arg value="../../doc/source/JmolDevelopersGuide_de.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+ </target>
+
+ <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"
+@@ -988,24 +892,6 @@ + <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />
+ <arg value="../${docbook-xsl}/html/docbook.xsl" />
+ </java>
+- <echo message="Generating applet guide (fr)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolAppletGuide_fr.html" />
+- <arg value="../../doc/source/JmolAppletGuide_fr.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+- <echo message="Generating applet guide (de)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolAppletGuide_de.html" />
+- <arg value="../../doc/source/JmolAppletGuide_de.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+ </target>
+
+ <target name="test" id="test" depends="main,compile-tests">
+@@ -1036,12 +922,4 @@ + <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />
+ </target>
+
+- <!-- i18n stuff -->
+- <target name="main-i18n" depends="classes">
+- <ant antfile="build-i18n.xml" target="main-i18n"/>
+- </target>
+- <target name="spotless-i18n">
+- <ant antfile="build-i18n.xml" target="spotless-i18n"/>
+- </target>
+-
+ </project>
diff --git a/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch new file mode 100644 index 000000000000..0a43faaf653d --- /dev/null +++ b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch @@ -0,0 +1,330 @@ +--- orig-build.xml 2012-05-31 13:42:43.943062427 -0500 ++++ build.xml 2012-05-31 14:01:01.691982062 -0500 +@@ -52,8 +52,6 @@ +
+ <property file="proxy.properties" />
+
+- <import file="tools/build-i18n.xml"/>
+-
+ <path id="project.class.path">
+ <fileset dir="${lib.dir}">
+ <include name="*.jar" />
+@@ -111,10 +109,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolGuide.docbook.xml, guide/*.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolUserGuide_fr/index.html">
+- <srcfiles dir="doc/source"
+- includes="JmolGuide_fr.docbook.xml, guide/*_fr.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -124,14 +118,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolHistory.xml,JmolHistoryToHtml.xsl,history/changes.xml" />
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolHistory_fr.xml,JmolHistoryToHtml.xsl,history/changes_fr.xml" />
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_nl.html">
+- <srcfiles dir="doc/source"
+- includes="JmolHistory_nl.xml,JmolHistoryToHtml.xsl,history/changes_nl.xml" />
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -141,14 +127,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolDevelopersGuide.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolDevelopersGuide_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolDevelopersGuide_fr.docbook.xml"/>
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolDevelopersGuide_de.html">
+- <srcfiles dir="doc/source"
+- includes="JmolDevelopersGuide_de.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -158,14 +136,6 @@ + <srcfiles dir="doc/source"
+ includes="JmolAppletGuide.docbook.xml, applet/*.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolAppletGuide_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolAppletGuide_fr.docbook.xml, applet/*_fr.docbook.xml"/>
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolAppletGuide_de.html">
+- <srcfiles dir="doc/source"
+- includes="JmolAppletGuide_de.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -388,17 +358,12 @@ + </target>
+
+ <target name="jar" id="jar"
+- depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">
++ depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars">
+ <copy todir="${classes.dir}/org/openscience/jmol/Data/guide" >
+ <fileset dir="build/doc/JmolUserGuide">
+ <include name="**/*.html" />
+ </fileset>
+ </copy>
+- <copy todir="${classes.dir}/org/openscience/jmol/Data/guide_fr" >
+- <fileset dir="build/doc/JmolUserGuide_fr">
+- <include name="**/*.html" />
+- </fileset>
+- </copy>
+ <copy todir="${classes.dir}/org/openscience/jmol/Data" >
+ <fileset dir="build/doc/JmolHistory">
+ <include name="**/*.html" />
+@@ -603,18 +568,6 @@ + <fileset dir="${appletjars.dir}" includes="**/*"/>
+ </jar>
+
+- <for list="${all.JmolApplet.languages}" delimiter=","
+- param="current.Jmol.language">
+- <sequential>
+- <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+- manifest="manifest/applet_i18n.txt" >
+- <fileset dir="${applet.classes.dir}">
+- <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
+- </fileset>
+- </jar>
+- </sequential>
+- </for>
+-
+ <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
+ <fileset dir="${applet.classes.dir}">
+ <include name="org/jmol/minimize/**" />
+@@ -729,7 +682,6 @@ + <include name="org/jmol/constant/**" />
+ <include name="org/jmol/g3d/**" />
+ <include name="org/jmol/geodesic/**" />
+- <include name="org/jmol/i18n/**" />
+ <include name="org/jmol/modelset/**" />
+ <include name="org/jmol/script/**" />
+ <include name="org/jmol/shape/**" />
+@@ -755,7 +707,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
+- <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
+ </indexjars>
+ </jar>
+ <!-- changes to this must be replicated below for the signed applet -->
+@@ -868,16 +819,6 @@ + keystore="selfSignedCertificate/selfSignedCertificate.store"
+ storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+
+- <for list="${all.JmolApplet.languages}" delimiter=","
+- param="current.Jmol.language">
+- <sequential>
+- <signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+- signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n_@{current.Jmol.language}.jar"
+- keystore="selfSignedCertificate/selfSignedCertificate.store"
+- storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+- </sequential>
+- </for>
+-
+ <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
+ <!-- this one must be treated specially because of jar indexing
+ we cannot simply rename the jar file, because the index has
+@@ -905,7 +846,6 @@ + <include name="org/jmol/shape/**" />
+ <include name="org/jmol/viewer/**" />
+ <include name="org/jmol/util/**" />
+- <include name="org/jmol/i18n/**" />
+ </fileset>
+ <indexjars>
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Console.jar" />
+@@ -924,7 +864,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSurface.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Symmetry.jar" />
+- <fileset dir="${jmol.applet.build.dir}" includes="JmolAppletSigned0_i18n_*.jar" />
+ </indexjars>
+ </jar>
+ <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"
+@@ -963,18 +902,6 @@ + </fileset>
+ </jar>
+
+- <for list="${all.JmolApplet.languages}" delimiter=","
+- param="current.Jmol.language">
+- <sequential>
+- <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+- manifest="manifest/applet_i18n.txt" >
+- <fileset dir="${applet.classes.dir}">
+- <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
+- </fileset>
+- </jar>
+- </sequential>
+- </for>
+-
+ <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
+ <fileset dir="${applet.classes.dir}">
+ <include name="org/jmol/minimize/**" />
+@@ -1088,7 +1015,6 @@ + <include name="org/jmol/constant/**" />
+ <include name="org/jmol/g3d/**" />
+ <include name="org/jmol/geodesic/**" />
+- <include name="org/jmol/i18n/**" />
+ <include name="org/jmol/modelset/**" />
+ <include name="org/jmol/script/**" />
+ <include name="org/jmol/shape/**" />
+@@ -1114,7 +1040,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
+- <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
+ </indexjars>
+ </jar>
+ <!-- changes to this must be replicated below for the signed applet -->
+@@ -1123,7 +1048,7 @@ + </target>
+
+ <target name="dist" id="dist"
+- depends="doc,main-i18n,main,signed-applet">
++ depends="doc,main,signed-applet">
+ <!-- first build binary distribution -->
+ <delete dir="build/dist/jmol-${version}"/>
+ <mkdir dir="build/dist/jmol-${version}"/>
+@@ -1183,7 +1108,6 @@ + <fileset dir=".">
+ <include name="applet.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -1278,7 +1202,6 @@ + <fileset dir=".">
+ <include name="apisio.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -1374,7 +1297,7 @@ + <target name="xclean" id="xclean">
+ </target>
+
+- <target name="spotless" id="spotless" depends="clean,spotless-i18n">
++ <target name="spotless" id="spotless" depends="clean">
+ <delete dir="build"/>
+ <delete dir="${javadoc.dir}"/>
+ <delete dir="packaging/rpm/dist"/>
+@@ -1438,16 +1361,6 @@ + <arg value="../../../doc/source/JmolGuide.docbook.xml" />
+ <arg value="../../${docbook-xsl}/html/chunk.xsl" />
+ </java>
+- <echo message="Generating user's guide (fr)" />
+- <mkdir dir="build/doc/JmolUserGuide_fr" />
+- <java fork="true" dir="build/doc/JmolUserGuide_fr"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <jvmarg value="${proxyHost}" />
+- <jvmarg value="${proxyPort}" />
+- <arg value="../../../doc/source/JmolGuide_fr.docbook.xml" />
+- <arg value="../../${docbook-xsl}/html/chunk.xsl" />
+- </java>
+ </target>
+
+ <target name="jmolHistory" id="jmolHistory"
+@@ -1462,26 +1375,6 @@ + <arg value="../../../doc/source/JmolHistory.xml" />
+ <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+ </java>
+- <echo message="Generating history of changes (fr)" />
+- <java fork="true" dir="build/doc/JmolHistory"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="ChangeLog_fr.html" />
+- <arg value="../../../doc/source/JmolHistory_fr.xml" />
+- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+- <arg value="lang=fr" />
+- </java>
+- <echo message="Generating history of changes (nl)" />
+- <java fork="true" dir="build/doc/JmolHistory"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="ChangeLog_nl.html" />
+- <arg value="../../../doc/source/JmolHistory_nl.xml" />
+- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+- <arg value="lang=nl" />
+- </java>
+ </target>
+
+ <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"
+@@ -1495,24 +1388,6 @@ + <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />
+ <arg value="../${docbook-xsl}/html/docbook.xsl" />
+ </java>
+- <echo message="Generating developer's guide (fr)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolDevelopersGuide_fr.html" />
+- <arg value="../../doc/source/JmolDevelopersGuide_fr.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+- <echo message="Generating developer's guide (de)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolDevelopersGuide_de.html" />
+- <arg value="../../doc/source/JmolDevelopersGuide_de.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+ </target>
+
+ <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"
+@@ -1526,24 +1401,6 @@ + <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />
+ <arg value="../${docbook-xsl}/html/docbook.xsl" />
+ </java>
+- <echo message="Generating applet guide (fr)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolAppletGuide_fr.html" />
+- <arg value="../../doc/source/JmolAppletGuide_fr.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+- <echo message="Generating applet guide (de)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolAppletGuide_de.html" />
+- <arg value="../../doc/source/JmolAppletGuide_de.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+ </target>
+
+ <target name="test" id="test" depends="main,compile-tests">
+@@ -1575,12 +1432,4 @@ + <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />
+ </target>
+
+- <!-- i18n stuff -->
+- <target name="main-i18n" depends="classes">
+- <ant antfile="tools/build-i18n.xml" target="main-i18n"/>
+- </target>
+- <target name="spotless-i18n">
+- <ant antfile="tools/build-i18n.xml" target="spotless-i18n"/>
+- </target>
+-
+ </project>
diff --git a/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild b/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild new file mode 100644 index 000000000000..589cc469b42f --- /dev/null +++ b/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild @@ -0,0 +1,100 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 +WEBAPP_OPTIONAL="yes" + +inherit eutils webapp java-pkg-2 java-ant-2 + +MY_P=Jmol + +DESCRIPTION="Java molecular viever for 3-D chemical structures" +HOMEPAGE="http://jmol.sourceforge.net/" +SRC_URI=" + mirror://sourceforge/${PN}/${MY_P}-${PV}-full.tar.gz + https://dev.gentoo.org/~jlec/distfiles/${PN}-selfSignedCertificate.store.tar" + +WEBAPP_MANUAL_SLOT="yes" +SLOT="0" +KEYWORDS="~amd64 ~x86" +LICENSE="LGPL-2.1" +IUSE="client-only vhosts" + +COMMON_DEP=" + dev-java/commons-cli:1 + dev-java/itext:0 + sci-libs/jmol-acme:0 + sci-libs/vecmath-objectclub:0" + +RDEPEND=">=virtual/jre-1.4 + ${COMMON_DEP}" +DEPEND=">=virtual/jdk-1.4 + !client-only? ( ${WEBAPP_DEPEND} ) + ${COMMON_DEP}" + +pkg_setup() { + use client-only || webapp_pkg_setup + java-pkg-2_pkg_setup +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}/${PN}-nointl.patch \ + "${FILESDIR}"/${PV}/${PN}-manifest.patch + + mkdir "${S}"/selfSignedCertificate || die "Failed to create Cert directory." + cp "${WORKDIR}"/selfSignedCertificate.store "${S}"/selfSignedCertificate/ \ + || die "Failed to install Cert file." + + rm -v "${S}"/*.jar "${S}"/plugin-jars/*.jar || die + cd "${S}/jars" + +# We still have to use netscape.jar on amd64 until a nice way to include plugin.jar comes along. + if use amd64; then + mv -v netscape.jar netscape.tempjar || die "Failed to move netscape.jar." + rm -v *.jar *.tar.gz || die "Failed to remove jars." + mv -v netscape.tempjar netscape.jar || die "Failed to move netscape.tempjar." + fi + + java-pkg_jar-from vecmath-objectclub vecmath-objectclub.jar vecmath1.2-1.14.jar + java-pkg_jar-from itext iText.jar itext-1.4.5.jar + java-pkg_jar-from jmol-acme jmol-acme.jar Acme.jar + java-pkg_jar-from commons-cli-1 commons-cli.jar commons-cli-1.0.jar + + mkdir -p "${S}/build/appjars" || die +} + +src_compile() { + # prevent absorbing dep's classes + eant -Dlibjars.uptodate=true main +} + +src_install() { + java-pkg_dojar build/Jmol.jar + dohtml -r build/doc/* || die "Failed to install html docs." + dodoc *.txt doc/*license* || die "Failed to install licenses." + + java-pkg_dolauncher ${PN} --main org.openscience.jmol.app.Jmol \ + --java_args "-Xmx512m" + + if ! use client-only ; then + webapp_src_preinst + cp Jmol.js build/Jmol.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp build/JmolApplet*.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp applet.classes "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp -r build/classes/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp -r build/appletjars/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp "${FILESDIR}"/caffeine.xyz "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp "${FILESDIR}"/index.html "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + + webapp_src_install + fi +} + +pkg_postinst() { + use client-only || webapp_pkg_postinst +} + +pkg_prerm() { + use client-only || webapp_pkg_prerm +} diff --git a/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild b/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild new file mode 100644 index 000000000000..2b78a243a22d --- /dev/null +++ b/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild @@ -0,0 +1,98 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 +WEBAPP_OPTIONAL="yes" + +inherit eutils webapp java-pkg-2 java-ant-2 + +MY_P=Jmol + +DESCRIPTION="Java molecular viever for 3-D chemical structures" +HOMEPAGE="http://jmol.sourceforge.net/" +SRC_URI=" + mirror://sourceforge/${PN}/${MY_P}-${PV}-full.tar.gz + https://dev.gentoo.org/~jlec/distfiles/${PN}-selfSignedCertificate.store.tar" + +LICENSE="LGPL-2.1" +KEYWORDS="~x86 ~amd64" +IUSE="+client-only vhosts" + +WEBAPP_MANUAL_SLOT="yes" +SLOT="0" + +COMMON_DEP=" + dev-java/commons-cli:1 + dev-java/itext:0 + sci-libs/jmol-acme:0 + sci-libs/vecmath-objectclub:0 + sci-libs/naga" +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEP}" +DEPEND=">=virtual/jdk-1.5 + dev-java/saxon:6.5 + !client-only? ( ${WEBAPP_DEPEND} ) + ${COMMON_DEP}" + +pkg_setup() { + use client-only || webapp_pkg_setup + java-pkg-2_pkg_setup +} + +src_prepare() { + epatch "${FILESDIR}"/${P}-nointl.patch + + rm -v "${S}"/*.jar "${S}"/plugin-jars/*.jar || die + cd "${S}/jars" + +# We still have to use netscape.jar on amd64 until a nice way to include plugin.jar comes along. + if use amd64; then + mv -v netscape.jar netscape.tempjar || die "Failed to move netscape.jar." + rm -v *.jar *.tar.gz || die "Failed to remove jars." + mv -v netscape.tempjar netscape.jar || die "Failed to move netscape.tempjar." + fi + + java-pkg_jar-from vecmath-objectclub vecmath-objectclub.jar vecmath1.2-1.14.jar + java-pkg_jar-from itext iText.jar itext-1.4.5.jar + java-pkg_jar-from jmol-acme jmol-acme.jar Acme.jar + java-pkg_jar-from commons-cli-1 commons-cli.jar commons-cli-1.0.jar + java-pkg_jar-from naga + java-pkg_jar-from --build-only saxon-6.5 saxon.jar + + mkdir -p "${S}/build/appjars" || die +} + +src_compile() { + # prevent absorbing dep's classes + eant -Dlibjars.uptodate=true main +} + +src_install() { + java-pkg_dojar build/Jmol.jar + dohtml -r build/doc/* || die "Failed to install html docs." + dodoc *.txt doc/*license* || die "Failed to install licenses." + + java-pkg_dolauncher ${PN} --main org.openscience.jmol.app.Jmol \ + --java_args "-Xmx512m" + + if ! use client-only ; then + webapp_src_preinst + cp Jmol.js build/Jmol.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp build/JmolApplet*.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp applet.classes "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp -r build/classes/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp -r build/appletjars/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp "${FILESDIR}"/caffeine.xyz "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp "${FILESDIR}"/index.html "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + + webapp_src_install + fi +} + +pkg_postinst() { + use client-only || webapp_pkg_postinst +} + +pkg_prerm() { + use client-only || webapp_pkg_prerm +} diff --git a/sci-chemistry/jmol/metadata.xml b/sci-chemistry/jmol/metadata.xml new file mode 100644 index 000000000000..888f06b55ce5 --- /dev/null +++ b/sci-chemistry/jmol/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="client-only">Install the viewer only, no applet files for httpd + </flag> + </use> + <upstream> + <remote-id type="sourceforge">jmol</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/ksdssp/Manifest b/sci-chemistry/ksdssp/Manifest new file mode 100644 index 000000000000..ddeeb5ddeca0 --- /dev/null +++ b/sci-chemistry/ksdssp/Manifest @@ -0,0 +1,6 @@ +DIST ksdssp-040728.shar 104347 SHA256 0e47de4147724035519f9e845724407c472b99219bbb41c35f3ae1150ae8ef4c SHA512 17c32bea1f32acfd31353d0378fe2a664a8922db8b929da4b9b10ac279013946911acd2a26ab3ab227ae160352c8313dcf742fae8c139a90ac11f772f17a1689 WHIRLPOOL a5f70b8268150388ec1e21e798c4e651b19503293f08ca581a9a9d73e9ffd40c1472988c12bcbac53bdbae5e1557a27f1a2846b28b96bc338500592cc6604748 +EBUILD ksdssp-040728-r1.ebuild 916 SHA256 d5b1500ef1a03dfb4c86400e89a80c906c4ef0f5c43aa4cd02bd346ea7935679 SHA512 90eeb66be6665ca20bbe2dfdf1515d4ff44480dba23c47511501750749f903c2a1f80394e7c026b0ed99f4e545dcf3d70c64bcf8f21b49d945ed6e99878b5d30 WHIRLPOOL e29d0072b5ea130fff81c0c678080e88b8b5594e2bdcd39da8a7e741ce1047490fd3d9a57b43eb8129ac57fe02b45d2e5263ae668e938d94e067a827b677bdd2 +EBUILD ksdssp-040728.ebuild 859 SHA256 be423fb98053392d3282425f150b4ff3b4283558ad3c5b0189a30376b312a4a6 SHA512 9c75d28ec520923f51d9b985d4de7f99a65496797bd897d837e9d6a2abc92fa73e90832451f0c5ee198c6d0bccb2ad79b9189e93dab8efdd40070c2555c325a2 WHIRLPOOL 83623919a1d18801a0c7f200a67d039cb29c8834b1685b78f1d308d1751b3559aa94a5e6205a008c1d2642443e997f82b0278a759153dd2a0c03b6ade8926275 +MISC ChangeLog 2629 SHA256 eb48f2a3e6dcb7a03fbdedc15316f1658f7036eca165ac0d8a1514952c821c2d SHA512 997b093922d1010151c3c9c4dd7f022df24018baa8912e757fad7719001c26d9dd834576766828c37f3131f175e3c39b162bc7451ac40d4d13dbccd339efaf7f WHIRLPOOL b92280037b30e20ee22f87342681d5b91456ae76490c3c7589ae3460d5136658bdf6842c900eb2d162c4f008b375393285abb6b94b4e79fe506f56eb5c8233dc +MISC ChangeLog-2015 905 SHA256 5627e6868ba5f3ac745be12299d4ff5de3ada9e1ce0e033120b48205ef6514d5 SHA512 b07122ee764db12c4f4e3ba387c758c6d1fb1a5d43ae725dd1d2815a99d267048d5b6da4ffab1ea3db3203d20a80ce32b57f87dbe7e2b2949d800fbe72dafc85 WHIRLPOOL 80da6bcc55c4790f12e1cc7a01a8a62c2fd434c95fe2f848c10b20a4d5010142bca7e8ce4ff42b21e52627b390d52096a9d2c1e0f4048d88a78d9e969b8602c1 +MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d diff --git a/sci-chemistry/ksdssp/ksdssp-040728-r1.ebuild b/sci-chemistry/ksdssp/ksdssp-040728-r1.ebuild new file mode 100644 index 000000000000..b5e9e772743f --- /dev/null +++ b/sci-chemistry/ksdssp/ksdssp-040728-r1.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit toolchain-funcs + +DESCRIPTION="An open source implementation of sci-chemistry/dssp" +HOMEPAGE="http://www.cgl.ucsf.edu/Overview/software.html" +SRC_URI="mirror://gentoo/${P}.shar" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="sci-libs/libpdb++" +DEPEND="${RDEPEND} + app-arch/sharutils" + +S="${WORKDIR}"/${PN} + +src_unpack() { + "${EPREFIX}/usr/bin/unshar" "${DISTDIR}"/${A} || die +} + +src_compile() { + emake \ + CXX="$(tc-getCXX)" \ + PDBINCDIR="${EPREFIX}/usr/include/libpdb++" \ + BINDIR="${EPREFIX}/usr/bin" \ + .TARGET="${PN}.csh" \ + .CURDIR="${S}" \ + CC="$(tc-getCXX)" \ + LINKER="$(tc-getCXX)" \ + OPT="${CXXFLAGS}" \ + LFLAGS="${LDFLAGS}" \ + ${PN} ${PN}.csh +} + +src_install() { + dobin ${PN}{,.csh} + dodoc README + dohtml ${PN}.html + doman ${PN}.1 +} diff --git a/sci-chemistry/ksdssp/ksdssp-040728.ebuild b/sci-chemistry/ksdssp/ksdssp-040728.ebuild new file mode 100644 index 000000000000..9dcb38c517d6 --- /dev/null +++ b/sci-chemistry/ksdssp/ksdssp-040728.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit toolchain-funcs + +DESCRIPTION="ksdssp is an open source implementation of dssp" +HOMEPAGE="http://www.cgl.ucsf.edu/Overview/software.html" +SRC_URI="mirror://gentoo/${P}.shar" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="BSD" +IUSE="" + +RDEPEND="sci-libs/libpdb++" +DEPEND=" + ${RDEPEND} + app-arch/sharutils" + +S="${WORKDIR}"/${PN} + +src_unpack() { + "${EPREFIX}"/usr/bin/unshar "${DISTDIR}"/${A} +} + +src_compile() { + emake \ + CXX="$(tc-getCXX)" \ + PDBINCDIR="${EPREFIX}/usr/include/libpdb++" \ + BINDIR="${EPREFIX}/usr/bin" \ + .TARGET="${PN}.csh" \ + .CURDIR="${S}" \ + CC="$(tc-getCXX)" \ + LINKER="$(tc-getCXX)" \ + OPT="${CXXFLAGS}" \ + LFLAGS="${LDFLAGS}" \ + ${PN} ${PN}.csh +} + +src_install() { + dobin ${PN}{,.csh} +} diff --git a/sci-chemistry/ksdssp/metadata.xml b/sci-chemistry/ksdssp/metadata.xml new file mode 100644 index 000000000000..da36ecbfcd6a --- /dev/null +++ b/sci-chemistry/ksdssp/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/mars/Manifest b/sci-chemistry/mars/Manifest new file mode 100644 index 000000000000..9a338b52c4dc --- /dev/null +++ b/sci-chemistry/mars/Manifest @@ -0,0 +1,5 @@ +DIST mars-1.2_linux.tar.gz 2058733 SHA256 c909aa781296d806f89c8d51d89b7345c3e94dd33fc8cc72554573a78ff21b2b SHA512 ba7ec4e94cf5918d22405022c75feabf3e5b345d96075eabf50eb24857101575bb41d15e5686822c2b2f25ba554aa7d7a2b65122dd47304939234a4a884ae4d2 WHIRLPOOL 3cbc59474d776cc79d3c392ae55ce6effe13ae088ff544afd3537daf157adc2c14e1074a38b937e197c87d262f37371dc7109d31f758d25c4c210847a5fb6a79 +EBUILD mars-1.2.ebuild 905 SHA256 22390a299499cb2363edbd0a7cc466eeacff5810e9afa12143d3be8947b28051 SHA512 c2abf892fa6fcbbafafe2dd6446679cd577dc85e744734ec36ebac42259e2e1de41704228ba99eef6da9eb465c3e2f65e0ea26a906da61290a97aa5c9a040ca9 WHIRLPOOL b8d091a4cdb60dfd63d8472aafab5d2854a1cba6aa8c7f423656aab40dab22d2ffa47a5a39742af4ca140064b510b0b40bd6641ab4fe96990ec4b4dc9f99fc60 +MISC ChangeLog 2559 SHA256 f21b13ac2b2fc01411e597932dcf1d1b87c08420320f7c4750f9e0242da10f44 SHA512 b668d3718c5d4582a7acee29f066bfc48114a25b7000fa795bfa68d03db47c212f5589faeba280de6f833a0ad5e6cdfc4702a54c7be1b9cd2bad5f04fc1496bf WHIRLPOOL 6525bb10d8b99ed69b613d59511feecae73688b23551eb7484d4c0bad17e6c023f35a78401aa1760941aa5ae87510cf0aace0a09ee4eacff634babe4240a4e47 +MISC ChangeLog-2015 1088 SHA256 b49db95e4d76f1c8c357d39e1f8f6734a37d91784de14fd87ba588db444dd1ac SHA512 af31fbcf1a876b4b7ff3429df4250b9eb2eef5a1c56103daa9796ac6cd9988d0f8dd1d208f596b3da1f6c7f783f2212291717233179044abd00d518492d936f0 WHIRLPOOL 5aa10a6149743331543205d170c0f8be1ea9624805d090d069b9ab9d68cffbbb42924e1d33c01adf8b89783e8b35f6e2fd6905a644cd22c3a6cd1fbc0e0fc9fd +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/mars/mars-1.2.ebuild b/sci-chemistry/mars/mars-1.2.ebuild new file mode 100644 index 000000000000..5fd849dc4cb1 --- /dev/null +++ b/sci-chemistry/mars/mars-1.2.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +MY_P="${P}_linux" + +DESCRIPTION="Robust automatic backbone assignment of proteins" +HOMEPAGE="http://www.mpibpc.mpg.de/groups/zweckstetter/_links/software_mars.htm" +SRC_URI="http://www.mpibpc.mpg.de/groups/zweckstetter/_software_files/_${PN}/${MY_P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="all-rights-reserved" +IUSE="examples" + +RDEPEND="sci-biology/psipred" +DEPEND="" + +RESTRICT=mirror + +S="${WORKDIR}"/${MY_P} + +QA_PREBUILT="opt/mars/*" + +src_install() { + dobin bin/runmars* + + exeinto /opt/${PN}/ + doexe bin/{${PN},calcJC-S2,runmars*,*.awk} *.awk + insinto /opt/${PN}/ + doins bin/*.{tab,txt} + if use examples; then + insinto /usr/share/${PN}/ + doins -r examples + fi + + cat >> "${T}"/23mars <<- EOF + MARSHOME="${EPREFIX}/opt/${PN}" + EOF + + doenvd "${T}"/23mars +} diff --git a/sci-chemistry/mars/metadata.xml b/sci-chemistry/mars/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/mars/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/massxpert/Manifest b/sci-chemistry/massxpert/Manifest new file mode 100644 index 000000000000..fa9f93013bdd --- /dev/null +++ b/sci-chemistry/massxpert/Manifest @@ -0,0 +1,6 @@ +AUX massxpert-3.4.0-gentoo.patch 2990 SHA256 f70439cd7a35b0582fa0adf862e858124dd0481ae00f455a953fa32a8b9f2aca SHA512 a3901821c803e28ff28f507ccf0509e58184c1ce02fcc76ebf4e36af4130ccee0cbe94212802b8caa03cfad2d09d926ed805b57eaf49ddc49e9045eeba0e6d25 WHIRLPOOL 615d0de16100b7d5324ef9123009c609bc60e8780457de24c919614de4dbef15a9bcba980e70980872306dc9c5d07be95bc423f6b2ce4cd6a6d277d605386622 +DIST massxpert-3.4.0.tar.bz2 16544044 SHA256 b06314722b4cbdf68dc76e55933a79487848c655fc65341a8dbc707ed89cc9e8 SHA512 50e8eaab145ab7fa225725b113d6840168b88db7d2ee194b176bc88eabf4f44c20f8dc0680986d659de1f94f2e0c6ae10d54e17e2d8b3b5aa6a9a9bf57a508de WHIRLPOOL 4578801c2dd4eee7390eadb299f3d55af29d0a48365f96ba6d6488a07792e47882e191f8eda05b6b261d9a972bf7f92f160d4a5fbbcc216ed7ffda32fcfee6ed +EBUILD massxpert-3.4.0.ebuild 1141 SHA256 b0ddfc938b7fd93fa2133c1e7f558f2cebdb8a7c5f7a0bff78f74ef3913c6959 SHA512 4dbcf7902d4722599fce2cf944aaa8df4fbe4dee16305a59f75dfc3d36f0f3ab5fa940e016430a9c43b402170866d74ee2a61407ccd73647ecc5ea17d89c289c WHIRLPOOL 95de82125b46b0528bab5bff4e2703c874367e15f21a7d449fbcefb1b5410b3f1f23925ac580829ce16351632f3563c8279620e3a34a01d84f08c07b792d0a71 +MISC ChangeLog 2860 SHA256 3958398fef3c60a7a0b82675cc34d828583f67cabeda8dbde05b01605deca306 SHA512 cc821191fcdf194f0b3f8198aff97241c1415e88aa5805cfe8d2952b6cf0574594b95f3714e965e20411778eb37c6cc4061b05c1442fa5d4424bb07df5cce8cf WHIRLPOOL 01a1c0fe26e03ae697ec8f4d1b41a318e52824e5cadf46857f75911ad3276c5373c4650b3910c9426d804c29d22cee7af3f613ffc369c1c85e0961552226e949 +MISC ChangeLog-2015 2478 SHA256 dda315b03dd952605e50d5ec8b630ddfde6b13e6fae46af1415497a2ea92ae23 SHA512 6d147c0b33e022d09e2a9c94fbdf546d6f87d2c8494bed149b285130f2abc7bbbfc61312b527675b220c3c75948570deb0e1362e4b234b9d7fafe1006fd76116 WHIRLPOOL b74c3b0f3868249b9a98dc7e6e2170ed068d35bda5d10e3db7a431aef2f6786aae3a742b5dc7db6dd42de693a651b431c82526deadd636a9be8428863239f4db +MISC metadata.xml 395 SHA256 ff36b506db8ce521f60da36cd854503e99050364101687450e46148b074d7db7 SHA512 52ea34dcafba93e544a877ffda573b2fe7f11e060ebf8a5cf193541c7c80642a1499d63980fcf12bdc8200a9e9ccce29c592ec7f6f3b8a6129a23b176f2012d0 WHIRLPOOL 05d83584d85ae6e8d5bca9bd84353d94c4b028a4eba394342179ea578416f9ce30398cdaea683234146f5516ef9ee9c7efdef65ea5b9d8ae45f3e76d367a5cc3 diff --git a/sci-chemistry/massxpert/files/massxpert-3.4.0-gentoo.patch b/sci-chemistry/massxpert/files/massxpert-3.4.0-gentoo.patch new file mode 100644 index 000000000000..fc0fc4f606cf --- /dev/null +++ b/sci-chemistry/massxpert/files/massxpert-3.4.0-gentoo.patch @@ -0,0 +1,91 @@ + CMakeLists.txt | 20 ++++---------------- + gui/configurationSettingsDlg.cpp | 10 ++++------ + 2 files changed, 8 insertions(+), 22 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index fec954b..b87d157 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -24,10 +24,10 @@ SET (CMAKE_VERBOSE_MAKEFILE ON) + ############################################################# + # Enable warnings and treat them as errors, on GNU/Linux only + IF (UNIX) +- SET (PEDANTIC TRUE CACHE BOOL "Should we compile with -Wall -Werror.") ++ SET (PEDANTIC TRUE CACHE BOOL "Should we compile with -Wall.") + + IF (PEDANTIC) +- ADD_DEFINITIONS (-Wall -Werror) ++ ADD_DEFINITIONS (-Wall) + ENDIF (PEDANTIC) + ENDIF (UNIX) + +@@ -64,12 +64,12 @@ IF (UNIX AND NOT APPLE) + # Plugin-specific stuff, some distros set CMAKE_INSTALL_LIBDIR to + # /usr/lib64 (Fedora64, for example) + IF (NOT CMAKE_INSTALL_LIBDIR) +- SET (CMAKE_INSTALL_LIBDIR ${CMAKE_INSTALL_PREFIX}/lib) ++ SET (CMAKE_INSTALL_LIBDIR ${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}) + ENDIF (NOT CMAKE_INSTALL_LIBDIR) + SET (MASSXPERT_PLUGIN_DIR ${CMAKE_INSTALL_LIBDIR}/massxpert/plugins) + + SET (MASSXPERT_LOCALE_DIR ${CMAKE_INSTALL_PREFIX}/share/massxpert/locales) +- SET (MASSXPERT_DOC_DIR ${CMAKE_INSTALL_PREFIX}/share/doc/massxpert) ++ SET (MASSXPERT_DOC_DIR ${CMAKE_INSTALL_PREFIX}/share/doc/massxpert-${VERSION}) + SET (MASSXPERT_USERMAN_DIR ${MASSXPERT_DOC_DIR}/usermanual) + ENDIF (UNIX AND NOT APPLE) + +@@ -144,10 +144,6 @@ IF (${BUILD_PROGRAM}) + ############### + # install stuff + +- # The license file +- INSTALL (FILES COPYING +- DESTINATION ${MASSXPERT_DOC_DIR}) +- + # The desktop file + IF (UNIX AND NOT APPLE) + INSTALL (FILES massxpert.desktop +@@ -185,10 +181,6 @@ IF (${BUILD_DATA}) + ############### + # install stuff + +- # The license file +- INSTALL (FILES COPYING +- DESTINATION ${MASSXPERT_DOC_DIR}) +- + # The manual pages (data) + IF (UNIX AND NOT APPLE) + INSTALL (FILES massxpert-data.7 +@@ -219,10 +211,6 @@ IF (${BUILD_USERMANUAL}) + ############### + # install stuff + +- # The license file +- INSTALL (FILES COPYING +- DESTINATION ${MASSXPERT_DOC_DIR}) +- + # The manual pages (user manual) + IF (UNIX AND NOT APPLE) + INSTALL (FILES massxpert-doc.7 +diff --git a/gui/configurationSettingsDlg.cpp b/gui/configurationSettingsDlg.cpp +index bf595d5..82cad21 100644 +--- a/gui/configurationSettingsDlg.cpp ++++ b/gui/configurationSettingsDlg.cpp +@@ -309,13 +309,11 @@ namespace massXpert + bool + ConfigurationSettingsDlg::checkLocalizationDir(const QDir &dir) + { +- // At the moment there is the french translation: massxpert_fr.qm ++ // Gentoo provides optional installing of translations. ++ // If you decide not to have translations, then this check ++ // would fail. + +- QString filePath(dir.absolutePath() + +- QDir::separator() + +- "massxpert_fr.qm"); +- +- return QFile::exists(filePath); ++ return true; + } + + diff --git a/sci-chemistry/massxpert/massxpert-3.4.0.ebuild b/sci-chemistry/massxpert/massxpert-3.4.0.ebuild new file mode 100644 index 000000000000..068f083b4bf2 --- /dev/null +++ b/sci-chemistry/massxpert/massxpert-3.4.0.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Software suite to predict/analyze mass spectrometric data on (bio)polymers" +HOMEPAGE="http://massxpert.org" +SRC_URI="http://download.tuxfamily.org/${PN}/source/${P}.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug doc" + +RDEPEND="dev-qt/qtsvg:4[debug?]" +DEPEND="${DEPEND} + doc? ( virtual/latex-base )" + +MASSXPERT_LANGS="fr" + +for L in ${MASSXPERT_LANGS}; do + IUSE="${IUSE} linguas_${L}" +done + +src_prepare() { + epatch "${FILESDIR}/${P}-gentoo.patch" + + local langs= + for lingua in ${LINGUAS}; do + if has ${lingua} ${MASSXPERT_LANGS}; then + langs="${langs} ${PN}_${lingua}.qm" + fi + done + + sed -i -e "s/\(SET (massxpert_TRANSLATIONS \).*/\1${langs})/" \ + gui/CMakeLists.txt || die "setting up translations failed" +} + +src_configure() { + local mycmakeargs=( + -DBUILD_PROGRAM=1 + -DBUILD_DATA=1 + ) + use doc && mycmakeargs+=( -DBUILD_USERMANUAL=1 ) + + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + doicon "gui/images/${PN}-icon-32.xpm" + dodoc TODO +} diff --git a/sci-chemistry/massxpert/metadata.xml b/sci-chemistry/massxpert/metadata.xml new file mode 100644 index 000000000000..33ffde3e6f9e --- /dev/null +++ b/sci-chemistry/massxpert/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription lang="en"> +Prediction and analysis of mass spectrometric data for proteomic projects. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/mdanalysis/Manifest b/sci-chemistry/mdanalysis/Manifest new file mode 100644 index 000000000000..997ce8dd6822 --- /dev/null +++ b/sci-chemistry/mdanalysis/Manifest @@ -0,0 +1,5 @@ +DIST MDAnalysis-0.7.7.tar.gz 3262287 SHA256 9dd72b776bf7f2be83da562a638895a94f629422798cc309c14965795847eac1 SHA512 c26085c767ec213d5aa27709029e5a3b9df786c10e23e3841ffc9644e2fd66c8add0358f013c51a95fa3452c5c900b44901db736830504b669916ea45a924712 WHIRLPOOL 2acaa02d641d67bef4cd9ec311c787f57884d83bf350b46af9e862ca6d3a03a6d4ff3d71a2e866f5ab57e29036c5a3182a167e3bcc492667e9a5a60778de0b39 +EBUILD mdanalysis-0.7.7.ebuild 876 SHA256 43ce1a47db5621a2ee7c5577b6903b945faa9acaba35e0c142e398b39c44d73c SHA512 f541e70a7c757fa5ba9a819e51c6a0c5042c3f72cac7c2624e499a472ca949ad9b1fe02da078dfca5fd17c01ed7d7be8b00710a20efb90a7c1e6abcc2a3cfcc2 WHIRLPOOL e8282e5dbc4a67f8f7fef341d47db40e243791a9efbc59e822a0a49050ffbf668814ada37481835a62891da401bb3ba75d9b19f160ae313eec26a6380b86cbd9 +MISC ChangeLog 2753 SHA256 db81c2ed89028683767bed60aa5fdda7fae3692a800b0e24b14cecaef6d86650 SHA512 80a7899447df98433322f2564f7b2d44ff2cc40934318f7a7f683525d8a0ef2d7f55783026e64be4fdafef3ce04fac66151d071aed224884c1d963888711fd55 WHIRLPOOL aef8b2c8d7362d9184ce6b76a5fb45b3d690963df9451f4de6adb902577ba3c78b201286826662988f7bc325b554c2cfd1c003264f61d268ebf815975c5e1854 +MISC ChangeLog-2015 483 SHA256 1fbd6370707b4a110ff6a86069989719cd766a69264b7f76d1d6641023341f41 SHA512 86ab28472b125d6379a8c97d4112b6da2c38090999af7c57e56e3fc3b517e3f5faa1bc2e21d471fc39672df79150deba9586f13642780be790ac37004b4a0321 WHIRLPOOL 2994606d428dddbef647ca2f4e2603945a7c965ed5f573a58edd695ee320f6ccea1d1cff999c683178930dc8aeae0204455171b17f51e911d665170763832ed3 +MISC metadata.xml 259 SHA256 bbfbeb80ffccffa8e7f837d2c93e994bbe024d565ae3a31d30c6646e80a684c8 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706 WHIRLPOOL 75b8dd1a97dde63f9cc9f73b5951eaf54579460763ef7cbe6f3a9a0739070601d762152ea00df8b476b80e92e5c29b611a494bac5ab747298942530cabe0ee84 diff --git a/sci-chemistry/mdanalysis/mdanalysis-0.7.7.ebuild b/sci-chemistry/mdanalysis/mdanalysis-0.7.7.ebuild new file mode 100644 index 000000000000..763061028d4e --- /dev/null +++ b/sci-chemistry/mdanalysis/mdanalysis-0.7.7.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +MY_PN="MDAnalysis" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="A python library to analyze and manipulate molecular dynamics trajectories" +HOMEPAGE="http://www.mdanalysis.org/" +SRC_URI="https://mdanalysis.googlecode.com/files/${MY_P}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + sci-biology/biopython[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/scientificpython[${PYTHON_USEDEP}] + dev-python/GridDataFormats[${PYTHON_USEDEP}] + dev-python/netcdf4-python[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND} + test? ( dev-python/nose[${PYTHON_USEDEP}] )" + +S="${WORKDIR}"/${MY_P} diff --git a/sci-chemistry/mdanalysis/metadata.xml b/sci-chemistry/mdanalysis/metadata.xml new file mode 100644 index 000000000000..8425c0d53cb0 --- /dev/null +++ b/sci-chemistry/mdanalysis/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/metadata.xml b/sci-chemistry/metadata.xml new file mode 100644 index 000000000000..c60d4c31553f --- /dev/null +++ b/sci-chemistry/metadata.xml @@ -0,0 +1,38 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE catmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<catmetadata> + <longdescription lang="en"> + The sci-chemistry category contains software that can be used + in chemistral scientific environments. + </longdescription> + <longdescription lang="de"> + Die Kategorie sci-chemistry enthält Software, welche in chemischen + und chemietechnischen Umgebungen genutzt werden kann. + </longdescription> + <longdescription lang="es"> + La categoría sci-chemistry contiene programas que pueden ser utilizados + en entornos relacionados con la química. + </longdescription> + <longdescription lang="ja"> + sci-chemistryカテゴリーには化学の科学的な分野に利用される + フトウェアが含まれています。 + </longdescription> + <longdescription lang="nl"> + De sci-chemistry categorie bevat software die in scheikundige omgevingen + gebruikt kan worden. + </longdescription> + <longdescription lang="vi"> + Nhóm sci-chemistry chứa các phần mềm dùng trong hoá học. + </longdescription> + <longdescription lang="it"> + La categoria sci-chemistry contiene programmi per la chimica. + </longdescription> + <longdescription lang="pt"> + A categoria sci-chemistry contém programas que podem ser usados + em ambientes relacionados a química. + </longdescription> + <longdescription lang="pl"> + Kategoria sci-chemistry zawiera programy naukowe związane z chemią. + </longdescription> +</catmetadata> + diff --git a/sci-chemistry/mm-align/Manifest b/sci-chemistry/mm-align/Manifest new file mode 100644 index 000000000000..c8f304163ef8 --- /dev/null +++ b/sci-chemistry/mm-align/Manifest @@ -0,0 +1,6 @@ +AUX CMakeLists.txt 142 SHA256 29f1003a81107cc60a17f0fe26fb59b91a28fb3e46224552b856bf505f777ae0 SHA512 edeaeed165d8b89edaf0f8e1e50870c61fa1446e3b8febb367451cf93d160679e042131256e3a5d52406a4f1731f94414550cacb8dc023246dbda12c6586a00c WHIRLPOOL ceb7508e26e61a3ad30ee623554877f95f9d01cb81963debdc6e912777d9bd365b0aafd6cfaa09f811f458b7d361578f018d6c39bce2f5e443d72175fcfde5f4 +DIST MM-align-20120321.tar.xz 20072 SHA256 0158a93a06257b885630ab7bed3b7bf8dca2ee12217c84d019829a1e34f3eeb3 SHA512 193c3b16b2d9fb0aaacf18b203fcf0240de7b11b4c0ce99fc571c277aa6e624b7b8b4df625e34433a5dec4349bb5bf6ae0368609c1738337923cf3b4d06428bc WHIRLPOOL 42ccb05d05d668f7a99c6d1f60ca55663e68568fb7b4277ac9db3c05c8739969c1a1c63dfd8edca7cd1fa0e064bc9a12721759a0418c6d3f7656cd775b89db87 +EBUILD mm-align-20120321.ebuild 512 SHA256 411bc93fcb20e8833d08f35062d215ea5887852a03df45a914c104cec3c86c6e SHA512 0da84f046c7aaa3023a0512397f09b298a5d99ea8623126aa1a4c2a18e3fc9b93eab635253a424e149013d39c47e1ab608edb68b540edb40fc3db7e055fdded8 WHIRLPOOL 6c97a424fe997b369dcec8ce6687439829300823c7fb6912bf71e226b1ae8056a86e565ceff44dca65cb3cbbb5487882160013ca239fc122c16e963d2755ccc5 +MISC ChangeLog 2632 SHA256 93f26f7e615f13894363b5ffecd0f564c6c954a2c3456e0eb6e287400905042c SHA512 2eab7ede7faa855c7f61d2e4577803f2da23d1116748255128ec541fa21270344a2374f59c459f328ac245535662ce13a86a59ce88ae7b667940c4e940e963bc WHIRLPOOL a7a5a8d78312d854c6b74dc86c26d572c6361005ae76c97ae4d236894a797ae66a8ad97b06edd9beaa38ed44aa7522ac5b3799c8b779d4464536989c7a133183 +MISC ChangeLog-2015 507 SHA256 0484f971d061116d2dd41688307a94cc7a9d1232734ef8cfa13b5690db496e40 SHA512 c3f5fd7c9c972ba91d6ac0a829b8676c212af917b47974d604ccadab9b45def6e046d5246504d4d13aebfdf20bfbff03d2d47a4778bc4531bcd7e8b0fb1bb533 WHIRLPOOL 67c7846e20f2986157f1c5c57262411ec6fc627172ef4e910096c3cd032264ff717f341304c1f7c04fefa271f7ba9d8176c76ae3eaa89d01c2cc5a9ca339af7a +MISC metadata.xml 1450 SHA256 cb612ac1f13c4c08f6dad283656dc57a7c720dba29192ad236751661e83ed894 SHA512 6769f81c777dc048f3342a308219623b2119e8f79502c98edab0ebdf0c4cc4584c504ce1c3e6d5e968ecdb9c83e0e40a3344205b0bf33870d3fab832707c62fa WHIRLPOOL 1b091ecf5728f911563a6ee3d0582c618bf7235eb153344f86318bade9c6d0ceb29d344825329435df6f9d278bd39a61b22bef75e168d905b581898743fa2a94 diff --git a/sci-chemistry/mm-align/files/CMakeLists.txt b/sci-chemistry/mm-align/files/CMakeLists.txt new file mode 100644 index 000000000000..635ffdd67418 --- /dev/null +++ b/sci-chemistry/mm-align/files/CMakeLists.txt @@ -0,0 +1,5 @@ +cmake_minimum_required (VERSION 2.6) +project (MM-align Fortran) +add_executable(MMalign MM-align.f) + +install (TARGETS MMalign DESTINATION bin) diff --git a/sci-chemistry/mm-align/metadata.xml b/sci-chemistry/mm-align/metadata.xml new file mode 100644 index 000000000000..5653687f9cfd --- /dev/null +++ b/sci-chemistry/mm-align/metadata.xml @@ -0,0 +1,26 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +MM-align is an algorithm for structurally aligning multiple-chain +protein-protein complexes. The algorithm is built on a heuristic +iteration of a modified Needleman-Wunsch dynamic programming (DP) +algorithm, with the alignment score specified by the inter-complex residue +distances. The multiple chains in each complex are first joined, in every +possible order, and then simultaneously aligned with cross-chain alignments +prevented. The alignments of interface residues are enhanced by an +interface-specific weighting factor. An optimal alignment between two complexes, +as well as the overall TM-score, will be reported for each comparison. +What is the difference between TM-align and MM-align? TM-align is for aligning +monomer protein structures while MM-align is designed for aligning +multiple-chain protein complex structures. Although one can still use TM-align +to align protein complexes after manually joining the chains, this will lead +to suboptimal alignments with unphysical cross alignments. Therefore, the +best result will be obtained if one uses TM-align to monomer structures and +MM-align for multimer structures. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/mm-align/mm-align-20120321.ebuild b/sci-chemistry/mm-align/mm-align-20120321.ebuild new file mode 100644 index 000000000000..d2b42fe2547e --- /dev/null +++ b/sci-chemistry/mm-align/mm-align-20120321.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils fortran-2 + +DESCRIPTION="Protein Complex Structural Alignment" +HOMEPAGE="http://zhanglab.ccmb.med.umich.edu/MM-align/" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/MM-align-${PV}.tar.xz" + +SLOT="0" +LICENSE="tm-align" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}" + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + + cmake-utils_src_prepare +} diff --git a/sci-chemistry/molden/Manifest b/sci-chemistry/molden/Manifest new file mode 100644 index 000000000000..8930478eab42 --- /dev/null +++ b/sci-chemistry/molden/Manifest @@ -0,0 +1,15 @@ +AUX molden-4.7-implicit-dec.patch 225 SHA256 368b5a83f8fae257a48c43f5d3cb10f5d8aedd345d5fdd7dbf73c99295bebeab SHA512 9a76dfdd434849532a8625459663ca81d8a948b20f7ea8296ae8d25a51f6c28b3cab2691be0f7683ff5d5b7ed8d84211ac26a5bb22c27891863a1c04299d8fea WHIRLPOOL 6b50616d308132c2d9082b9a3c0c177422796b1a9539e1766f54597a06d2f4caee19ba92ffebe0741fda49b79c8f74e36212f9323b95f5c744d7b9e398fffc28 +AUX molden-4.8-ambfor.patch 480 SHA256 d3b0f3a1ec8fe2b31dc94e1138b4eafd6b5f105ca637ec773a6d37b2c12872b1 SHA512 9fe52f994e621e4ce578a8cdfa9074ceda522c2426c4b15c4d1de38832eef936de54bd07021489e0e12f420b25179b7a3cb615512d77d4457d9e7c9adae0f475 WHIRLPOOL 02986dc7c849db2a22480ece79c6d0644378e0869f3bec55bdc79aea94c7648b66fcbef7a53adacfcf3fabd02da6f8ff17eab7d303d96702b78eaf535dafa76c +AUX molden-4.8-ldflags.patch 866 SHA256 14346b0f255ac2e7c85321a13112af857c4f55dd5574f007a3a32e61006c947b SHA512 427ec1da9e71b2097164f8fb7448713961f7fdb63b8a51dee23490d6d305129dd12a9e782033588304406dd35aa18ceb7040c32fa09ea38b339f9dc47e0a24a9 WHIRLPOOL c6d98799019a03efa81d32bd5f8922ad1e549b36636cb35cbf8f34a3926ca8ea4f1f6f7f91e8671bb42b0cc44c77e45b8f059e0c5fbb7ecfaf99ddbf1c572d0a +AUX molden-4.8-overflow.patch 714 SHA256 bf25341d0b7dc8f4dd61bb160c345d29fad5e303309c0690d64ad9f69f5b2b79 SHA512 ecc4f4501166a4ed4a1c451901d3aed49e3ad7fd3833cb4419a62b1864e689399ca68562fbc82784813881a003a405d4eea5d0e351a9181cbb164beb702d3765 WHIRLPOOL cc3b75e4ea04aa84fdac498e398dd51ac73657139e8eb663b37924416473d0a86fccf7dc64082a981b701c90d771a98b1cf189cf04b8e3ff9eaaea58db1c7285 +AUX molden-5.0-ambfor.patch 523 SHA256 65611167c51b773f1b64468712a0e075be673d7d460b73629ce85b202b19ebf6 SHA512 f531d3bd50374bf658e710f2e4b649559503b378ab663f03cd9259b9105b6c25eab61318bb3d02814425ecb596802569aa3281741d611d4e1c8fc4da771fd481 WHIRLPOOL 4d4af0277f3680b5814368a2f1db5cca140219cd310d9b1ad54273c35a8eb9975b3a1923ef3a98c0ab7c47a12df7c0960eb8e2dd6218b49e37c23f519c3bee21 +AUX molden-5.0-overflow.patch 341 SHA256 c004c35f1b5c4ff8ae262382e0cac375bd6d6ababad359ad28dcbcaeb223283f SHA512 342b7531179b8a3c3aedff085022d972bd795d2c56ebf4b49fce5ff60e6cc9ea48ed18258af53042ad72aae400f694aec9692bc0b1abfa960bc100ee02f57981 WHIRLPOOL 5f208d32f531bf6a906e1ea68f473836432fae446a1db5644c6f3c4bdf4e154419a628dc81d19e9941f9a4ded6db0d616aeebcaa62c942ac270cef0364c14f4d +DIST molden4.8.tar.gz 2969701 SHA256 314d9b9bdede2fd63d1e2f26e0212711576952244634fc28ea6c97ce2f7029b1 SHA512 11f2406e54a077d044369b5eee4a8a1c1b10f052188d33d4162af0151a1e76a1d5274d8788bbc3610905ff271b0bd2100990b77540a0290ad608bd5c29b839e3 WHIRLPOOL 838d66a4e17651dfd2bab893fa9b36ca8d722c879b9f10adb00c3c4e59974ae73e13060e6a559286c651ab35e1cea084049677277cc4b455e68a95c6c210dcf9 +DIST molden5.0.tar.gz 3063244 SHA256 c9cf8f656adf2f2c7a8b8b64fa07b5feaa9c3ca36c4803e1f58ac33de1cffdc4 SHA512 bf45849bf4efb67bc552767c28a6df6e5106a7d8ac2d73db2c7218412fb6cd2f2785c2be83a8589a5664ba9c0ca052cef5eb155c665ee1f3d6c7fe208f806a6b WHIRLPOOL ab7f1118b000a8df36cbaf23fddabb21bd291a2388e3aa5599e609ffa792bec01bf7df52a98f7e70125b504f7866e48ec6d5ce029ecd0e40c7bab7b8627c5c86 +DIST molden5.5.tar.gz 4934764 SHA256 6514a317486fb4087d94afc929a646c4f30cab7ff79651deeecb30f03212c059 SHA512 45269d2c7a52b3b2bf4fdb5f4ca3912637b3414ff9dfcd0d4f23815b3dcf7a53ffee717420d4fbf286b71c972539e756a440f5e37b7b7325ab312c25fc6c47b0 WHIRLPOOL 952382f26e227236e98deec5350e2617c68003098a8954ee6eebb10c89039ae0abf60aa117f73e02662153838f26bc724f7b16e6facc0cf07d86ba38fa0c03aa +EBUILD molden-4.8-r2.ebuild 1726 SHA256 1798515a1c9351372d7fc3a6b6a0ce2447299b14cc4ec6f7af7b1a364b268d28 SHA512 ca0772ada2086f91150f8a0ab2a86c9a9a6169a89e2c8c0f6b4ab4d368906f5d5d2807cd228e1f42292c6562d980a0e206f568433b396d23c7846beb65dd6f5a WHIRLPOOL d9f4ae3b1353923890cc7eafe9db40aa16a00ed75e841f989e87c84ee7eccd8e55080d8c7481b578feff4c6087c8da87bec3f73abdcb8f028066eeb92dc94a33 +EBUILD molden-5.0.ebuild 1733 SHA256 ccfb1fa9432f29ce6798316291a263084b687e75f060b772fd8c4571b3fedf3f SHA512 0584ad6f157bab063a79b8e095dedec04e6a2f1d05d5483027dc8c7b0b8455956140ae69f9d6749b47ce69db30d62d391e9f7a7e00dba696d73687861d6bd604 WHIRLPOOL 9f062d9279100e5c4b23b7347933a5b46f376c48591001782fc01a351aedee3c37a9fc25ac224a7672d415021c253a7174c9f23688469a884d3395468b016a5e +EBUILD molden-5.5.ebuild 1540 SHA256 448268966551cb3d533261801309a1d545240d3ca3f92e93b9a1f8b2e1b59d3c SHA512 01705f51b1b6992dbbb8e2fcab6cb43f40a3cbf6da1023a0ea12ef626d1995327ee0afd39bd70e0520a8fad015a1a76d5d1e9f3886ef5195fa6b9713d6bcf334 WHIRLPOOL c22f7a9bc26c90c1a479e3625f6bb33ab5ca53314dbf3ae15b03e84b544dcd33883d18fe2d71c496bda93ad59a97f7757f78d6c466a50ce64e933ebc58a01900 +MISC ChangeLog 3477 SHA256 d1245101b44a87ba10f549bad185971f53a35a26e7712c164f35c50724f8a60a SHA512 76269fdf77c0fb13fc8017a3b41cf9d22003e3faefb03a37505628d2485ea870fa29de5a1ae97d4ac632c2cf03076dc93ef11b4755b02c1bfe9b917303d765e4 WHIRLPOOL 623950943678d7d42dd24fbb0b663b8dc841ad453e3609dfc5b7696358025474f313878d48af3f178d8f781fa6102b360900082ea65d4350ac3807e37353af37 +MISC ChangeLog-2015 9211 SHA256 e1334e7e4501109e15dd1abff5d1bd1cd6a192245d4cb01245a69b01f86c9049 SHA512 1b801696d1b4aace4d3e8641dcd4aad87d1ab583708e7061b8ced140d8808d2e6edeaced04fbb557f5982b8f253ace6898eacaa8c7e0eb043a97cf7603b1b741 WHIRLPOOL 8147a0f6963cf3118ca285261b83ca96344e8afac8052e9b81a176a48912cca23b30728d7055b3aa7a408a0268db8162cdcb2c68e9a27e17ee7de795948b718d +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/molden/files/molden-4.7-implicit-dec.patch b/sci-chemistry/molden/files/molden-4.7-implicit-dec.patch new file mode 100644 index 000000000000..dd5aba4f17da --- /dev/null +++ b/sci-chemistry/molden/files/molden-4.7-implicit-dec.patch @@ -0,0 +1,12 @@ +diff --git a/silly.c b/silly.c +index 57d07e8..102156a 100644 +--- a/silly.c ++++ b/silly.c +@@ -13,6 +13,7 @@ + #include <stdio.h> + #include <stdlib.h> + #include <math.h> ++#include <string.h> + + #ifndef WIN32 + #include <GL/gl.h> diff --git a/sci-chemistry/molden/files/molden-4.8-ambfor.patch b/sci-chemistry/molden/files/molden-4.8-ambfor.patch new file mode 100644 index 000000000000..1ececa7f57e9 --- /dev/null +++ b/sci-chemistry/molden/files/molden-4.8-ambfor.patch @@ -0,0 +1,12 @@ +diff -Naur molden4.8/ambfor/makefile molden4.8.new/ambfor/makefile +--- molden4.8/ambfor/makefile 2009-12-19 06:14:32.000000000 -0500 ++++ molden4.8.new/ambfor/makefile 2010-02-25 22:33:41.000000000 -0500 +@@ -32,7 +32,7 @@ + $(LDR) -o ambmd md.o verlet.o allocmd.o $(OBJS) $(LIBS) + + ambfor.o: ambfor.f +- ${FC} -c -g -ffast-math -funroll-loops -m32 -o ambfor.o ambfor.f ++ ${FC} $(FFLAGS) -c ambfor.f -o ambfor.o + + allocmd.o: alloc.c + $(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o diff --git a/sci-chemistry/molden/files/molden-4.8-ldflags.patch b/sci-chemistry/molden/files/molden-4.8-ldflags.patch new file mode 100644 index 000000000000..92fa6c665f3f --- /dev/null +++ b/sci-chemistry/molden/files/molden-4.8-ldflags.patch @@ -0,0 +1,26 @@ +diff --git a/makefile b/makefile +index 81147a3..9e2353e 100644 +--- a/makefile ++++ b/makefile +@@ -224,10 +224,10 @@ all: molden gmolden ambfor/ambfor ambfor/ambmd surf/surf + + + molden: $(OBJS) mpdum.o xwin.o +- $(LDR) -o molden $(OBJS) mpdum.o xwin.o $(LIBS) ++ $(LDR) $(LDFLAGS) -o molden $(OBJS) mpdum.o xwin.o $(LIBS) + + gmolden: $(OBJS) mpdum.o xwingl.o +- $(LDR) -o gmolden $(OBJS) mpdum.o xwingl.o $(LIBSG) ++ $(LDR) $(LDFLAGS) -o gmolden $(OBJS) mpdum.o xwingl.o $(LIBSG) + + ambfor/ambfor: ambfor/*.f ambfor/*.c + $(MAKE) -C ambfor FC=${FC} FFLAGS="${FFLAGS}" LDR="${LDR}" CFLAGS="${CFLAGS}" +@@ -269,7 +269,7 @@ short_wrl: short_wrl.o + # Moldens OpenGL helper program + + moldenogl: oglmol.o silly.o +- $(CC) -o moldenogl oglmol.o silly.o $(LIBSOGL) ++ $(CC) $(LDFLAGS) -o moldenogl oglmol.o silly.o $(LIBSOGL) + + # conversion of CADPAC output to molden format + diff --git a/sci-chemistry/molden/files/molden-4.8-overflow.patch b/sci-chemistry/molden/files/molden-4.8-overflow.patch new file mode 100644 index 000000000000..7cbd7f436f57 --- /dev/null +++ b/sci-chemistry/molden/files/molden-4.8-overflow.patch @@ -0,0 +1,38 @@ + xwin.c | 10 ++++++---- + 1 files changed, 6 insertions(+), 4 deletions(-) + +diff --git a/xwin.c b/xwin.c +index f395909..092edff 100644 +--- a/xwin.c ++++ b/xwin.c +@@ -13552,7 +13552,7 @@ void NewActiveStruct() + #ifdef CRAY + _fcd ztr; + #else +- char ztr; ++ char ztr[4]; + #endif + #endif + +@@ -13650,8 +13650,10 @@ void NewActiveStruct() + */ + clfpstr->ihashz = 0; + #else +- strncpy(&ztr,HetAtm[j],3); +- parhet_(&j1,&ztr); ++ if (HetAtm[j] != NULL) { ++ strncpy(ztr,HetAtm[j],3); ++ parhet_(&j1,ztr); ++ } + #endif + #endif + } +@@ -27353,7 +27355,7 @@ char *errstr; + UpdateZME(); + RedrawScroll(&zscroll); + } +- strcpy(ZMEerr,errstr); ++ strncpy(ZMEerr,errstr,MAXZMEERR); + RedrawStatus(); + } + diff --git a/sci-chemistry/molden/files/molden-5.0-ambfor.patch b/sci-chemistry/molden/files/molden-5.0-ambfor.patch new file mode 100644 index 000000000000..9656ff7a79be --- /dev/null +++ b/sci-chemistry/molden/files/molden-5.0-ambfor.patch @@ -0,0 +1,16 @@ + ambfor/makefile | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/ambfor/makefile b/ambfor/makefile +index 8627a11..dbc23a1 100644 +--- a/ambfor/makefile ++++ b/ambfor/makefile +@@ -47,7 +47,7 @@ ambmd: md.o verlet.o qvdw.o allocmd.o $(OBJS) + $(LDR) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS) + + ambfor.o: ambfor.f +- ${FC} -c -g -ffast-math -funroll-loops -o ambfor.o ambfor.f ++ ${FC} $(FFLAGS) -c -o ambfor.o ambfor.f + + allocmd.o: alloc.c + $(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o diff --git a/sci-chemistry/molden/files/molden-5.0-overflow.patch b/sci-chemistry/molden/files/molden-5.0-overflow.patch new file mode 100644 index 000000000000..4fc406266935 --- /dev/null +++ b/sci-chemistry/molden/files/molden-5.0-overflow.patch @@ -0,0 +1,16 @@ + xwin.c | 10 ++++++---- + 1 files changed, 6 insertions(+), 4 deletions(-) + +diff --git a/xwin.c b/xwin.c +index f395909..092edff 100644 +--- a/xwin.c ++++ b/xwin.c +@@ -27353,7 +27355,7 @@ char *errstr; + UpdateZME(); + RedrawScroll(&zscroll); + } +- strcpy(ZMEerr,errstr); ++ strncpy(ZMEerr,errstr,MAXZMEERR); + RedrawStatus(); + } + diff --git a/sci-chemistry/molden/metadata.xml b/sci-chemistry/molden/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/molden/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/molden/molden-4.8-r2.ebuild b/sci-chemistry/molden/molden-4.8-r2.ebuild new file mode 100644 index 000000000000..f00761130395 --- /dev/null +++ b/sci-chemistry/molden/molden-4.8-r2.ebuild @@ -0,0 +1,76 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils fortran-2 flag-o-matic toolchain-funcs + +MY_P="${PN}${PV}" + +DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac" +HOMEPAGE="http://www.cmbi.ru.nl/molden/" +SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molgraph/${PN}/${MY_P}.tar.gz" + +LICENSE="MOLDEN" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="opengl" + +RDEPEND=" + x11-libs/libXmu + virtual/glu + opengl? ( + media-libs/freeglut + virtual/opengl )" +DEPEND="${RDEPEND} + x11-misc/gccmakedep + app-editors/vim" + # vim provides ex, which the build system uses (surf/Makefile, at least) + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-ambfor.patch \ + "${FILESDIR}"/${P}-overflow.patch \ + "${FILESDIR}"/${P}-ldflags.patch \ + "${FILESDIR}"/${PN}-4.7-implicit-dec.patch + sed \ + -e 's:makedepend:gccmakedep:g' \ + -e "s:/usr/include/sgidefs.h::g" \ + -i surf/Makefile || die + sed 's:shell g77:shell $(FC):g' -i makefile || die +} + +src_compile() { + # Use -mieee on alpha, according to the Makefile + use alpha && append-flags -mieee + + # Honor CC, CFLAGS, FC, and FFLAGS from environment; + # unfortunately a bash bug prevents us from doing typeset and + # assignment on the same line. + typeset -a args + args=( + CC="$(tc-getCC) ${CFLAGS}" \ + FC="$(tc-getFC)" \ + LDR="$(tc-getFC)" \ + FFLAGS="${FFLAGS}" ) + + einfo "Building Molden..." + emake -j1 "${args[@]}" + if use opengl ; then + einfo "Building Molden OpenGL helper..." + emake -j1 "${args[@]}" moldenogl + fi +} + +src_install() { + dobin ${PN} g${PN} + if use opengl ; then + dobin ${PN}ogl + fi + + dodoc HISTORY README REGISTER + cd doc + uncompress * && dodoc * +} diff --git a/sci-chemistry/molden/molden-5.0.ebuild b/sci-chemistry/molden/molden-5.0.ebuild new file mode 100644 index 000000000000..52f4ccdcfed0 --- /dev/null +++ b/sci-chemistry/molden/molden-5.0.ebuild @@ -0,0 +1,76 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils fortran-2 flag-o-matic toolchain-funcs + +MY_P="${PN}${PV}" + +DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac" +HOMEPAGE="http://www.cmbi.ru.nl/molden/" +SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molgraph/${PN}/${MY_P}.tar.gz" + +LICENSE="MOLDEN" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="opengl" + +RDEPEND=" + x11-libs/libXmu + virtual/glu + opengl? ( + media-libs/freeglut + virtual/opengl )" +DEPEND="${RDEPEND} + x11-misc/gccmakedep + app-editors/vim" + # vim provides ex, which the build system uses (surf/Makefile, at least) + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-ambfor.patch \ + "${FILESDIR}"/${P}-overflow.patch \ + "${FILESDIR}"/${PN}-4.8-ldflags.patch \ + "${FILESDIR}"/${PN}-4.7-implicit-dec.patch + sed \ + -e 's:makedepend:gccmakedep:g' \ + -e "s:/usr/include/sgidefs.h::g" \ + -i surf/Makefile || die + sed 's:shell g77:shell $(FC):g' -i makefile || die +} + +src_compile() { + # Use -mieee on alpha, according to the Makefile + use alpha && append-flags -mieee + + # Honor CC, CFLAGS, FC, and FFLAGS from environment; + # unfortunately a bash bug prevents us from doing typeset and + # assignment on the same line. + typeset -a args + args=( + CC="$(tc-getCC) ${CFLAGS}" \ + FC="$(tc-getFC)" \ + LDR="$(tc-getFC)" \ + FFLAGS="${FFLAGS}" ) + + einfo "Building Molden..." + emake -j1 "${args[@]}" + if use opengl ; then + einfo "Building Molden OpenGL helper..." + emake -j1 "${args[@]}" moldenogl + fi +} + +src_install() { + dobin ${PN} g${PN} + if use opengl ; then + dobin ${PN}ogl + fi + + dodoc HISTORY README REGISTER + cd doc + uncompress * && dodoc * +} diff --git a/sci-chemistry/molden/molden-5.5.ebuild b/sci-chemistry/molden/molden-5.5.ebuild new file mode 100644 index 000000000000..9bc1635e9353 --- /dev/null +++ b/sci-chemistry/molden/molden-5.5.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils fortran-2 flag-o-matic toolchain-funcs + +MY_P="${PN}${PV}" + +DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac" +HOMEPAGE="http://www.cmbi.ru.nl/molden/" +SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molgraph/${PN}/${MY_P}.tar.gz" + +LICENSE="MOLDEN" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="opengl" + +RDEPEND=" + x11-libs/libXmu + virtual/glu + opengl? ( + media-libs/freeglut + virtual/opengl )" +DEPEND="${RDEPEND} + x11-misc/gccmakedep + app-editors/vim" + # vim provides ex, which the build system uses (surf/Makefile, at least) + +S="${WORKDIR}/${MY_P}" + +PATCHES=( + "${FILESDIR}"/${PN}-5.0-ambfor.patch + "${FILESDIR}"/${PN}-5.0-overflow.patch + "${FILESDIR}"/${PN}-4.8-ldflags.patch + "${FILESDIR}"/${PN}-4.7-implicit-dec.patch +) + +src_prepare() { + default + sed \ + -e 's:makedepend:gccmakedep:g' \ + -i surf/Makefile || die + sed 's:shell g77:shell $(FC):g' -i makefile || die +} + +src_compile() { + local args=() + + # Use -mieee on alpha, according to the Makefile + use alpha && append-flags -mieee + + args=( + CC="$(tc-getCC) ${CFLAGS}" + FC="$(tc-getFC)" + LDR="$(tc-getFC)" + FFLAGS="${FFLAGS}" + ) + + einfo "Building Molden..." + emake -j1 "${args[@]}" + if use opengl ; then + einfo "Building Molden OpenGL helper..." + emake -j1 "${args[@]}" moldenogl + fi +} + +src_install() { + dobin ${PN} g${PN} $(usex opengl ${PN}ogl "") + + dodoc HISTORY README REGISTER + cd doc || die + uncompress * && dodoc * +} diff --git a/sci-chemistry/moldy/Manifest b/sci-chemistry/moldy/Manifest new file mode 100644 index 000000000000..1966e387b8d1 --- /dev/null +++ b/sci-chemistry/moldy/Manifest @@ -0,0 +1,6 @@ +AUX 2.16e-as-needed.patch 3226 SHA256 304343516efed00901c996a8948705047a7fa46a4b5c26243ded0bf73118e98b SHA512 b32461bb052c908106f0f8d74be4eba52daa41ba592a7ba6083edc2a54c4a14003cf33560572e57f2b370ad5ea1f703e388855e8e7fa67ccec40e3015a8f5803 WHIRLPOOL bdef755c8d8dd0e6ccfaa20537b211a44886e8c6db1c704bec0c5457662e320c9a3127c1f5dbc9a7ca4cd1350f27e13787f8c734a41b2e9fc1f6d5df6c52052e +DIST moldy-2.16e.tar.gz 488410 SHA256 51abefc5e7de355022f48084382c30e72738cc1f21cd3d67fde7f047f1822ea8 SHA512 b672f4e5c8843277d1b66eedf5f7ad87be0b4c014e0d6bfda4ef941cd9bfeec68d94a361e28531cc3794ee2e4a6937f15c462c69f9adcfcfe5254c3c677fe877 WHIRLPOOL 390237d87580d2f6e438dfcc01e5f47353f72392090c576785f0143482fced508c4a7cff737c9134ecda0b467565260fdb97dcc45b2b64909641da6f8d031448 +EBUILD moldy-2.16e-r2.ebuild 1811 SHA256 d352c930e7585a67ebbe0862ba477477d018981a97a8041137481341fa6e1628 SHA512 6f6280a30cef11539d27b6efa5326f3ca5b365e179dbc3f3e2b5b237b92e66786f4969ebd7ff1d67b3e3f53f2c52a3bc46ccb5ba45078db17e7d325c4640fff0 WHIRLPOOL afdf9d73d931de6d3e034fd18869ed9c1566e6bf6d6ccb8c34f4335db69704c3cf2056013eefcb0044630aa1636a0e750ed8659228e97cf2af70b42e61a3ce98 +MISC ChangeLog 2462 SHA256 cba96a830b9a475ac248ca7f51c62de46372967f328749eecbe77fff1df0eded SHA512 4e584b34d985666849087406f4ea049a4dba0cdadeb0c82ebc5f2e5545fbe40191eceef923b8a2699e7831e938cdbb20936fe11d54cd3434b7853a2c2b83a8ec WHIRLPOOL eb2786390b446556792de8f948a5bb69ef37e1b44c6314c31fd8de776c37af822fdb505be39cf6bf6fc85004bfb911b8e42cbb635b6af2e70ab2f7b43c5616a2 +MISC ChangeLog-2015 4173 SHA256 c32e66feea954789bdef0e3903bb406af1fc1661ee258d020a9138a63be2fbb6 SHA512 3bdb6d9e787956d2ef14f3cb8296637f08750e8fa28ade69b478c0320e7ee5e206960dc9147a1bf9d42f52b5796569eb948409b492af1ff3d23e310f9fe5785d WHIRLPOOL 639c1d1745433d4a08cb729b92ddb30e0f42c2e70927c8362564ce6812f889ee0e5b798a40f90d0ae76540648c1d324c40cbb7a6a6e4e6b701320ff6288751eb +MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d diff --git a/sci-chemistry/moldy/files/2.16e-as-needed.patch b/sci-chemistry/moldy/files/2.16e-as-needed.patch new file mode 100644 index 000000000000..67399e08560e --- /dev/null +++ b/sci-chemistry/moldy/files/2.16e-as-needed.patch @@ -0,0 +1,65 @@ +diff --git a/Makefile.in b/Makefile.in +index 0b02f00..ec588a8 100644 +--- a/Makefile.in ++++ b/Makefile.in +@@ -115,25 +115,25 @@ VMSBUILD= compile_moldy.com link_moldy.com defcomm.com\ + + DOSBUILD= Makefile.mak OFILES.RSP SHAKOBJS.RSP Makefile.w32 + +-all: moldy utilities Makefile ++all: moldy utilities + + moldy: $(OFILES) $(EXTRA_OBJ) $(HFILES) +- $(CC) -o moldy $(LDFLAGS) $(OFILES) $(EXTRA_OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) -o moldy $(LDFLAGS) $(OFILES) $(EXTRA_OBJ) $(LIBS) + + moldyext: moldyext.c $(LIBOBJS) $(HFILES) +- $(CC) $(CFLAGS) -o moldyext $(OPT) $(DEFS) $(LDFLAGS1) moldyext.c $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o moldyext $(OPT) $(DEFS) $(LDFLAGS1) moldyext.c $(LIBOBJS) $(LIBS) + + manalyze: manalyze.c $(HFILES) +- $(CC) $(CFLAGS) -o manalyze $(OPT) $(DEFS) $(LDFLAGS1) manalyze.c $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o manalyze $(OPT) $(DEFS) $(LDFLAGS1) manalyze.c $(LIBS) + + dumpanal: dumpanal.c xdr.o $(HFILES) +- $(CC) $(CFLAGS) -o dumpanal $(OPT) $(DEFS) $(LDFLAGS1) dumpanal.c xdr.o $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o dumpanal $(OPT) $(DEFS) $(LDFLAGS1) dumpanal.c xdr.o $(LIBS) + + dumpext: dumpext.c xdr.o utlsup.o matrix.o $(LIBOBJS) $(HFILES) +- $(CC) $(CFLAGS) -o dumpext $(OPT) $(DEFS) $(LDFLAGS1) dumpext.c xdr.o utlsup.o matrix.o $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o dumpext $(OPT) $(DEFS) $(LDFLAGS1) dumpext.c xdr.o utlsup.o matrix.o $(LIBOBJS) $(LIBS) + + dumpconv: dumpconv.c xdr.o $(HFILES) +- $(CC) $(CFLAGS) -o dumpconv $(OPT) $(DEFS) $(LDFLAGS1) dumpconv.c xdr.o $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o dumpconv $(OPT) $(DEFS) $(LDFLAGS1) dumpconv.c xdr.o $(LIBS) + + #mdtraj: mdtraj.o $(SHAKOBJS) $(LIBOBJS) + # $(CC) -o mdtraj $(LDFLAGS) mdtraj.o $(SHAKOBJS) $(LIBOBJS) $(LIBS) +@@ -142,21 +142,21 @@ mdshak: mdshak.o $(SHAKOBJS) $(LIBOBJS) + $(CC) -o mdshak $(LDFLAGS) mdshak.o $(SHAKOBJS) $(LIBOBJS) $(LIBS) + + msd: msd.o $(SHAKOBJS) $(LIBOBJS) +- $(CC) -o msd $(LDFLAGS1) msd.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o msd $(LDFLAGS1) msd.o $(SHAKOBJS) $(LIBOBJS) $(LIBS) + + mdvaf: mdvaf.o $(SHAKOBJS) $(LIBOBJS) +- $(CC) -o mdvaf $(LDFLAGS1) mdvaf.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o mdvaf $(LDFLAGS1) mdvaf.o $(SHAKOBJS) $(LIBOBJS) $(LIBS) + mdavpos: mdavpos.o $(SHAKOBJS) $(LIBOBJS) +- $(CC) -o mdavpos $(LDFLAGS1) mdavpos.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o mdavpos $(LDFLAGS1) mdavpos.o $(SHAKOBJS) $(LIBOBJS) $(LIBS) + + mdbond: mdbond.o $(SHAKOBJS) $(LIBOBJS) +- $(CC) -o mdbond $(LDFLAGS1) mdbond.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o mdbond $(LDFLAGS1) mdbond.o $(SHAKOBJS) $(LIBOBJS) $(LIBS) + + bdist: bdist.c $(HFILES) +- $(CC) $(CFLAGS) -o bdist $(OPT) $(DEFS) $(LDFLAGS1) bdist.c $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o bdist $(OPT) $(DEFS) $(LDFLAGS1) bdist.c $(LIBOBJS) $(LIBS) + + ransub: ransub.o $(SHAKOBJS) $(LIBOBJS) +- $(CC) -o ransub $(LDFLAGS1) ransub.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o ransub $(LDFLAGS1) ransub.o $(SHAKOBJS) $(LIBOBJS) $(LIBS) + + utilities: $(UTILS) $(UTILS2) + diff --git a/sci-chemistry/moldy/metadata.xml b/sci-chemistry/moldy/metadata.xml new file mode 100644 index 000000000000..da36ecbfcd6a --- /dev/null +++ b/sci-chemistry/moldy/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/moldy/moldy-2.16e-r2.ebuild b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild new file mode 100644 index 000000000000..8ba71f621898 --- /dev/null +++ b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Molecular dynamics simulations platform" +HOMEPAGE="http://www.ccp5.ac.uk/moldy/moldy.html" +SRC_URI="ftp://ftp.earth.ox.ac.uk/pub/keith/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc examples" + +DEPEND="doc? ( virtual/latex-base )" +RDEPEND="" + +S="${WORKDIR}" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-as-needed.patch + sed \ + -e 's:-O2::g' \ + -e 's:-ffast-math::g' \ + -i configure || die +} + +src_configure() { + #Individuals may want to edit the OPT* variables below. + #From the READ.ME: + #You may need to "hand-tune" compiler or optimization options, + #which may be specified by setting the OPT and OPT2 environment + #variables. OPT2 is used to compile only the most performance-critical + #modules and usually will select a very high level of optimization. + #It should be safe to select an optimization which means "treat all + #function arguments as restricted pointers which are not aliased to + #any other object". OPT is used for less preformance-critical modules + #and may be set to a lower level of optimization than OPT2. + + OPT="${CFLAGS}" \ + OPT2="${CFLAGS} ${CFLAGS_OPT}" \ + CC=$(tc-getCC) \ + econf +} + +src_compile() { + emake + # To prevent sandbox violations by metafont + if use doc; then + VARTEXFONTS="${T}"/fonts emake moldy.pdf + fi +} + +src_install() { + dodir /usr/bin + emake prefix="${ED}"/usr install + dodoc BENCHMARK READ.ME RELNOTES + + if use examples; then + rm Makefile.in configure.in config.h.in + insinto /usr/share/${PN}/examples/ + doins *.in *.out control.* || die + fi + if use doc; then + insinto /usr/share/doc/${PF}/pdf + newins moldy.pdf moldy-manual.pdf + fi +} diff --git a/sci-chemistry/molequeue/Manifest b/sci-chemistry/molequeue/Manifest new file mode 100644 index 000000000000..d343031b7b78 --- /dev/null +++ b/sci-chemistry/molequeue/Manifest @@ -0,0 +1,5 @@ +DIST molequeue-0.8.0.tar.gz 643072 SHA256 c191e396f3d882c911e331e6325ed4e2666b70d4316e458964e61d5af7c8cbba SHA512 b9539d2ad2c67188ad254f186c1d67c122a15a32047801c632a1613a4f9c887f38baf2da1bb80cb123391948c2a44604fb1082e475ca6de1e683fbe51266ac84 WHIRLPOOL 4ea157d2c644ab3e35648d731f9e48f0b4f4a05f70055646f55474ef37500626794e7def8dba8bdd1d60e1d98724fd5886995d1680e47a8c9e834833ba545e41 +EBUILD molequeue-0.8.0.ebuild 1530 SHA256 482b18ceb3d51df56355b7643d95f8145f80b33f7a93629996b82725fe9cee83 SHA512 f7028e71bdd7d4a62874e8619095d6d66eb728fcea4dfb65c72b9033a0f8d55e39698c429c253ff34d3b35ed732b583808eb846653119c1a1d0a628c6f9e487a WHIRLPOOL d23fd58a61fb38c3f1a568b8af151e699712e8baecad1063b43d5e979efab82f82644d04c9f1ec7cee2c89bead8b82354bf3524c56ff541ef479c73be00b2c38 +MISC ChangeLog 3325 SHA256 737af742a1d77e0cb7e8a955a437a70378af0946195ef73df61e83500ee9f653 SHA512 a545b03668684fb79f0028e6fef1339d2c96f50c7b3fd6324f35d68cdb9cc23588d600665a08691b2c819836a7918086e045d36ea094c88288b2364aa6ef94a2 WHIRLPOOL f38a481cdcf984fe1f771234428a10ff187990cc82c87751ce487d9148c604ce6ae02bc64606eaa62bcc52931e191a40c2bf84486b3002b9ac2973192974cd90 +MISC ChangeLog-2015 1304 SHA256 10ee349ac3ced4ff23cb2d9ba1a6d14695d164e19ff2552d6a2d34c4faa074c6 SHA512 e22eba76addf13e18ffd5978897ec40078a76977f73dfbbe6b7ac3b3fbd229087467a7c172d35fe0588b57627c30e955a556f84cd46edff82495e48fa99619a4 WHIRLPOOL 33d23b069eccd1502dd69c0dac90439a132abdb5ff20d524c6e26d5eac807d6d06cc30c6c0b2251854d55d7660ed536980cc2d97b46449de460c2999f4fbef23 +MISC metadata.xml 1257 SHA256 ee04d7205957acf0e4726c11a2a6a425923bc95e6680a8217629c4b2f5267dc2 SHA512 10e3dd48ec1e54bc0d47d4c2f0aca427875cc0ceb59a93ab41ab2734607aa6474e80f3ae622e45fa319753591f16439118dd0b301068cb3e16fd79ff11a4f058 WHIRLPOOL b3abfcc44a1c8178df97410e3ba89cdd504da76760d507882255cf6d11fe5146faacdd0564a350aa95c0998d1d735615e026ebca6babf39125bd39f82208b56d diff --git a/sci-chemistry/molequeue/metadata.xml b/sci-chemistry/molequeue/metadata.xml new file mode 100644 index 000000000000..070683db0c10 --- /dev/null +++ b/sci-chemistry/molequeue/metadata.xml @@ -0,0 +1,27 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription> +MoleQueue is an open-source, cross-platform, system-tray resident desktop +application for abstracting, managing, and coordinating the execution of tasks +both locally and on remote computational resources. It is built and tested and +Linux, Mac OS X, and Windows, with nightly binaries currently available for +Mac OS X and Windows. Users can set up local and remote queues that describe +where the task will be executed. Each queue can have programs, with templates +to facilitate the execution of the program. Input files can be staged, and +output files collected using a standard interface. + </longdescription> + <use> + <flag name="zeromq">Build with <pkg>net-libs/zeromq</pkg> support</flag> + <flag name="client">Build the client application</flag> + <flag name="server">Build the serve application</flag> + </use> + <upstream> + <remote-id type="sourceforge">molequeue</remote-id> + <remote-id type="github">OpenChemistry/molequeue</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/molequeue/molequeue-0.8.0.ebuild b/sci-chemistry/molequeue/molequeue-0.8.0.ebuild new file mode 100644 index 000000000000..1454d2636c13 --- /dev/null +++ b/sci-chemistry/molequeue/molequeue-0.8.0.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils multilib python-single-r1 versionator virtualx + +DESCRIPTION="Abstract, manage and coordinate execution of tasks" +HOMEPAGE="http://www.openchemistry.org/OpenChemistry/project/molequeue.html" +SRC_URI="https://github.com/OpenChemistry/molequeue/archive/${PV}.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+client doc server test +zeromq" + +REQUIRED_USE="${PYTHON_REQUIRED_USE} + server? ( client ) + test? ( server )" + +RDEPEND="${PYTHON_DEPS} + dev-qt/qtcore:5 + dev-qt/qtnetwork:5 + dev-qt/qtwidgets:5 + zeromq? ( net-libs/cppzmq:0= )" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen )" + +src_prepare() { + # delete bundled Qt5Json library + rm -r thirdparty || die +} + +src_configure() { + local mycmakeargs=( + $(cmake-utils_use_enable test TESTING) + $(cmake-utils_use_use zeromq ZERO_MQ) + $(cmake-utils_use_build doc DOCUMENTATION) + $(cmake-utils_use client MoleQueue_BUILD_CLIENT) + $(cmake-utils_use server MoleQueue_BUILD_APPLICATION) + -DINSTALL_LIBRARY_DIR=$(get_libdir) + ) + use zeromq && \ + mycmakeargs+=( -DZeroMQ_ROOT_DIR=\"${EPREFIX}/usr\" ) + + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile all $(usex doc documentation "") +} + +src_test() { + VIRTUALX_COMMAND=cmake-utils_src_test + virtualmake +} + +src_install() { + use doc && HTML_DOCS=( "${BUILD_DIR}"/docs/html/. ) + cmake-utils_src_install +} diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest new file mode 100644 index 000000000000..a2ea2253be38 --- /dev/null +++ b/sci-chemistry/molmol/Manifest @@ -0,0 +1,17 @@ +AUX cast.patch 519 SHA256 25acec7df7e5739e2e4664672e979636ccd13c68b2ce5d26e555b3d619be0e77 SHA512 4c57ee9b61a81c8e3b43527914bb3bb16e53083cafacb65fa77e3dd630ec76289e0dbbac62a013b6245c6a5460e0fb40d515af1e5273f8088165e272caecbe17 WHIRLPOOL 38637d00c9d30f71ac23ce6cfc1936dd42837e2d484a083f8324d71ef021d8bc5e13c6ceee006602b75386a24e57d9ff5aa09ae73dd319ca18158e2496b7c608 +AUX ldflags.patch 435 SHA256 cbae8934e2be43ceac0f541ed14e843ed76baf86219e0f669eab0af6d5714c64 SHA512 32c266444bf4341bf2db3fb3330c240729f7a538750c0962ee6b128947c5895fa84425a380a9f0897dacfe95bdc8d395e56e62a44c070513274000d5a493e0e3 WHIRLPOOL 39e7ec799e81a814e8f75e33b9996f82f0ecfde31cb4d0d02a01a98b1ac93cdd57879b58c57941b86ae67047f7d235af18844370474f9409c09397ff11f4d2c0 +AUX libpng15.patch 826 SHA256 656a088b11f0ce171ab666aed8de36e3eeac3576322055ab0036794b02c370ed SHA512 df973c637f09225d3f193bb6f977df515b9d475fb47d3a5e6288daaf1cea79afc1fe022803f9cbc1331b373c6ac1e52056e1fbb8e909562065347cf1ae87a205 WHIRLPOOL 54ba85edd7481a6532cba1ffbf007ec408d27965aa19a8ca358140b137ffee2a69237443ad25698b9ab1ce2bc36cd71914af62889c4be219a2584411ddfcba41 +AUX molmol-2k_p2-fink.patch 12821 SHA256 b7ddc4d48e6149f6ced7e287bf7b72b798394d17d01dee373d2615bf6407f04b SHA512 5646ae8f4801d53f1673c0656b3e5d152767a7cd6b85adec0d13fcb8e60a39e825ac733d18ed14ee1ef738d24841061f7fac2f6aa02cae78bead7f6b39a0a77f WHIRLPOOL 539b94c01fd7333b778b9c534bbc0c3c19c93331170c5afa8f2c4ea5e945a4398ab238fa5b988ff81f7d580b4f677e74e391174ab92f0de5986ceb6caba94c28 +AUX opengl.patch 2420 SHA256 9822e1c30f2efe559cdff4d1071f8777ab8e4555b35fa163018620f44471ee3b SHA512 d9898dc60da99d898365717293913df5dbdd35d381a3eb31f010988c042e83a7d06db3a2261c8d2bf21fe5a26b3860cf45e0761f3c12d92cf85742b92c7cfece WHIRLPOOL 373d010afb1b2d6a97bab587ad364055375207ca7a648469c857686bbc32ee25573e64d558a1b0ec7c1d3f51c3e616fce1447af2ce1fdfc950dd7139ee800adc +AUX pjf_RH9_molmol2k2.diff 3138 SHA256 5b7c3ede5714b123824cc0b8533f679d22d1c5219bf88e8d6a4cebe8e245aeb9 SHA512 93b78202d7bb705e253f2111eeda64c44269e2662c44e2ad5e02a0db9eaa62a7ef3efa25463668a17be9dcc39c81ac1f1875ac7d1990ee537c3dcbd53258bece WHIRLPOOL 9b5a9f5576535e96f23046ca4ce5c9b3e34167818b8c8fa469c4fdf10549e33d75fb4a290547791bb37d7c7ad07e297fc63659bf1c87eafc468b6b2fca4b7b76 +AUX prefix.patch 513 SHA256 efcb5d3fa7258cf88f02b63d1df3100eb0b73848c0ebabb59c84cb9ea082d8e7 SHA512 5e566b80238a5caf1f1d6de4d14ce4088b38dd5f1263390afa4304853f2b8bd71285da21cd14bf56c44211781593686696571e283915f528cffa8d6d3b8f12a4 WHIRLPOOL ac502216971039b07e43596d545b05b52b8a94e32339883c3cfaa46264d8b0992f39beb149b7d5bbb650500cc6040876d0e0818317e34db7abf193813c5f0744 +AUX wild.patch 50572 SHA256 8833f7495314f7fbe4065c3a2a77f08cbfa731c996d797f141bf85cb234694ad SHA512 3b61c046ee230cfd22d6964246c8965adf817563d3dc56e92895e7715df02f89c55d51f3cc9a01858e857c89331baa8aabd75827a5683a6f827836fdd86187da WHIRLPOOL f5952ba2bcefe61931477ab25ca356af0978201b7d56bbbd7947b0a78f0b9d3b9af8f2c562c019e21fa8c7c7eb9e4989166872fce16d9b851b505cdb2e25c8ba +DIST molmol-2k.2.0-doc.tar.gz 1062297 SHA256 07e1c3fd04ffe7c9e9d91eaefa0bf72e6d0913a981eec3bf0879bfc65537a6be SHA512 131f747a5762859398ebe9b676a07df56c82c8864ecc035ec914f1dea74dafcd67f87993421dfe5899c640470c7e1e1ef03ae262b04a9b360ae329eb19a331fe WHIRLPOOL b74f47149c4dce8199722075fda17c9cbe22263eec57b647ef543b15386d53b267ee85d5a2c44a4fda7e533fd6ccdafb82fbbbd71e671ec4e1fd58e07363677c +DIST molmol-2k.2.0-src.tar.gz 1088805 SHA256 1104dcb1b2517581c7d6b1695ff2e92f4076ad34afc48dd896eec38e5acf2287 SHA512 6ab01a6fd3d19752634a2cf22919a20e43d195768bd4bdacd5f0bbe016c3058c94915bad4c7fa64dcd86576be39cad0ae112cb62f5e69ffb10041518101e7a9b WHIRLPOOL e258ede83ac4a8fe9b4a9274588ced7e1294415d864c909ed83e3e56d36512e1388e6f77e45da614bc19992a265d32b739c54aace7faa28971c61a01bba27541 +EBUILD molmol-2k_p2-r2.ebuild 1692 SHA256 bd4feca46efdf75a59ac864bd4b3c5e90997779681c296e871dccdf305bb512e SHA512 60a0fa252d9a6e59d17eb0a5f1df819170e95c1a4857187c5620dc33a01113a87001eff940983861db4b2137fc56026b0a19092681b9738d2055421ba7c0d10a WHIRLPOOL f0578627c681faf49953ed86351bea08706c3f7938a6909989b77afdbe0162a456e2fc1b48510ab601476b4063c5929b2404e9bdf497f307d60080a73358e833 +EBUILD molmol-2k_p2-r3.ebuild 1817 SHA256 9409a09878d0eba2510638843ed671e3c900001f20f778c2db57d95648303ec1 SHA512 723d3cff895cc9a7037de631027485ce35ac3a1ce4621f72cfe9eb26bbbb7554dbea8bce33898ff4c0e7c25addea5f844ba17e4e526689bbd9bcc4f999d78964 WHIRLPOOL 8105575d069f277115165d85d89ca20752e98b3aac74dc0e5082a97b38b0607474782ec6c14c6d39815df28e9cdc72c68d7ebb30638034b068e47c4d42a3dadc +EBUILD molmol-2k_p2-r4.ebuild 1834 SHA256 fa9dbf6e0d1e1e8ed4a5b2a84b7db3cef9fa716e398037ebedd26a4778777b8f SHA512 7f995739ff9ef95bf9408245957a4a282dd23a309ad8eb791ad688ecac0af51229638c078e924572032d281ff4f1b31b4ad9a97d35cf20c21639b244e2c28c8d WHIRLPOOL fa7d6d1a08bed868dda749ecb071e342c5f5b906d5cf277efb6b38fb1a3a907c1d5ec6f0a855dd23c93411a86b828490e14848d3ceb79f5be8237457ff139ac9 +EBUILD molmol-2k_p2-r5.ebuild 1842 SHA256 77271b14705603d0f8198db6b7f5884ed34a04de1066a2a224135932e071437b SHA512 29e216d410dac3ce982010ace56a02f23d35b3dddc04ad773a5d2a6d1c0e4a002fd0ef8f486c7c6d872800a590cfb996c7d354670e09ce9de578c55fc1548bc9 WHIRLPOOL 3bf1f853446979be17c8674676a9e72e0e185edbf5469230f575fcb8c7fb732cd8c0db170f24d3351caf8eeade8af0a3f55db3735ea5867ead09a4ab6e8893fd +MISC ChangeLog 3059 SHA256 c09731a5cd875e00a43dc23970cf08d7d30eae68ff674688f7d7e8170dc1c1a3 SHA512 bd7b1586db627d7f9ddeca3bc80febad1ba7073f3e8bc667fba6d3c9608850fec131ac8082845d3b35037267c60caff6b59aa325b10dba6c33cea98e3edfa758 WHIRLPOOL 16df2bdef50a933b13ea413fd3d4e4b4b79237f8c567d8c4863fda6cc063682360e66a235b9cb1c2f1d981092a9d70eda1f4394cf1af3c66cbb2624f71c73096 +MISC ChangeLog-2015 5362 SHA256 5495e3b639f2c394d2a1c373fe680282178d7fe0ac0ec529daa6219b6f2eb1c9 SHA512 e7d0079ecc3703857100d349db4750104ba00fa677827134d1b446ce1c1049dabad667df9513a7e8d08d622d8ca06aa91cceb15fa5cd6dc15e2d105008b44a64 WHIRLPOOL ce38ea072497b114bdc1e67d35155fa6f7b3f4a294810ab2b81b94599617b1dc3a21481bf60189672c352a723163cc015dceca448a702c9bfe42a15d56e99e42 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/molmol/files/cast.patch b/sci-chemistry/molmol/files/cast.patch new file mode 100644 index 000000000000..16ac411c76e5 --- /dev/null +++ b/sci-chemistry/molmol/files/cast.patch @@ -0,0 +1,21 @@ +diff --git a/src/data/DataDist.c b/src/data/DataDist.c +index 7f7121f..18eef33 100644 +--- a/src/data/DataDist.c ++++ b/src/data/DataDist.c +@@ -27,6 +27,7 @@ + + #include <stdio.h> + #include <stdlib.h> ++#include <stdint.h> + + #include <hashtab.h> + +@@ -89,7 +90,7 @@ hashInter(void *p, unsigned size) + { + TabEntryInter *entryP = p; + +- return ((unsigned) entryP->atom1P + (unsigned) entryP->atom2P) % size; ++ return ((unsigned)(uintptr_t) entryP->atom1P + (unsigned)(uintptr_t) entryP->atom2P) % size; + } + + static int diff --git a/sci-chemistry/molmol/files/ldflags.patch b/sci-chemistry/molmol/files/ldflags.patch new file mode 100644 index 000000000000..ff6e06ef490c --- /dev/null +++ b/sci-chemistry/molmol/files/ldflags.patch @@ -0,0 +1,13 @@ +diff --git a/src/main/Makefile b/src/main/Makefile +index 74530fa..102d1b7 100644 +--- a/src/main/Makefile ++++ b/src/main/Makefile +@@ -22,7 +22,7 @@ SRC = $(OBJ:.o=.c) + default: $(PROGRAM) + + $(PROGRAM): $(OBJ) $(LIBS) $(SGLIB) $(TOOLSLIB) +- $(CC) -o $@ $(CFLAGS) $(OBJ) $(LIBS) $(SGLIB) $(TOOLSLIB) $(SYSLIB) ++ $(CC) $(CFLAGS) ${LDFLAGS} -o $@ $(OBJ) $(LIBS) $(SGLIB) $(TOOLSLIB) $(SYSLIB) + + clean: + rm -f $(OBJ) $(PROGRAM) core *.ps diff --git a/sci-chemistry/molmol/files/libpng15.patch b/sci-chemistry/molmol/files/libpng15.patch new file mode 100644 index 000000000000..cd27e4906608 --- /dev/null +++ b/sci-chemistry/molmol/files/libpng15.patch @@ -0,0 +1,32 @@ +--- src/motogl/MotOGLDump.c ++++ src/motogl/MotOGLDump.c +@@ -248,7 +248,7 @@ + pngErrHand(png_structp pngStrucP, char *errMsg) + { + IORaiseError(errMsg); +- longjmp(pngStrucP->jmpbuf, 1); ++ longjmp(png_jmpbuf(pngStrucP), 1); + } + #endif + +@@ -357,7 +357,7 @@ + return IO_RES_ERR; + } + +- if (setjmp(pngStrucP->jmpbuf)) { ++ if (setjmp(png_jmpbuf(pngStrucP))) { + if (cBuf != NULL) + free(cBuf); + if (fBuf != NULL) +@@ -368,10 +368,7 @@ + + png_init_io(pngStrucP, ImgFileP); + +- pngInfoP->width = imgW; +- pngInfoP->height = imgH; +- pngInfoP->bit_depth = 8; +- pngInfoP->color_type = PNG_COLOR_TYPE_RGB; ++ png_set_IHDR(pngStrucP, pngInfoP, imgW, imgH, 8, PNG_COLOR_TYPE_RGB, 0, PNG_COMPRESSION_TYPE_DEFAULT, PNG_FILTER_TYPE_DEFAULT); + png_write_info(pngStrucP, pngInfoP); + } + #endif diff --git a/sci-chemistry/molmol/files/molmol-2k_p2-fink.patch b/sci-chemistry/molmol/files/molmol-2k_p2-fink.patch new file mode 100644 index 000000000000..14cc83b63e9e --- /dev/null +++ b/sci-chemistry/molmol/files/molmol-2k_p2-fink.patch @@ -0,0 +1,356 @@ + src/calc/CalcRmsd.c | 8 ++++---- + src/cmdfig/FigUtil.c | 46 +++++++++++++++++++++++----------------------- + src/cmdio/ExWriteSec.c | 6 +++--- + src/data/DataDist.c | 2 +- + src/data/DataHand.c | 8 ++++---- + src/expr/ExprScan.c | 2 +- + src/iodev/IODev.c | 2 -- + src/motif/MotifDial.c | 2 +- + src/motif/MotifMainW.c | 4 ++-- + src/os/GFile.c | 2 +- + src/prim/PrimDraw.c | 2 +- + src/prim/RibbonCalc.c | 12 ++++++------ + src/pudev/PuMainW.c | 2 +- + src/tty/TTY.c | 2 +- + tools/src/IsoSurface.c | 22 +++++++++++----------- + 15 files changed, 60 insertions(+), 62 deletions(-) + +diff --git a/src/calc/CalcRmsd.c b/src/calc/CalcRmsd.c +index 0e4629e..ed99e76 100644 +--- a/src/calc/CalcRmsd.c ++++ b/src/calc/CalcRmsd.c +@@ -1025,10 +1025,10 @@ CalcRmsd(BOOL fitPairs, char *range, char *glob1, char *glob2, + } + + for (propI = 0; propI < 2; propI++) { +- if (groupNo == 0 || propI == 0 && ! calc1) ++ if (groupNo == 0 || (propI == 0 && ! calc1)) + continue; + +- if (groupNo == 0 || propI == 1 && ! calc2) ++ if (groupNo == 0 || (propI == 1 && ! calc2)) + continue; + + Report("\nAverage RMSD, dev., min. and max of "); +@@ -1052,8 +1052,8 @@ CalcRmsd(BOOL fitPairs, char *range, char *glob1, char *glob2, + Report(" "); + + for (groupI2 = 0; groupI2 < groupNo; groupI2++) { +- if (groupI1 < groupI2 && +- groupInfoP[groupI1].membNo != groupInfoP[groupI2].membNo || ++ if (((groupI1 < groupI2) && ++ (groupInfoP[groupI1].membNo != groupInfoP[groupI2].membNo)) || + groupInfoP[groupI1].membNo == 0 || + groupInfoP[groupI2].membNo == 0) { + groupInfoP[groupI2].stat.avg = 0.0f; +diff --git a/src/cmdfig/FigUtil.c b/src/cmdfig/FigUtil.c +index 20d403a..b8dc3a6 100644 +--- a/src/cmdfig/FigUtil.c ++++ b/src/cmdfig/FigUtil.c +@@ -44,29 +44,29 @@ typedef struct { + } TabEntry; + + static TabEntry GreekTab[] = { +- "ALPHA", 'a', +- "BETA", 'b', +- "CHI", 'c', +- "DELTA", 'd', +- "EPSILON", 'e', +- "PHI" , 'f', +- "GAMMA", 'g', +- "ETA", 'h', +- "IOTA", 'i', +- "KAPPA", 'k', +- "LAMBDA", 'l', +- "MU", 'm', +- "NU", 'n', +- "PI", 'p', +- "THETA", 'q', +- "RHO", 'r', +- "SIGMA", 's', +- "TAU", 't', +- "UPSILON", 'u', +- "OMEGA", 'w', +- "XI", 'x', +- "PSI", 'y', +- "ZETA", 'z' ++ {"ALPHA", 'a'}, ++ {"BETA", 'b'}, ++ {"CHI", 'c'}, ++ {"DELTA", 'd'}, ++ {"EPSILON", 'e'}, ++ {"PHI" , 'f'}, ++ {"GAMMA", 'g'}, ++ {"ETA", 'h'}, ++ {"IOTA", 'i'}, ++ {"KAPPA", 'k'}, ++ {"LAMBDA", 'l'}, ++ {"MU", 'm'}, ++ {"NU", 'n'}, ++ {"PI", 'p'}, ++ {"THETA", 'q'}, ++ {"RHO", 'r'}, ++ {"SIGMA", 's'}, ++ {"TAU", 't'}, ++ {"UPSILON", 'u'}, ++ {"OMEGA", 'w'}, ++ {"XI", 'x'}, ++ {"PSI", 'y'}, ++ {"ZETA", 'z'} + }; + + int +diff --git a/src/cmdio/ExWriteSec.c b/src/cmdio/ExWriteSec.c +index 7f705d4..8da8336 100644 +--- a/src/cmdio/ExWriteSec.c ++++ b/src/cmdio/ExWriteSec.c +@@ -250,9 +250,9 @@ writeSecondary(DhResP *resPA, int resNo) + + if (neighLStart != NO_RES) { + if (num != neighLEnd + 1 || +- neighNum != neighREnd + 1 && neighNum != neighREnd - 1 || +- neighREnd > neighRStart && neighNum != neighREnd + 1 || +- neighREnd < neighRStart && neighNum != neighREnd - 1) { ++ (neighNum != neighREnd + 1 && neighNum != neighREnd - 1) || ++ (neighREnd > neighRStart && neighNum != neighREnd + 1) || ++ (neighREnd < neighRStart && neighNum != neighREnd - 1)) { + writeNeigh(neighLStart, neighLEnd, neighRStart, neighREnd); + neighLStart = NO_RES; + } else { +diff --git a/src/data/DataDist.c b/src/data/DataDist.c +index 18eef33..c683f9e 100644 +--- a/src/data/DataDist.c ++++ b/src/data/DataDist.c +@@ -117,7 +117,7 @@ fillIntra(TabEntryIntra *entryP, DhAtomP atom1P, DhAtomP atom2P) + entryP->atom2I = DhAtomGetNumber(atom2P); + + if (entryP->res1I > entryP->res2I || +- entryP->res1I == entryP->res2I && entryP->atom1I > entryP->atom2I) { ++ (entryP->res1I == entryP->res2I && entryP->atom1I > entryP->atom2I)) { + t = entryP->res1I; + entryP->res1I = entryP->res2I; + entryP->res2I = t; +diff --git a/src/data/DataHand.c b/src/data/DataHand.c +index b20e29c..368aad3 100644 +--- a/src/data/DataHand.c ++++ b/src/data/DataHand.c +@@ -2043,8 +2043,8 @@ applyBondList(PropRefP refP, LINLIST bondL, int groupNum, + groupNum1 = getGroupNum(bondAddP->res1P->molP); + groupNum2 = getGroupNum(bondAddP->res2P->molP); + if (atom1P->state == AS_VALID && atom2P->state == AS_VALID && +- (groupNum1 == groupNum && groupNum2 == groupNum || +- groupNum < 0 && groupNum1 != groupNum2)) ++ ((groupNum1 == groupNum && groupNum2 == groupNum) || ++ (groupNum < 0 && groupNum1 != groupNum2))) + applyF(bondP, atom1P, atom2P, clientData); + } + bondAddP = nextBondAddP; +@@ -2367,8 +2367,8 @@ callDistApply(PropRefP refP, DhDistP distP, int groupNum, + groupNum1 = getGroupNum(distP->res1P->molP); + groupNum2 = getGroupNum(distP->res2P->molP); + if (atom1P->state == AS_VALID && atom2P->state == AS_VALID && +- (groupNum1 == groupNum && groupNum2 == groupNum || +- groupNum < 0 && groupNum1 != groupNum2)) ++ ((groupNum1 == groupNum && groupNum2 == groupNum) || ++ (groupNum < 0 && groupNum1 != groupNum2))) + applyF(distP, atom1P, atom2P, clientData); + } + } +diff --git a/src/expr/ExprScan.c b/src/expr/ExprScan.c +index dcef69e..6266b4d 100644 +--- a/src/expr/ExprScan.c ++++ b/src/expr/ExprScan.c +@@ -221,7 +221,7 @@ ExprScanGetSym(void) + for (;;) { + if (isdigit(ch)) { + DStrAppChar(StrVal, ch); +- } else if (ch == '.' && ExprStr[1] != '.' || ++ } else if ((ch == '.' && ExprStr[1] != '.') || + ch == 'e' || ch == 'E') { + DStrAppChar(StrVal, ch); + isFloat = TRUE; +diff --git a/src/iodev/IODev.c b/src/iodev/IODev.c +index 9c04ce8..aa4f9a7 100644 +--- a/src/iodev/IODev.c ++++ b/src/iodev/IODev.c +@@ -44,7 +44,6 @@ extern void IOMotifGLDSetDev(void); + #endif + #ifdef IO_DEV_MOTIF_OGL + extern void IOMotifOGLSetDev(void); +-extern void IOMotifOGLDSetDev(void); + #endif + #ifdef IO_DEV_MOTIF_XGL + extern void IOMotifXGLSetDev(void); +@@ -76,7 +75,6 @@ static DevListEntry DevList[] = { + #endif + #ifdef IO_DEV_MOTIF_OGL + {"Motif/OpenGL", IOMotifOGLSetDev}, +- {"Motif/OpenGLD", IOMotifOGLDSetDev}, + #endif + #ifdef IO_DEV_MOTIF_XGL + {"Motif/XGL", IOMotifXGLSetDev}, +diff --git a/src/motif/MotifDial.c b/src/motif/MotifDial.c +index 2514549..6e3bfd7 100644 +--- a/src/motif/MotifDial.c ++++ b/src/motif/MotifDial.c +@@ -1323,7 +1323,7 @@ PuMotifAddGizmoCB(PuGizmo gizmo, PuGizmoCBType type, + + switch (type) { + case PU_CT_ACTIVATE: +- if (gType == GIZMO_TEXT_FIELD || GIZMO_TEXT) ++ if (gType == (GIZMO_TEXT_FIELD | GIZMO_TEXT)) + XtAddCallback(gizmo, XmNactivateCallback, textActivateCB, infoP); + else if (gType == GIZMO_BUTTON) + XtAddCallback(gizmo, XmNactivateCallback, gizmoGenCB, infoP); +diff --git a/src/motif/MotifMainW.c b/src/motif/MotifMainW.c +index abbb444..77ce8fd 100644 +--- a/src/motif/MotifMainW.c ++++ b/src/motif/MotifMainW.c +@@ -80,8 +80,8 @@ checkPressOrExpose(Display *dpy, XEvent *eventP, XPointer arg) + { + Window *winP = (Window *) arg; + +- return eventP->type == ButtonPress && eventP->xbutton.window == *winP || +- eventP->type == Expose && eventP->xexpose.window == *winP; ++ return (eventP->type == ButtonPress && eventP->xbutton.window == *winP) || ++ (eventP->type == Expose && eventP->xexpose.window == *winP); + } + + static void +diff --git a/src/os/GFile.c b/src/os/GFile.c +index d0d63b6..08d48c7 100644 +--- a/src/os/GFile.c ++++ b/src/os/GFile.c +@@ -385,7 +385,7 @@ GFileEOF(GFile gf) + { + if (gf->format == GF_FORMAT_MEMORY) + return gf->currP == NULL || +- gf->currP->nextP == NULL && gf->currPos == gf->currP->len; ++ (gf->currP->nextP == NULL && gf->currPos == gf->currP->len); + else + return feof(gf->fp); + } +diff --git a/src/prim/PrimDraw.c b/src/prim/PrimDraw.c +index 32bd593..ba89c57 100644 +--- a/src/prim/PrimDraw.c ++++ b/src/prim/PrimDraw.c +@@ -461,7 +461,7 @@ drawRibbon(PrimObjP primP) + } + + if (partP->paint == RP_ATOM || +- partP->paint == RP_ATOM_SMOOTH && partP->polyNo > 0) ++ (partP->paint == RP_ATOM_SMOOTH && partP->polyNo > 0)) + SgSetColor(attrP->colR, attrP->colG, attrP->colB); + + if (partP->paint == RP_ATOM_SMOOTH) +diff --git a/src/prim/RibbonCalc.c b/src/prim/RibbonCalc.c +index 09874cf..0849d03 100644 +--- a/src/prim/RibbonCalc.c ++++ b/src/prim/RibbonCalc.c +@@ -907,7 +907,7 @@ calcStrips(PrimObjP primP, PrimObjP prevP) + getSplinePoints(partP, ribbonP, ePar, partP->endPar, ePNo + 1, + parA + sPNo + mPNo - 1, xA + sPNo + mPNo - 1, dzA + sPNo + mPNo - 1); + +- if (partP->style == RS_ROUND && partP->midRad == 0.0f || ++ if ((partP->style == RS_ROUND && partP->midRad == 0.0f) || + BreakInterrupted()) { + /* draw only one line */ + partP->traceNo = 1; +@@ -1128,15 +1128,15 @@ calcStrips(PrimObjP primP, PrimObjP prevP) + Vec3Copy(partP->traceA[traceI].nvA[pointI], nv); + } + +- if (pointI == 0 && partP->startStyle == RE_SHARP || +- pointI == pointNo - ePNo && partP->endStyle == RE_ARROW) ++ if ((pointI == 0 && partP->startStyle == RE_SHARP) || ++ (pointI == pointNo - ePNo && partP->endStyle == RE_ARROW)) + Vec3Copy(partP->polyA[polyI].xA[traceNo - 1 - traceI], x); + else if (pointI == pointNo - 1 && partP->endStyle == RE_SHARP) + Vec3Copy(partP->polyA[polyI].xA[traceI], x); + } + +- if (pointI == 0 && partP->startStyle == RE_SHARP || +- pointI == pointNo - ePNo && partP->endStyle == RE_ARROW) { ++ if ((pointI == 0 && partP->startStyle == RE_SHARP) || ++ (pointI == pointNo - ePNo && partP->endStyle == RE_ARROW)) { + Vec3Copy(x, dy); + Vec3Cross(x, dx); + Vec3Copy(partP->polyA[polyI].nv, x); +@@ -1327,7 +1327,7 @@ RibbonCalc(PrimObjP primP) + + if (! partP->pointValid || prec != partP->prec || + startRad != partP->startRad || +- partP->style == RS_ROUND && midRad != partP->midRad || ++ (partP->style == RS_ROUND && midRad != partP->midRad) || + endRad != partP->endRad || radChanged) { + for (i = 0; i < partP->traceNo; i++) { + free(partP->traceA[i].xA); +diff --git a/src/pudev/PuMainW.c b/src/pudev/PuMainW.c +index 73d183b..d287345 100644 +--- a/src/pudev/PuMainW.c ++++ b/src/pudev/PuMainW.c +@@ -57,7 +57,7 @@ PuSetTextField(PuTextFieldChoice fieldChoice, char *text) + if (text[0] != LOCK_CHAR) + return; + text++; +- if (text[0] == '\0' || text[0] == ' ' && text[1] == '\0') { ++ if (text[0] == '\0' || (text[0] == ' ' && text[1] == '\0')) { + StatusLocked = FALSE; + text = " "; + } +diff --git a/src/tty/TTY.c b/src/tty/TTY.c +index 0090f75..22adfef 100644 +--- a/src/tty/TTY.c ++++ b/src/tty/TTY.c +@@ -164,7 +164,7 @@ PuTTYSwitchFullscreen(BOOL onOff) + void + PuTTYSetTextField(PuTextFieldChoice fieldChoice, char *text) + { +- if (text[0] == '\0' || text[0] == ' ' && text[1] == '\0') ++ if (text[0] == '\0' || (text[0] == ' ' && text[1] == '\0')) + return; + + switch (fieldChoice) { +diff --git a/tools/src/IsoSurface.c b/tools/src/IsoSurface.c +index 5e11a98..09f89d0 100644 +--- a/tools/src/IsoSurface.c ++++ b/tools/src/IsoSurface.c +@@ -104,19 +104,19 @@ typedef struct { + } Strip; + + static CubeDesc CubeEven = { +- 0, 3, 5, 6, {{D_0, 1}, {D_0, 2}, {D_0, 3}, {D_0, 4}}, +- 3, 0, 5, 1, {{D_0, 0}, {D_MZ, 4}, {D_MY, 1}, {D_PX, 2}}, +- 0, 3, 6, 2, {{D_0, 0}, {D_MZ, 3}, {D_PY, 2}, {D_MX, 1}}, +- 3, 5, 6, 7, {{D_0, 0}, {D_PX, 3}, {D_PZ, 1}, {D_PY, 4}}, +- 5, 0, 6, 4, {{D_0, 0}, {D_MY, 3}, {D_MX, 4}, {D_PZ, 2}} ++ {{0, 3, 5, 6, {{D_0, 1}, {D_0, 2}, {D_0, 3}, {D_0, 4}}}, ++ {3, 0, 5, 1, {{D_0, 0}, {D_MZ, 4}, {D_MY, 1}, {D_PX, 2}}}, ++ {0, 3, 6, 2, {{D_0, 0}, {D_MZ, 3}, {D_PY, 2}, {D_MX, 1}}}, ++ {3, 5, 6, 7, {{D_0, 0}, {D_PX, 3}, {D_PZ, 1}, {D_PY, 4}}}, ++ {5, 0, 6, 4, {{D_0, 0}, {D_MY, 3}, {D_MX, 4}, {D_PZ, 2}}}} + }; + + static CubeDesc CubeOdd = { +- 1, 2, 7, 4, {{D_0, 1}, {D_0, 2}, {D_0, 3}, {D_0, 4}}, +- 2, 1, 7, 3, {{D_0, 0}, {D_MZ, 3}, {D_PX, 2}, {D_PY, 1}}, +- 1, 2, 4, 0, {{D_0, 0}, {D_MZ, 4}, {D_MX, 1}, {D_MY, 2}}, +- 2, 7, 4, 6, {{D_0, 0}, {D_PY, 4}, {D_PZ, 2}, {D_MX, 3}}, +- 7, 1, 4, 5, {{D_0, 0}, {D_PX, 4}, {D_MY, 3}, {D_PZ, 1}} ++ {{1, 2, 7, 4, {{D_0, 1}, {D_0, 2}, {D_0, 3}, {D_0, 4}}}, ++ {2, 1, 7, 3, {{D_0, 0}, {D_MZ, 3}, {D_PX, 2}, {D_PY, 1}}}, ++ {1, 2, 4, 0, {{D_0, 0}, {D_MZ, 4}, {D_MX, 1}, {D_MY, 2}}}, ++ {2, 7, 4, 6, {{D_0, 0}, {D_PY, 4}, {D_PZ, 2}, {D_MX, 3}}}, ++ {7, 1, 4, 5, {{D_0, 0}, {D_PX, 4}, {D_MY, 3}, {D_PZ, 1}}}} + }; + + static BOOL Initialized = FALSE; +@@ -158,7 +158,7 @@ fillFaces(TetDesc *tetP) + static BOOL + equalPair(int i00, int i01, int i10, int i11) + { +- return i00 == i10 && i01 == i11 || i00 == i11 && i01 == i10; ++ return (i00 == i10 && i01 == i11) || (i00 == i11 && i01 == i10); + } + + static int diff --git a/sci-chemistry/molmol/files/opengl.patch b/sci-chemistry/molmol/files/opengl.patch new file mode 100644 index 000000000000..c1db35d9013d --- /dev/null +++ b/sci-chemistry/molmol/files/opengl.patch @@ -0,0 +1,96 @@ + molmol | 65 +++++++++-------------------------------------------------------- + 1 file changed, 9 insertions(+), 56 deletions(-) + +diff --git a/molmol b/molmol +index 7863225..b6c75ce 100755 +--- a/molmol ++++ b/molmol +@@ -11,55 +11,8 @@ ostype=`uname` + osrel=`uname -r` + osmaj=`echo $osrel | awk -F. '{print $1}'` + osmin=`echo $osrel | awk -F. '{print $2}'` +-localdev= +-glxdev= +- +-if [ $ostype = "IRIX" -o $ostype = "IRIX64" ]; then +- if [ $osmaj -eq 6 -a $osmin -ge 2 -o $osmaj -gt 6 ]; then +- arch=sgi6 +- localdev=Motif/OpenGL +- glxdev=Motif/OpenGL +- elif [ $osmaj -eq 5 -a $osmin -ge 3 -o $osmaj -gt 5 ]; then +- arch=sgi5 +- localdev=Motif/OpenGL +- glxdev=Motif/OpenGL +- else +- arch=sgi4 +- localdev=Motif/GL +- fi +- MONITOR=72HZ; export MONITOR +-elif [ $ostype = "AIX" ]; then +- arch=aix +- localdev=Motif/OpenGL +-elif [ $ostype = "HP-UX" ]; then +- arch=hp +- localdev=Motif/OpenGL +- glxdev=Motif/OpenGL +-elif [ $ostype = "OSF1" ]; then +- arch=dec +- localdev=Motif/OpenGL +-elif [ $ostype = "Linux" ]; then +- arch=lnx +- localdev=Motif/OpenGL +-elif [ $ostype = "SunOS" ]; then +- if [ $osmaj -eq 5 -a $osmin -ge 4 -o $osmaj -gt 5 ]; then +- arch=sol +- localdev=Motif/OpenGL +- else +- arch=sun +- fi +-else +- arch=unknown +-fi +- +-if [ $ostype = "SunOS" ]; then +- xdpy=/usr/openwin/bin/xdpyinfo +-elif [ $ostype = "HP-UX" ]; then +- xdpy=/usr/contrib/bin/X11/xdpyinfo +-else +- xdpy=/usr/bin/X11/xdpyinfo +-fi +- ++localdev=Motif/OpenGL ++glxdev=Motif/OpenGL + printUsage () { + echo "Usage: molmol -ht2as [-o dev] [-r range] [-f macro] files" + echo "" +@@ -121,15 +74,15 @@ done + + magictmp=/tmp/molmol_magic$$ + +-if [ ! -d $HOME/molmol ]; then +- mkdir $HOME/molmol ++if [ ! -d $HOME/.molmol ]; then ++ mkdir $HOME/.molmol + fi +-startmacro=$HOME/molmol/options.mac ++startmacro=$HOME/.molmol/options.mac + cp /dev/null $startmacro + + if [ -n "$*" ]; then +- if [ -f $HOME/molmol/dump ]; then +- mv -f $HOME/molmol/dump $HOME/molmol/dump.old ++ if [ -f $HOME/.molmol/dump ]; then ++ mv -f $HOME/.molmol/dump $HOME/.molmol/dump.old + fi + echo "0 long 0x3b7a12f9 MOLMOL" > $magictmp + echo "0 long 0xf9127a3b MOLMOL" >> $magictmp +@@ -209,7 +162,7 @@ elif [ -x $xdpy ]; then + fi + + if [ "$input" = "-" -o -n "$nograph" ]; then +- $MOLMOLHOME/molmol.$arch $xopt ++ $MOLMOLHOME/molmol $xopt + else +- $MOLMOLHOME/molmol.$arch $xopt < /dev/null ++ $MOLMOLHOME/molmol $xopt < /dev/null + fi diff --git a/sci-chemistry/molmol/files/pjf_RH9_molmol2k2.diff b/sci-chemistry/molmol/files/pjf_RH9_molmol2k2.diff new file mode 100644 index 000000000000..0ad57d93e107 --- /dev/null +++ b/sci-chemistry/molmol/files/pjf_RH9_molmol2k2.diff @@ -0,0 +1,103 @@ +Only in molmol_rh9: makedef +diff -ru molmol_rh9_unpatched/makedef.lnx molmol_rh9/makedef.lnx +--- molmol_rh9_unpatched/makedef.lnx 2003-01-20 16:10:18.000000000 -0500 ++++ molmol_rh9/makedef.lnx 2003-05-06 10:40:08.000000000 -0400 +@@ -1,31 +1,38 @@ + # definitions for Linux + +-MISSFUNC = -Dsqrtf=sqrt -Dexpf=exp -Dlogf=log -Dpowf=pow \ +- -Dsinf=sin -Dcosf=cos -Dtanf=tan \ +- -Dasinf=asin -Dacosf=acos -Datanf=atan -Datan2f=atan2 \ +- -Dfabsf=fabs -Dceilf=ceil +-MCPPFLAGS = $(MISSFUNC) +-MCFLAGS = -O2 +- +-RANLIB = /bin/true +-WAIT = /usr/bin/sleep 2 +-SHELL = /bin/sh +-CPP = /lib/cpp +-CC = /usr/bin/gcc ++#TIFFDIR = $(TOP)/tiff-v3.4/libtiff ++#JPEGDIR = $(TOP)/../libjpeg/jpeg-6a ++#PNGDIR = $(TOP)/../libpng/libpng-0.89c ++#ZLIBDIR = $(TOP)/../libpng/zlib-1.0.2 ++ ++IMGDEF = -DTIFF_SUPPORT -DJPEG_SUPPORT -DPNG_SUPPORT ++IMGLIB = -ltiff -ljpeg -lpng -lz ++IMGINCL = # -I$(TIFFDIR) -I$(JPEGDIR) -I$(PNGDIR) -I$(ZLIBDIR) ++ ++XINCL = -I/usr/X11R6/include ++ ++CC=gcc ++MCPPFLAGS = ++MCFLAGS =-pipe -O3 -ffast-math -march=i686 -mcpu=i686 ++ ++RANLIB = /bin/true ++WAIT = sleep 2 ++SHELL = /bin/sh ++CPP = /lib/cpp + +-SGDEVDIR = x11 no pov rib vrml1 vrml2 ps fm +- +-SGDEVDEF = -DSG_DEV_X11 -DSG_DEV_NO -DSG_DEV_POV -DSG_DEV_RIB -DSG_DEV_VRML1 -DSG_DEV_VRML2 -DSG_DEV_PS -DSG_DEV_CPS -DSG_DEV_FM3 -DSG_DEV_FM4 ++SGDEVDIR = ogl x11 no pov rib vrml1 vrml2 ps fm ++SGDEVDEF = -DSG_DEV_OGL -DSG_DEV_X11 -DSG_DEV_NO -DSG_DEV_POV -DSG_DEV_RIB -DSG_DEV_VRML1 -DSG_DEV_VRML2 -DSG_DEV_PS -DSG_DEV_CPS -DSG_DEV_FM3 -DSG_DEV_FM4 + + PUDEVDIR = motif tty + PUDEVDEF = -DPU_DEV_MOTIF -DPU_DEV_TTY + +-IODEVDIR = motx11 ttyno +-IODEVDEF = -DIO_DEV_MOTIF_X11 -DIO_DEV_TTY_NO ++IODEVDIR = motogl motx11 ttyno ++IODEVDEF = -DIO_DEV_MOTIF_OGL -DIO_DEV_MOTIF_X11 -DIO_DEV_TTY_NO + ++OPENGLDEF = -DOPENGL_SGI_STEREO + MOTIFDEF = -DFUNCPROTO + +-SYSLIB = -L/usr/X11R6/lib -lXm -lXt -lXpm -lX11 -lm -lc -lieee ++SYSLIB = -lGLw -lGLU -lGL -lXm -lXpm -lXt -lXext -lX11 -lm + + TOOLSDIR = $(TOP)/tools +-SGDIR = $(TOP)/sg ++SGDIR = $(TOP)/sg +diff -ru molmol_rh9_unpatched/src/motogl/MotOGL.c molmol_rh9/src/motogl/MotOGL.c +--- molmol_rh9_unpatched/src/motogl/MotOGL.c 2000-05-29 12:31:51.000000000 -0400 ++++ molmol_rh9/src/motogl/MotOGL.c 2003-05-06 11:51:05.000000000 -0400 +@@ -31,7 +31,7 @@ + #include <Xm/XmStrDefs.h> + + #define BOOL MOTIF_BOOL /* hack to avoid naming conflict */ +-#include <X11/GLw/GLwMDrawA.h> ++#include <GL/GLwMDrawA.h> + #undef BOOL + + #include <sg.h> +diff -ru molmol_rh9_unpatched/src/os/GFile.c molmol_rh9/src/os/GFile.c +--- molmol_rh9_unpatched/src/os/GFile.c 2001-06-17 14:59:17.000000000 -0400 ++++ molmol_rh9/src/os/GFile.c 2003-05-06 12:34:34.000000000 -0400 +@@ -30,6 +30,7 @@ + #include <string.h> + #include <memory.h> + #include <ctype.h> ++#include <errno.h> + + #include <linlist.h> + +@@ -38,7 +39,7 @@ + const INT32 GFMagic = 0x3b7a12f9; + + #ifndef __linux__ +-extern char *sys_errlist[]; ++extern char *strerror(); + #endif + extern int errno; + +@@ -81,7 +82,7 @@ + { + if (msg == NULL) { + if (NextMsg == NULL) +- msg = sys_errlist[errno]; ++ msg = strerror(errno); + else + msg = NextMsg; + } diff --git a/sci-chemistry/molmol/files/prefix.patch b/sci-chemistry/molmol/files/prefix.patch new file mode 100644 index 000000000000..89f17b2e984e --- /dev/null +++ b/sci-chemistry/molmol/files/prefix.patch @@ -0,0 +1,22 @@ +diff --git a/molmol b/molmol +index e774abf..9f10558 100755 +--- a/molmol ++++ b/molmol +@@ -57,7 +57,7 @@ if [ $ostype = "SunOS" ]; then + elif [ $ostype = "HP-UX" ]; then + xdpy=/usr/contrib/bin/X11/xdpyinfo + else +- xdpy=/usr/bin/X11/xdpyinfo ++ xdpy=@GENTOO_PORTAGE_EPREFIX@/usr/bin/xdpyinfo + fi + + printUsage () { +@@ -119,7 +119,7 @@ while [ -n "$*" ]; do + esac + done + +-magictmp=/tmp/molmol_magic$$ ++magictmp=@GENTOO_PORTAGE_EPREFIX@/tmp/molmol_magic$$ + + if [ ! -d $HOME/molmol ]; then + mkdir $HOME/molmol diff --git a/sci-chemistry/molmol/files/wild.patch b/sci-chemistry/molmol/files/wild.patch new file mode 100644 index 000000000000..8be9baf92203 --- /dev/null +++ b/sci-chemistry/molmol/files/wild.patch @@ -0,0 +1,1866 @@ + include/cmd_dial.h | 1 + + include/cmd_io.h | 7 +- + include/cmd_struc.h | 1 + + include/curr_dir.h | 1 + + include/data_hand.h | 6 + + src/cip/cmd_tab.h | 3 + + src/cmddial/ExDialColor.c | 314 +++++++++++++++++++++++++++++++----------- + src/cmddial/ExDialRes.c | 340 ++++++++++++++++++++++++++++++++++++++++++++++ + src/cmddial/Makefile | 2 +- + src/cmdio/ExPdb.c | 70 +++++++++- + src/cmdstruc/ExBuild.c | 123 +++++++++++++++++ + src/data/DataHand.c | 114 +++++++++++++++- + src/iodev/IODev.c | 2 + + src/main/MolInit.c | 5 +- + src/main/MolMol.c | 2 +- + src/motif/MotifDial.c | 32 ++--- + src/motogl/MotOGLDump.c | 2 +- + src/os/CurrDir.c | 46 ++----- + src/os/ProgDir.c | 25 +++- + src/win/WinDial.c | 255 +++++++++++++++++----------------- + src/winogl/WinOGLDump.c | 7 +- + 21 files changed, 1073 insertions(+), 285 deletions(-) + +diff --git a/include/cmd_dial.h b/include/cmd_dial.h +index f60e918..47fb8f8 100644 +--- a/include/cmd_dial.h ++++ b/include/cmd_dial.h +@@ -29,6 +29,7 @@ extern ErrCode ExUserInterface(char *); + + extern ErrCode ExDialColor(char *); + extern ErrCode ExDialMol(char *); ++extern ErrCode ExDialRes(char *); + extern ErrCode ExDialMeasure(char *); + extern ErrCode ExDialRmsd(char *); + extern ErrCode ExDialSelect(char *); +diff --git a/include/cmd_io.h b/include/cmd_io.h +index 79b173c..9a7b12c 100644 +--- a/include/cmd_io.h ++++ b/include/cmd_io.h +@@ -30,15 +30,16 @@ extern ErrCode ExReadAng(char *); + extern ErrCode ExReadDg(char *); + extern ErrCode ExReadDump(char *); + extern ErrCode ExReadLib(char *); +-extern ErrCode ExReadPdb(char *); +-extern ErrCode ExReadSeq(char *); +-extern ErrCode ExReadShift(char *); + extern ErrCode ExReadLimit(char *); + extern ErrCode ExReadListAng(char *); + extern ErrCode ExReadListDg(char *); + extern ErrCode ExReadListPdb(char *); ++extern ErrCode ExReadOldPdb(char *); + extern ErrCode ExReadOmap(char *); ++extern ErrCode ExReadPdb(char *); + extern ErrCode ExReadPot(char *); ++extern ErrCode ExReadSeq(char *); ++extern ErrCode ExReadShift(char *); + extern ErrCode ExReadSybyl(char *); + extern ErrCode ExReadXyz(char *); + extern ErrCode ExWriteAng(char *); +diff --git a/include/cmd_struc.h b/include/cmd_struc.h +index e0d729f..f4950b9 100644 +--- a/include/cmd_struc.h ++++ b/include/cmd_struc.h +@@ -33,6 +33,7 @@ extern ErrCode ExAddDist(char *); + extern ErrCode ExAddLimit(char *); + extern ErrCode ExAddPseudo(char *); + extern ErrCode ExAddRes(char *); ++extern ErrCode ExMakeMolCyclic(char *); + extern ErrCode ExChangeRes(char *); + extern ErrCode ExFirstMol(char *); + extern ErrCode ExFlipAtom(char *); +diff --git a/include/curr_dir.h b/include/curr_dir.h +index c7895c4..04e404d 100644 +--- a/include/curr_dir.h ++++ b/include/curr_dir.h +@@ -26,6 +26,7 @@ + #ifndef _CURR_DIR_H_ + #define _CURR_DIR_H_ + ++extern void CurrDirSet(char *dir); + extern char *CurrDirGet(void); + + #endif /* _CURR_DIR_H_ */ +diff --git a/include/data_hand.h b/include/data_hand.h +index 4462328..74a716a 100644 +--- a/include/data_hand.h ++++ b/include/data_hand.h +@@ -112,6 +112,7 @@ extern void DhMolMoveFirst(DhMolP); + extern void DhMolDestroy(DhMolP); + + extern DhResP DhResNew(DhMolP, DhResDefP, DhSeqPos); ++extern DhResP DhResNewCyclic(DhMolP, DhResDefP, DhSeqPos); + extern void DhResMutate(DhResP, DhResDefP, DhMutationKind); + extern void DhResSetNeigh(DhResP, DhNeighChoice, DhResP); + extern BOOL DhResDestroy(DhResP); +@@ -287,6 +288,7 @@ extern void DhMolGetTransVect(DhMolP, Vec3); + extern MolAttrP DhMolGetAttr(DhMolP); + + extern DSTR DhResGetName(DhResP); ++extern DhAtomP DhResGetAtomA(DhResP); + extern int DhResGetNumber(DhResP); + + extern DSTR DhAtomGetName(DhAtomP); +@@ -335,6 +337,10 @@ extern void DhResAnglesChanged(DhResP); + extern void DhResDockPrev(DhResP); + extern void DhResDockNext(DhResP); + extern void DhResCalcAtom(DhResP, DSTR); ++extern DhResP DhResPrev(DhResP resP); ++extern DhResP DhResNext(DhResP resP); ++extern DhResP DhResFirst(DhMolP molP); ++extern DhResP DhResLast(DhMolP molP); + + /* dump/undump */ + +diff --git a/src/cip/cmd_tab.h b/src/cip/cmd_tab.h +index 0b73f65..cf7bc2a 100644 +--- a/src/cip/cmd_tab.h ++++ b/src/cip/cmd_tab.h +@@ -108,6 +108,7 @@ static CmdTabEntry BuiltinCmdTab[] = { + {"DialColor", ExDialColor, US_NONE}, + {"DialMeasure", ExDialMeasure, US_NONE}, + {"DialMol", ExDialMol, US_NONE}, ++ {"DialRes", ExDialRes, US_NONE}, + {"DialRmsd", ExDialRmsd, US_NONE}, + {"DialSelect", ExDialSelect, US_NONE}, + {"DialStyle", ExDialStyle, US_NONE}, +@@ -164,6 +165,7 @@ static CmdTabEntry BuiltinCmdTab[] = { + {"ListSelectedDist", ExListSelected, US_NONE}, + {"ListSelectedMol", ExListSelected, US_NONE}, + {"ListSelectedRes", ExListSelected, US_NONE}, ++ {"MakeMolCyclic", ExMakeMolCyclic, US_ALL}, + {"MaterialAtom", ExMaterial, US_ALL}, + {"MaterialBond", ExMaterial, US_ALL}, + {"MaterialDist", ExMaterial, US_ALL}, +@@ -213,6 +215,7 @@ static CmdTabEntry BuiltinCmdTab[] = { + {"ReadListDg", ExReadListDg, US_ALL}, + {"ReadListPdb", ExReadListPdb, US_ALL}, + {"ReadLol", ExReadLimit, US_ALL}, ++ {"ReadOldPdb", ExReadOldPdb, US_ALL}, + {"ReadOmap", ExReadOmap, US_ALL}, + {"ReadPdb", ExReadPdb, US_ALL}, + {"ReadPot", ExReadPot, US_ALL}, +diff --git a/src/cmddial/ExDialColor.c b/src/cmddial/ExDialColor.c +index f960e1d..e827c4f 100644 +--- a/src/cmddial/ExDialColor.c ++++ b/src/cmddial/ExDialColor.c +@@ -43,6 +43,9 @@ + #define NAME_LEN 100 + #define NUM_LEN 6 + #define CMD_NO 7 ++#define MAXRGBVALUE 255 ++#define ICOLOR(c) (int) ((float)c * (float)MAXRGBVALUE) ++#define FCOLOR(c) (float) ((float)c / (float)MAXRGBVALUE) + + #define EPS ((float) 1.0e-5) + +@@ -56,8 +59,8 @@ typedef struct { + static ColorDesc *ColorList; + static int ColorNo = 0; + static BOOL DialOn = FALSE; +-static PuGizmo DialGizmo = NULL, NameGizmo, RGizmo, GGizmo, BGizmo, ColGizmo; +-static DSTR NameStr = NULL, RStr, GStr, BStr; ++static PuGizmo DialGizmo = NULL, NameGizmo, RGizmo, GGizmo, BGizmo, ColGizmo, rGizmo, gGizmo, bGizmo; ++static DSTR NameStr = NULL, RStr, GStr, BStr, rStr, gStr, bStr; + + static char *LabelList[] = { + "Back", +@@ -136,22 +139,50 @@ editCB(PuGizmo g, char *name, void *clientData, void *callData) + char *field = clientData; + PuTextCBStruc *callP = callData; + +- if (field[0] == 'N') ++ if (field[0] == 'N') { + DStrAssignStr(NameStr, callP->newText); +- else if (field[0] == 'R') ++ } ++ else if (field[0] == 'R') { + DStrAssignStr(RStr, callP->newText); +- else if (field[0] == 'G') ++ } ++ else if (field[0] == 'G') { + DStrAssignStr(GStr, callP->newText); +- else ++ } ++ else if (field[0] == 'B') { + DStrAssignStr(BStr, callP->newText); ++ } ++ else if (field[0] == 'r') { ++ DStrAssignStr(rStr, callP->newText); ++ } ++ else if (field[0] == 'g') { ++ DStrAssignStr(gStr, callP->newText); ++ } ++ else if (field[0] == 'b') { ++ DStrAssignStr(bStr, callP->newText); ++ } + } + + static void + updateFields(int colorI) + { ++ char buf[10]; ++ float f; ++ + PuSetStr(RGizmo, PU_SC_TEXT, ColorList[colorI].r); + PuSetStr(GGizmo, PU_SC_TEXT, ColorList[colorI].g); + PuSetStr(BGizmo, PU_SC_TEXT, ColorList[colorI].b); ++ ++ f = atof(ColorList[colorI].r); ++ (void) sprintf(buf, "%i", ICOLOR(f)); ++ PuSetStr(rGizmo, PU_SC_TEXT, buf); ++ ++ f = atof(ColorList[colorI].g); ++ (void) sprintf(buf, "%i", ICOLOR(f)); ++ PuSetStr(gGizmo, PU_SC_TEXT, buf); ++ ++ f = atof(ColorList[colorI].b); ++ (void) sprintf(buf, "%i", ICOLOR(f)); ++ PuSetStr(bGizmo, PU_SC_TEXT, buf); + } + + static void +@@ -190,17 +221,96 @@ activateCB(PuGizmo g, char *name, void *clientData, void *callData) + { + char *field = clientData; + int i; ++ float f; ++ char buf[10]; + + if (field[0] == 'N') { + for (i = 0; i < ColorNo; i++) + if (strcmp(ColorList[i].name, DStrToStr(NameStr)) == 0) { +- updateFields(i); +- break; ++ updateFields(i); ++ break; + } + } else { ++ if (field[0] == 'R') { ++ f = atof(DStrToStr(RStr)); ++ if (f>1.0) { ++ f=1.0; ++ i=MAXRGBVALUE; ++ sprintf(buf,"%1.3f", FCOLOR(i)); ++ DStrAssignStr(RStr, buf); ++ PuSetStr(RGizmo, PU_SC_TEXT, buf); ++ } ++ sprintf(buf,"%i", ICOLOR(f)); ++ DStrAssignStr(rStr, buf); ++ PuSetStr(rGizmo, PU_SC_TEXT, buf); ++ } ++ else if (field[0] == 'G') { ++ f = atof(DStrToStr(GStr)); ++ if (f>1.0) { ++ f=1.0; ++ i=MAXRGBVALUE; ++ sprintf(buf,"%1.3f", FCOLOR(i)); ++ DStrAssignStr(GStr, buf); ++ PuSetStr(GGizmo, PU_SC_TEXT, buf); ++ } ++ sprintf(buf,"%i", ICOLOR(f)); ++ DStrAssignStr(gStr, buf); ++ PuSetStr(gGizmo, PU_SC_TEXT, buf); ++ } ++ else if (field[0] == 'B') { ++ f = atof(DStrToStr(BStr)); ++ if (f>1.0) { ++ f=1.0; ++ i=MAXRGBVALUE; ++ sprintf(buf,"%1.3f", FCOLOR(i)); ++ DStrAssignStr(BStr, buf); ++ PuSetStr(BGizmo, PU_SC_TEXT, buf); ++ } ++ sprintf(buf,"%i", ICOLOR(f)); ++ DStrAssignStr(bStr, buf); ++ PuSetStr(bGizmo, PU_SC_TEXT, buf); ++ } ++ else if (field[0] == 'r') { ++ i = atoi(DStrToStr(rStr)); ++ if (i>MAXRGBVALUE) { ++ f=1.0; ++ i=MAXRGBVALUE; ++ sprintf(buf,"%i", ICOLOR(f)); ++ DStrAssignStr(rStr, buf); ++ PuSetStr(rGizmo, PU_SC_TEXT, buf); ++ } ++ sprintf(buf,"%1.3f", FCOLOR(i)); ++ DStrAssignStr(RStr, buf); ++ PuSetStr(RGizmo, PU_SC_TEXT, buf); ++ } ++ else if (field[0] == 'g') { ++ i = atoi(DStrToStr(gStr)); ++ if (i>MAXRGBVALUE) { ++ f=1.0; ++ i=MAXRGBVALUE; ++ sprintf(buf,"%i", ICOLOR(f)); ++ DStrAssignStr(gStr, buf); ++ PuSetStr(gGizmo, PU_SC_TEXT, buf); ++ } ++ sprintf(buf,"%1.3f", FCOLOR(i)); ++ DStrAssignStr(GStr, buf); ++ PuSetStr(GGizmo, PU_SC_TEXT, buf); ++ } ++ else if (field[0] == 'b') { ++ i = atoi(DStrToStr(bStr)); ++ if (i>MAXRGBVALUE) { ++ f=1.0; ++ i=MAXRGBVALUE; ++ sprintf(buf,"%i", ICOLOR(f)); ++ DStrAssignStr(bStr, buf); ++ PuSetStr(bGizmo, PU_SC_TEXT, buf); ++ } ++ sprintf(buf,"%1.3f", FCOLOR(i)); ++ DStrAssignStr(BStr, buf); ++ PuSetStr(BGizmo, PU_SC_TEXT, buf); ++ } + showName(); + } +- + showColor(); + } + +@@ -258,13 +368,20 @@ showAttr(AttrP attrP) + { + char buf[10]; + +- (void) sprintf(buf, "%5.3f", attrP->colR); ++ (void) sprintf(buf, "%1.3f", attrP->colR); + PuSetStr(RGizmo, PU_SC_TEXT, buf); +- (void) sprintf(buf, "%5.3f", attrP->colG); ++ (void) sprintf(buf, "%1.3f", attrP->colG); + PuSetStr(GGizmo, PU_SC_TEXT, buf); +- (void) sprintf(buf, "%5.3f", attrP->colB); ++ (void) sprintf(buf, "%1.3f", attrP->colB); + PuSetStr(BGizmo, PU_SC_TEXT, buf); + ++ (void) sprintf(buf, "%i", ICOLOR(attrP->colR)); ++ PuSetStr(rGizmo, PU_SC_TEXT, buf); ++ (void) sprintf(buf, "%i", ICOLOR(attrP->colG)); ++ PuSetStr(gGizmo, PU_SC_TEXT, buf); ++ (void) sprintf(buf, "%i", ICOLOR(attrP->colB)); ++ PuSetStr(bGizmo, PU_SC_TEXT, buf); ++ + showName(); + showColor(); + } +@@ -315,107 +432,152 @@ buildDial(void) + PuGizmo g; + PuConstraints con; + int i; +- +- DialGizmo = PuCreateDialog("Color Dialog", 7, 5); +- PuSetBool(DialGizmo, PU_BC_PLACE_OUTSIDE, TRUE); +- +- con.x = 0; +- con.w = 1; +- con.h = 1; +- +- g = PuCreateLabel(DialGizmo, "Name"); +- con.y = 0; +- PuSetConstraints(g, con); +- PuSwitchGizmo(g, TRUE); +- +- g = PuCreateLabel(DialGizmo, "Red"); +- con.y = 1; +- PuSetConstraints(g, con); +- PuSwitchGizmo(g, TRUE); +- +- g = PuCreateLabel(DialGizmo, "Green"); +- con.y = 2; +- PuSetConstraints(g, con); +- PuSwitchGizmo(g, TRUE); +- +- g = PuCreateLabel(DialGizmo, "Blue"); +- con.y = 3; +- PuSetConstraints(g, con); +- PuSwitchGizmo(g, TRUE); +- +- con.x = 1; +- con.w = 2; +- con.h = 1; +- + NameStr = DStrNew(); ++ + RStr = DStrNew(); + GStr = DStrNew(); + BStr = DStrNew(); ++ rStr = DStrNew(); ++ gStr = DStrNew(); ++ bStr = DStrNew(); ++ + DStrAssignStr(RStr, "0.0"); + DStrAssignStr(GStr, "0.0"); + DStrAssignStr(BStr, "0.0"); ++ DStrAssignStr(rStr, "0"); ++ DStrAssignStr(gStr, "0"); ++ DStrAssignStr(bStr, "0"); + ++ DialGizmo = PuCreateDialog("Color Dialog", 3, 20); ++ PuSetBool(DialGizmo, PU_BC_PLACE_OUTSIDE, TRUE); ++ ++ con.x = 1; ++ con.y = 0; ++ con.w = 2; ++ con.h = 3; ++ ColGizmo = PuCreateColorField(DialGizmo, "Color"); ++ PuSetConstraints(ColGizmo, con); ++ PuSetConstraints(ColGizmo, con); ++ showColor(); ++ PuSwitchGizmo(ColGizmo, TRUE); ++ ++ con.x = 0; ++ con.y = 4; ++ con.w = 1; ++ con.h = 1; ++ g = PuCreateLabel(DialGizmo, "Name"); ++ PuSetConstraints(g, con); ++ PuSwitchGizmo(g, TRUE); ++ con.x = 1; ++ con.w = 2; ++ con.h = 1; + NameGizmo = PuCreateTextField(DialGizmo, "Name", DStrToStr(NameStr)); +- con.y = 0; + PuSetConstraints(NameGizmo, con); +- PuSetInt(NameGizmo, PU_IC_TEXT_WIDTH, 13); ++ PuSetInt(NameGizmo, PU_IC_TEXT_WIDTH, 10); + PuAddGizmoCB(NameGizmo, PU_CT_MODIFY, editCB, "N", NULL); + PuAddGizmoCB(NameGizmo, PU_CT_ACTIVATE, activateCB, "N", NULL); + showName(); + PuSwitchGizmo(NameGizmo, TRUE); + +- RGizmo = PuCreateTextField(DialGizmo, "Red", DStrToStr(RStr)); +- con.y = 1; ++ con.x = 1; ++ con.y = 5; ++ con.w = 2; ++ con.h = 5; ++ g = PuCreateList(DialGizmo, "Color List"); ++ for (i = 0; i < ColorNo; i++) ++ PuAddListEntry(g, ColorList[i].name, FALSE); ++ PuSetConstraints(g, con); ++ PuSetBool(g, PU_BC_AUTO_DESEL, TRUE); ++ PuAddGizmoCB(g, PU_CT_SELECT, selectCB, NULL, NULL); ++ PuSwitchGizmo(g, TRUE); ++ ++ con.x = 1; ++ con.y = 11; ++ con.w = 1; ++ con.h = 1; ++ g = PuCreateLabel(DialGizmo, "Float"); ++ PuSetConstraints(g, con); ++ PuSwitchGizmo(g, TRUE); ++ con.x = 2; ++ con.y = 11; ++ g = PuCreateLabel(DialGizmo, "RGB"); ++ PuSetConstraints(g, con); ++ PuSwitchGizmo(g, TRUE); ++ ++ con.x = 0; ++ con.y = 12; ++ con.w = 1; ++ con.h = 1; ++ g = PuCreateLabel(DialGizmo, "Red"); ++ PuSetConstraints(g, con); ++ PuSwitchGizmo(g, TRUE); ++ con.x = 1; ++ RGizmo = PuCreateTextField(DialGizmo, "RED", DStrToStr(RStr)); + PuSetConstraints(RGizmo, con); + PuSetInt(RGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); + PuAddGizmoCB(RGizmo, PU_CT_MODIFY, editCB, "R", NULL); + PuAddGizmoCB(RGizmo, PU_CT_ACTIVATE, activateCB, "R", NULL); + PuSwitchGizmo(RGizmo, TRUE); ++ con.x = 2; ++ rGizmo = PuCreateTextField(DialGizmo, "red", DStrToStr(rStr)); ++ PuSetConstraints(rGizmo, con); ++ PuSetInt(rGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); ++ PuAddGizmoCB(rGizmo, PU_CT_MODIFY, editCB, "r", NULL); ++ PuAddGizmoCB(rGizmo, PU_CT_ACTIVATE, activateCB, "r", NULL); ++ PuSwitchGizmo(rGizmo, TRUE); + +- GGizmo = PuCreateTextField(DialGizmo, "Green", DStrToStr(GStr)); +- con.y = 2; ++ con.x = 0; ++ con.y = 13; ++ con.w = 1; ++ con.h = 1; ++ g = PuCreateLabel(DialGizmo, "Green"); ++ PuSetConstraints(g, con); ++ PuSwitchGizmo(g, TRUE); ++ con.x = 1; ++ GGizmo = PuCreateTextField(DialGizmo, "GREEN", DStrToStr(GStr)); + PuSetConstraints(GGizmo, con); + PuSetInt(GGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); + PuAddGizmoCB(GGizmo, PU_CT_MODIFY, editCB, "G", NULL); + PuAddGizmoCB(GGizmo, PU_CT_ACTIVATE, activateCB, "G", NULL); + PuSwitchGizmo(GGizmo, TRUE); ++ con.x = 2; ++ gGizmo = PuCreateTextField(DialGizmo, "green", DStrToStr(gStr)); ++ PuSetConstraints(gGizmo, con); ++ PuSetInt(gGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); ++ PuAddGizmoCB(gGizmo, PU_CT_MODIFY, editCB, "g", NULL); ++ PuAddGizmoCB(gGizmo, PU_CT_ACTIVATE, activateCB, "g", NULL); ++ PuSwitchGizmo(gGizmo, TRUE); + +- BGizmo = PuCreateTextField(DialGizmo, "Blue", DStrToStr(BStr)); +- con.y = 3; ++ con.x = 0; ++ con.y = 14; ++ con.w = 1; ++ con.h = 1; ++ g = PuCreateLabel(DialGizmo, "Blue"); ++ PuSetConstraints(g, con); ++ PuSwitchGizmo(g, TRUE); ++ con.x = 1; ++ BGizmo = PuCreateTextField(DialGizmo, "BLUE", DStrToStr(BStr)); + PuSetConstraints(BGizmo, con); + PuSetInt(BGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); + PuAddGizmoCB(BGizmo, PU_CT_MODIFY, editCB, "B", NULL); + PuAddGizmoCB(BGizmo, PU_CT_ACTIVATE, activateCB, "B", NULL); + PuSwitchGizmo(BGizmo, TRUE); ++ con.x = 2; ++ bGizmo = PuCreateTextField(DialGizmo, "blue", DStrToStr(bStr)); ++ PuSetConstraints(bGizmo, con); ++ PuSetInt(bGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); ++ PuAddGizmoCB(bGizmo, PU_CT_MODIFY, editCB, "b", NULL); ++ PuAddGizmoCB(bGizmo, PU_CT_ACTIVATE, activateCB, "b", NULL); ++ PuSwitchGizmo(bGizmo, TRUE); + +- ColGizmo = PuCreateColorField(DialGizmo, "Color"); +- con.x = 3; +- con.y = 0; +- con.w = 2; +- con.h = 4; +- PuSetConstraints(ColGizmo, con); +- showColor(); +- PuSwitchGizmo(ColGizmo, TRUE); +- +- g = PuCreateList(DialGizmo, "Color List"); +- for (i = 0; i < ColorNo; i++) +- PuAddListEntry(g, ColorList[i].name, FALSE); +- con.x = 5; +- con.y = 0; +- con.w = 2; +- con.h = 4; +- PuSetConstraints(g, con); +- PuSetBool(g, PU_BC_AUTO_DESEL, TRUE); +- PuAddGizmoCB(g, PU_CT_SELECT, selectCB, NULL, NULL); +- PuSwitchGizmo(g, TRUE); +- +- con.y = 4; ++ con.x = 0; ++ con.y = 15; + con.w = 1; + con.h = 1; +- + for (i = 0; i < CMD_NO; i++) { + g = PuCreateButton(DialGizmo, LabelList[i]); +- con.x = i; ++ con.x = i%3; ++ if (i%3 == 0) con.y++; + PuSetConstraints(g, con); + PuAddGizmoCB(g, PU_CT_ACTIVATE, cmdCB, NULL, NULL); + PuSwitchGizmo(g, TRUE); +diff --git a/src/cmddial/ExDialRes.c b/src/cmddial/ExDialRes.c +new file mode 100644 +index 0000000..06925ff +--- /dev/null ++++ b/src/cmddial/ExDialRes.c +@@ -0,0 +1,340 @@ ++/* ++************************************************************************ ++* ++* ExDialMol.c - DialMol command ++* ++* Copyright (c) 1994-98 ++* ++* ETH Zuerich ++* Institut fuer Molekularbiologie und Biophysik ++* ETH-Hoenggerberg ++* CH-8093 Zuerich ++* ++* SPECTROSPIN AG ++* Industriestr. 26 ++* CH-8117 Faellanden ++* ++* All Rights Reserved ++* ++* Date of last modification : 98/08/17 ++* Pathname of SCCS file : /tmp_mnt/net/sn/homeb/rkoradi/molmol-master/src/cmddial/SCCS/s.ExDialMol.c ++* SCCS identification : 1.10 ++* ++************************************************************************ ++*/ ++ ++#include <cmd_dial.h> ++ ++#include <stdio.h> ++#include <string.h> ++#include <stdlib.h> ++ ++#include <break.h> ++#include <pu.h> ++#include <arg.h> ++#include <cip.h> ++#include <data_hand.h> ++ ++#define PROP_NO 3 ++ ++typedef struct { ++ char *label; ++ char *propName; ++ char *cmd; ++} PropDesc; ++typedef struct { ++ char *name; ++ BOOL active; ++} Residue; ++ ++static BOOL DialOn = FALSE; ++static PuGizmo DialGizmo = NULL, ListGizmo; ++static int CurrProp; ++static PropRefP CurrRefP; ++static int MolNo, MolI; ++static BOOL *MolStateA; ++static BOOL SuppressUpdate = FALSE; ++static PropDesc PropTab[] = { ++ {"sel", PROP_SELECTED, "SelectRes"}, ++ {"disp", PROP_DISPLAYED, "DefPropRes 'displayed'"}, ++ {"move", PROP_MOVABLE, "DefProRes 'movable'"} ++}; ++static Residue ResidueTab[] = { ++ {"ARG", FALSE}, ++ {"CYS", FALSE}, ++ {"PRO", FALSE}, ++ {"ASP", FALSE}, ++ {"PHE", FALSE}, ++ {"LEU", FALSE}, ++ {"GLU", FALSE}, ++ {"PRO", FALSE}, ++ {"TYR", FALSE}, ++ {"GLY", FALSE}, ++ {"ASN", FALSE}, ++ {"ALA", FALSE}, ++ {"SER", FALSE}, ++ {"THR", FALSE}, ++ {"LYS", FALSE}, ++ {"ILE", FALSE} ++}; ++ ++static void ++countMol(DhResP molP, void *clientData) ++{ ++ MolNo++; ++} ++ ++ ++ ++static void ++addMol(DhResP molP, void *clientData) ++{ ++ ++ ++ DSTR name; ++ DSTR residue; ++ char buf[10]; ++ char buf2[5]; ++ BOOL propVal; ++ int j; ++ name = DStrNew(); ++ residue = DStrNew(); ++ ++ ++ j= DhResGetNumber(molP); ++ (void) sprintf(buf, "%5d " , j); ++ ++ DStrAssignStr(name, buf); ++ DStrAssignStr(residue, buf2); ++ DStrAppStr(name, " "); ++ ++ DStrAppDStr(residue, DhResGetName(molP)); ++ DStrAppDStr(name, DhResGetName(molP)); ++ propVal = DhResGetProp(CurrRefP, molP); ++ ++ ++ ++ if (! BreakCheck(10)){ ++ PuAddListEntry(ListGizmo, DStrToStr(name), propVal); ++ ++ } ++ ++ ++ ++ MolStateA[MolI] = propVal; ++ ++ DStrFree(name); ++ ++ MolI++; ++} ++ ++static void ++selectMolCB(PuGizmo g, char *name, void *clientData, void *callData) ++{ ++ PuSelectCBStruc *callP = callData; ++ DSTR cmd; ++ BOOL isFirst; ++ char buf[10]; ++ int num, startI, i; ++ ++ (void) sscanf(name, "%d", &num); ++ MolStateA[num - 1] = callP->onOff; ++ ++ if (! callP->last) ++ return; ++ ++ cmd = DStrNew(); ++ DStrAssignStr(cmd, PropTab[CurrProp].cmd); ++ isFirst = TRUE; ++ ++ for (i = 0; i < MolNo; i++) { ++ if (i == 0 || ! MolStateA[i - 1]) ++ startI = i; ++ if (MolStateA[i] && (i == MolNo - 1 || ! MolStateA[i + 1])) { ++ if (isFirst) ++ DStrAppStr(cmd, " 'num = "); ++ else ++ DStrAppStr(cmd, ","); ++ (void) sprintf(buf, "%d", startI + 1); ++ DStrAppStr(cmd, buf); ++ if (i > startI) { ++ DStrAppStr(cmd, ".."); ++ (void) sprintf(buf, "%d", i + 1); ++ DStrAppStr(cmd, buf); ++ } ++ ++ isFirst = FALSE; ++ } ++ } ++ ++ if (isFirst) ++ DStrAppStr(cmd, " '0'"); ++ else ++ DStrAppStr(cmd, "'"); ++ ++ SuppressUpdate = TRUE; ++ CipExecCmd(DStrToStr(cmd)); ++ SuppressUpdate = FALSE; ++ ++ DStrFree(cmd); ++} ++ ++static void ++buildList(void) ++{ ++ int lineNo; ++ ++ MolNo = 0; ++ DhApplyRes(PropGetRef(PROP_ALL, FALSE), countMol, NULL); ++ if (MolNo > 0) { ++ if (MolStateA == NULL) ++ MolStateA = malloc(MolNo * sizeof(*MolStateA)); ++ else ++ MolStateA = realloc(MolStateA, MolNo * sizeof(*MolStateA)); ++ lineNo = MolNo; ++ if (lineNo > 40) ++ lineNo = 40; ++ } else { ++ lineNo = 1; ++ } ++ ++ PuSetInt(ListGizmo, PU_IC_ENTRY_NO, lineNo); ++ ++ MolI = 0; ++ BreakActivate(TRUE); ++ DhApplyRes(PropGetRef(PROP_ALL, FALSE), addMol, NULL); ++ BreakActivate(FALSE); ++ ++ PuSwitchGizmo(ListGizmo, TRUE); ++} ++ ++static void ++updateList(void) ++{ ++ if (SuppressUpdate) ++ return; ++ ++ PuSwitchGizmo(ListGizmo, FALSE); ++ PuRemoveListEntries(ListGizmo, 0, MolNo); ++ buildList(); ++} ++ ++static void ++selectPropCB(PuGizmo g, char *name, void *clientData, void *callData) ++{ ++ PuSelectCBStruc *callP = callData; ++ PropRefP newPropP; ++ int i; ++ ++ if (! callP->onOff) ++ return; ++ ++ for (i = 0; i < PROP_NO; i++) ++ if (strcmp(name, PropTab[i].label) == 0) ++ break; ++ ++ newPropP = PropGetRef(PropTab[i].propName, FALSE); ++ ++ if (newPropP != CurrRefP) { ++ CurrRefP = newPropP; ++ CurrProp = i; ++ updateList(); ++ } ++} ++ ++static void ++popdownCB(PuGizmo g, char *name, void *clientData, void *callData) ++{ ++ PuSwitchGizmo(DialGizmo, FALSE); ++ DialOn = FALSE; ++} ++ ++static void ++listCB(void *clientData) ++{ ++ updateList(); ++} ++ ++static void ++helpCB(PuGizmo g, char *name, void *clientData, void *callData) ++{ ++ CipShowHelpFile(DialGizmo, "DialMol"); ++} ++ ++static void ++buildDial(void) ++{ ++ ++ PuGizmo g; ++ int i; ++ ++ CurrProp = 0; ++ CurrRefP = PropGetRef(PropTab[CurrProp].propName, FALSE); ++ ++ DialGizmo = PuCreateDialog("Residue Dialog", 0, 0); ++ PuSetBool(DialGizmo, PU_BC_PLACE_OUTSIDE, TRUE); ++ ++ g = PuCreateRadioBox(DialGizmo, "Property"); ++ for (i = 0; i < PROP_NO; i++) ++ PuAddToggle(g, PropTab[i].label, i == 0); ++ PuAddGizmoCB(g, PU_CT_SELECT, selectPropCB, NULL, NULL); ++ PuSwitchGizmo(g, TRUE); ++ ++ ListGizmo = PuCreateList(DialGizmo, "Molecules"); ++ PuAddGizmoCB(ListGizmo, PU_CT_SELECT, selectMolCB, NULL, NULL); ++ PuSetBool(ListGizmo, PU_BC_MULT_SEL, TRUE); ++ buildList(); ++ ++ PuAddGizmoCB(DialGizmo, PU_CT_CLOSE, popdownCB, NULL, NULL); ++ PuAddGizmoCB(DialGizmo, PU_CT_HELP, helpCB, NULL, NULL); ++ ++} ++ ++ErrCode ++ExDialRes(char *cmd) ++{ ++ ArgDescr arg; ++ EnumEntryDescr enumEntry[2]; ++ ErrCode errCode; ++ ++ arg.type = AT_ENUM; ++ ++ ArgInit(&arg, 1); ++ ++ arg.prompt = "Residue Dialog"; ++ arg.u.enumD.entryP = enumEntry; ++ arg.u.enumD.n = 2; ++ ++ enumEntry[0].str = "off"; ++ enumEntry[1].str = "on"; ++ ++ enumEntry[0].onOff = DialOn; ++ enumEntry[1].onOff = ! DialOn; ++ if (DialOn) ++ arg.v.intVal = 0; ++ else ++ arg.v.intVal = 1; ++ ++ errCode = ArgGet(&arg, 1); ++ if (errCode != EC_OK) { ++ ArgCleanup(&arg, 1); ++ return errCode; ++ } ++ ++ DialOn = (arg.v.intVal == 1); ++ ++ ArgCleanup(&arg, 1); ++ ++ if (DialOn) { ++ if (DialGizmo == NULL) { ++ buildDial(); ++ DhAddMolListCB(listCB, NULL); ++ } ++ PuSwitchGizmo(DialGizmo, TRUE); ++ } else { ++ if (DialGizmo != NULL) ++ PuSwitchGizmo(DialGizmo, FALSE); ++ } ++ ++ return EC_OK; ++} +\ No newline at end of file +diff --git a/src/cmddial/Makefile b/src/cmddial/Makefile +index d94609d..66fdea9 100644 +--- a/src/cmddial/Makefile ++++ b/src/cmddial/Makefile +@@ -8,7 +8,7 @@ CPPFLAGS = $(INCLUDES) $(MCPPFLAGS) + CFLAGS = $(CPPFLAGS) $(MCFLAGS) + + OBJ = ExDialColor.o ExDialSelect.o ExDialStyle.o ExDialMol.o ExDialMeas.o \ +- ExDialRmsd.o ExUserInterf.o ExRecordMac.o ++ ExDialRes.o ExDialRmsd.o ExUserInterf.o ExRecordMac.o + SRC = $(OBJ:.o=.c) + + default: $(LIBDIR)/libcmd.a +diff --git a/src/cmdio/ExPdb.c b/src/cmdio/ExPdb.c +index 8447c4c..fde9c73 100644 +--- a/src/cmdio/ExPdb.c ++++ b/src/cmdio/ExPdb.c +@@ -1,7 +1,7 @@ + /* + ************************************************************************ + * +-* ExPdb.c - ReadPdb, ReadListPdb and WritePdb commands ++* ExPdb.c - ReadPdb, ReadOldPdb, ReadListPdb and WritePdb commands + * + * Copyright (c) 1994-98 + * +@@ -105,7 +105,7 @@ compFunc(void *p1, void *p2) + } + + static void +-readTransTab(BOOL pdbToIntern) ++readTransTab(BOOL pdbToIntern, BOOL isNewNomenclature) + { + GFile gf; + GFileRes res; +@@ -114,7 +114,7 @@ readTransTab(BOOL pdbToIntern) + + TransTab = TreeOpen(sizeof(TransTabEntry), compFunc); + gf = SetupOpen(PN_PDB_ATOMS, "PdbAtoms", FALSE); +- if (gf == NULL) ++ if (gf == NULL || isNewNomenclature) + return; + + if (pdbToIntern) { +@@ -675,7 +675,7 @@ ExReadPdb(char *cmd) + return errCode; + } + +- readTransTab(TRUE); ++ readTransTab(TRUE, TRUE); + UnknownErrInit(); + + if (replace) { +@@ -755,7 +755,7 @@ ExReadListPdb(char *cmd) + + FileNamePath(fileName); + +- readTransTab(TRUE); ++ readTransTab(TRUE,TRUE); + UnknownErrInit(); + inName = DStrNew(); + pdbName = DStrNew(); +@@ -932,7 +932,7 @@ ExWritePdb(char *cmd) + if (gf == NULL) + return EC_ERROR; + +- readTransTab(FALSE); ++ readTransTab(FALSE,TRUE); + + CHECK_RES(GFileWriteStr(gf, "HEADER Structure from")); + CHECK_RES(GFileWriteStr(gf, PROG_NAME)); +@@ -987,3 +987,61 @@ ExWritePdb(char *cmd) + + return EC_OK; + } ++ ++ErrCode ++ExReadOldPdb(char *cmd) ++{ ++ BOOL replace; ++ DSTR name; ++ int molNo, readNo; ++ DhMolP *molPA; ++ ErrCode errCode; ++ DSTR errStr; ++ ++ replace = (strncmp(cmd, "Replace", 7) == 0); ++ ++ name = DStrNew(); ++ errCode = ArgGetFilename(name, CurrDirGet(), "*.pdb", TRUE); ++ if (errCode != EC_OK) { ++ DStrFree(name); ++ return errCode; ++ } ++ ++ readTransTab(TRUE, FALSE); ++ UnknownErrInit(); ++ ++ if (replace) { ++ molNo = SelMolGet(NULL, 0); ++ if (molNo > 0) { ++ molPA = malloc(molNo * sizeof(*molPA)); ++ (void) SelMolGet(molPA, molNo); ++ } ++ } else { ++ molNo = 0; ++ molPA = NULL; ++ } ++ ++ BreakActivate(TRUE); ++ errCode = readFile(molPA, molNo, name, &readNo); ++ BreakActivate(FALSE); ++ ++ DStrFree(name); ++ TreeClose(TransTab); ++ if (molNo > 0) ++ free(molPA); ++ ++ if (errCode != EC_OK) ++ return EC_ERROR; ++ ++ if (replace) ++ GraphMolChanged(PROP_SELECTED); ++ ++ errStr = UnknownErrGet(); ++ if (errStr != NULL) { ++ CipSetError(DStrToStr(errStr)); ++ DStrFree(errStr); ++ return EC_WARNING; ++ } ++ ++ return EC_OK; ++} +diff --git a/src/cmdstruc/ExBuild.c b/src/cmdstruc/ExBuild.c +index 32bc650..7f003b2 100644 +--- a/src/cmdstruc/ExBuild.c ++++ b/src/cmdstruc/ExBuild.c +@@ -31,11 +31,16 @@ + #include <data_hand.h> + #include <data_sel.h> + #include <graph_draw.h> ++#include <pu.h> + + #define ARG_NUM 1 + + static int CurrPos = 1; + static int CurrKind = 0; ++static PuTextWindow TextW; ++static DhMolP LastMolP=NULL; ++static BOOL messageWindowCreated=FALSE; ++static BOOL cyclicResidueFound=FALSE; + + ErrCode + ExNewMol(char *cmd) +@@ -206,3 +211,121 @@ ExChangeRes(char *cmd) + + return EC_OK; + } ++ ++static void ++writeInt(int num) ++{ ++ char buf[10]; ++ (void) sprintf(buf, "%5d ", num); ++ PuWriteStr(TextW, buf); ++} ++ ++static void ++checkMolCyclic(DhMolP molP, void *clientData) ++{ ++ DhResP resP; ++ DSTR resName = DStrNew(); ++ DStrAssignStr(resName, "XXX"); ++ ++ resP = DhResFirst(molP); ++ while (resP != NULL) { ++ if (DStrCmp(resName, DhResGetName(resP)) == 0) { ++ cyclicResidueFound=TRUE; ++ } ++ resP = DhResNext(resP); ++ } ++ ++ if (cyclicResidueFound && !messageWindowCreated) { ++ TextW = PuCreateTextWindow("MakeMolCyclic"); ++ PuWriteStr(TextW, "--------------------------------------------------\n"); ++ messageWindowCreated=TRUE; ++ } ++ if (cyclicResidueFound) { ++ PuWriteStr(TextW, "Error -"); ++ writeInt(DhMolGetNumber(molP) + 1); ++ PuWriteStr(TextW, DStrToStr(DhMolGetName(molP))); ++ PuWriteStr(TextW, " already made cyclic!\n"); ++ } ++} ++ ++static void ++makeMolCyclic(DhMolP molP, void *clientData) ++{ ++ DhResP xResP, yResP; ++ Vec3 firstCoord, lastCoord, midCoord; ++ DhResP firstResP, lastResP; ++ DhAtomP caAtomP; ++ DSTR atomName = DStrNew(); ++ DhResDefP resDefP = (DhResDefP) clientData; ++ ++ DStrAssignStr(atomName, "CA"); ++ ++ xResP = DhResNewCyclic(molP, resDefP, SP_FIRST); ++ DhResInit(xResP); ++ yResP = DhResNewCyclic(molP, resDefP, SP_LAST); ++ DhResInit(yResP); ++ ++ xResP = DhResFirst(molP); ++ ++ firstResP = DhResNext(xResP); ++ caAtomP = NULL; ++ while (caAtomP == NULL && firstResP != NULL) { ++ caAtomP = DhAtomFindName(firstResP, atomName, FALSE); ++ firstResP = DhResNext(firstResP); ++ } ++ if (caAtomP == NULL) { ++ return; ++ } ++ DhAtomGetCoord(caAtomP, firstCoord); ++ ++ yResP = DhResLast(molP); ++ lastResP = DhResPrev(yResP); ++ caAtomP = NULL; ++ while (caAtomP == NULL && lastResP != NULL) { ++ caAtomP = DhAtomFindName(lastResP, atomName, FALSE); ++ lastResP = DhResPrev(lastResP); ++ } ++ if (caAtomP == NULL) { ++ return; ++ } ++ ++ DhAtomGetCoord(caAtomP, lastCoord); ++ ++ midCoord[0] = (firstCoord[0]+lastCoord[0])/2; ++ midCoord[1] = (firstCoord[1]+lastCoord[1])/2; ++ midCoord[2] = (firstCoord[2]+lastCoord[2])/2; ++ ++ DhAtomSetCoord(DhResGetAtomA(xResP), midCoord); ++ DhAtomSetCoord(DhResGetAtomA(yResP), midCoord); ++} ++ ++ErrCode ++ExMakeMolCyclic(char *cmd) ++{ ++ int ind=0; ++ DhResDefP resDefP; ++ DSTR resName = DStrNew(); ++ ++ messageWindowCreated=FALSE; ++ cyclicResidueFound=FALSE; ++ DhApplyMol(PropGetRef(PROP_SELECTED, FALSE), checkMolCyclic, NULL); ++ if (cyclicResidueFound) { ++ DSTR msg = DStrNew(); ++ DStrAssignStr(msg, "Error cyclic molecules selected"); ++ PuSetTextField(PU_TF_STATUS, DStrToStr(msg)); ++ DStrFree(msg); ++ return EC_OK; ++ } ++ ++ DStrAssignStr(resName, "XXX"); ++ resDefP = DhResDefGet(resName); ++ if (resDefP == NULL) { ++ CipSetError("error cyclic marker residue 'XXX' not found in residue library"); ++ return EC_ERROR; ++ } ++ ++ DhApplyMol(PropGetRef(PROP_SELECTED, FALSE), makeMolCyclic, resDefP); ++ GraphMolChanged(PROP_SELECTED); ++ GraphRedrawNeeded(); ++ return EC_OK; ++} +diff --git a/src/data/DataHand.c b/src/data/DataHand.c +index 368aad3..d020c20 100644 +--- a/src/data/DataHand.c ++++ b/src/data/DataHand.c +@@ -994,9 +994,11 @@ BOOL + DhResDestroy(DhResP resP) + { + /* can only destroy first or last residue of molecule! */ ++ DhMolP molP; + if (resP == ListFirst(resP->molP->resL)) { ++ molP = resP->molP; + ListRemove(resP->molP->resL, resP); +- setEquivI(ListFirst(resP->molP->resL), NULL); ++ setEquivI((DhResP)ListFirst(molP->resL), NULL); + return TRUE; + } else if (resP == ListLast(resP->molP->resL)) { + ListRemove(resP->molP->resL, resP); +@@ -2842,6 +2844,18 @@ DhResGetName(DhResP resP) + return resP->defP->name; + } + ++DhAtomP ++DhResGetAtomA(DhResP resP) ++{ ++ return resP->atomA; ++} ++ ++DhResDefP ++DhResGetDefP(DhResP resP) ++{ ++ return resP->defP; ++} ++ + int + DhResGetNumber(DhResP resP) + { +@@ -3313,3 +3327,101 @@ DhAltCoordListGet(void) + { + return AltCoordList; + } ++ ++static void ++initResCyclic(DhResP resP) ++{ ++ DhResDefP defP; ++ DhResP prevResP, nextResP; ++ DhAtomP atomP, equivAtomP; ++ int i; ++ ++ defP = resP->defP; ++ ++ resP->neighLeftP = NULL; ++ resP->neighRightP = NULL; ++ ++ resP->atomA = malloc(defP->atomNo * sizeof(*resP->atomA)); ++ resP->bondA = malloc(defP->bondNo * sizeof(*resP->bondA)); ++ resP->angleA = malloc(defP->angleNo * sizeof(*resP->angleA)); ++ ++ for (i = 0; i < defP->atomNo; i++) ++ initAtom(resP->atomA + i, resP); ++ ++ for (i = defP->firstBondI; i <= defP->lastBondI; i++) ++ initBond(resP->bondA + i, resP); ++ ++ for (i = 0; i < defP->angleNo; i++) { ++ resP->angleA[i].resP = resP; ++ resP->angleA[i].val = 0.0f; ++ resP->angleA[i].minVal = DH_ANGLE_MIN; ++ resP->angleA[i].maxVal = DH_ANGLE_MAX; ++ resP->angleA[i].changed = FALSE; ++ resP->angleA[i].propTab = PropNewTab(FALSE); ++ } ++ ++ resP->propTab = PropNewTab(FALSE); ++ ++ for (i = 0; i < EQUIV_NO; i++) { ++ resP->equivI[i] = -1; ++ } ++ ++ prevResP = ListPrev(resP->molP->resL, resP); ++ nextResP = ListNext(resP->molP->resL, resP); ++} ++ ++DhResP ++DhResNewCyclic(DhMolP molP, DhResDefP defP, DhSeqPos pos) ++{ ++ struct DhResS resS; ++ DhResP resP, prevResP, nextResP; ++ ++ resS.molP = molP; ++ resS.defP = defP; ++ ++ if (pos == SP_FIRST) { ++ nextResP = ListFirst(molP->resL); ++ if (nextResP == NULL) ++ resS.num = 1; ++ else ++ resS.num = nextResP->num - 1; ++ ++ resP = ListInsertFirst(molP->resL, &resS); ++ } else { ++ prevResP = ListLast(molP->resL); ++ if (prevResP == NULL) ++ resS.num = 1; ++ else ++ resS.num = prevResP->num + 1; ++ ++ resP = ListInsertLast(molP->resL, &resS); ++ } ++ ++ initResCyclic(resP); ++ ++ return resP; ++} ++ ++DhResP ++DhResPrev(DhResP resP) ++{ ++ return (DhResP) ListPrev(resP->molP->resL, resP); ++} ++ ++DhResP ++DhResNext(DhResP resP) ++{ ++ return (DhResP) ListNext(resP->molP->resL, resP); ++} ++ ++DhResP ++DhResFirst(DhMolP molP) ++{ ++ return (DhResP) ListFirst(molP->resL); ++} ++ ++DhResP ++DhResLast(DhMolP molP) ++{ ++ return (DhResP) ListLast(molP->resL); ++} +diff --git a/src/iodev/IODev.c b/src/iodev/IODev.c +index aa4f9a7..9c04ce8 100644 +--- a/src/iodev/IODev.c ++++ b/src/iodev/IODev.c +@@ -44,6 +44,7 @@ extern void IOMotifGLDSetDev(void); + #endif + #ifdef IO_DEV_MOTIF_OGL + extern void IOMotifOGLSetDev(void); ++extern void IOMotifOGLDSetDev(void); + #endif + #ifdef IO_DEV_MOTIF_XGL + extern void IOMotifXGLSetDev(void); +@@ -75,6 +76,7 @@ static DevListEntry DevList[] = { + #endif + #ifdef IO_DEV_MOTIF_OGL + {"Motif/OpenGL", IOMotifOGLSetDev}, ++ {"Motif/OpenGLD", IOMotifOGLDSetDev}, + #endif + #ifdef IO_DEV_MOTIF_XGL + {"Motif/XGL", IOMotifXGLSetDev}, +diff --git a/src/main/MolInit.c b/src/main/MolInit.c +index a7c467a..fccccd3 100644 +--- a/src/main/MolInit.c ++++ b/src/main/MolInit.c +@@ -313,8 +313,9 @@ MolInit(char *defaultDev, int argc, char *argv[], char *macroName) + + SgSetDoubleBuffer(TRUE); + +- ProgDirSet("MOLMOLHOME", "/usr/molmol"); ++ ProgDirSet("MOLMOLHOME", argv[0]); + SetupSetDir("setup"); ++ CurrDirSet(getenv("HOME")); +- UserFileSetDir(CurrDirGet(), "molmol"); ++ UserFileSetDir(CurrDirGet(), ".molmol"); + GFileSetErrorHandler(handleFileError); + +@@ -326,7 +327,7 @@ MolInit(char *defaultDev, int argc, char *argv[], char *macroName) + IOSetErrorHandler(handleIOError); + + PuSetTextField(PU_TF_TITLE, +- "MOLMOL - MOLecule analysis and MOLecule display"); ++ "MOLMOL - MOLecule analysis and MOLecule display - JCU V1.0.8"); + + gf = UserFileOpenRead("par"); + if (gf != NULL) { +diff --git a/src/main/MolMol.c b/src/main/MolMol.c +index 6f825e8..902b50a 100644 +--- a/src/main/MolMol.c ++++ b/src/main/MolMol.c +@@ -30,5 +30,5 @@ + int + main(int argc, char *argv[]) + { +- return MolInit("Motif/X11", argc, argv, NULL); ++ return MolInit("Motif/OpenGL", argc, argv, NULL); + } +diff --git a/src/motif/MotifDial.c b/src/motif/MotifDial.c +index 6e3bfd7..8fe0c5a 100644 +--- a/src/motif/MotifDial.c ++++ b/src/motif/MotifDial.c +@@ -1115,26 +1115,24 @@ PuMotifSetStr(PuGizmo gizmo, PuStrChoice choice, char *val) + void + PuMotifSetColor(PuGizmo gizmo, float r, float g, float b) + { +- Display *dpy; +- int screen; +- Pixel pix; +- XColor col; ++ Display *display; ++ Pixel pixel; ++ XColor color; ++ Colormap colormap; + +- dpy = XtDisplay(gizmo); +- screen = DefaultScreen(dpy); +- XtVaGetValues(gizmo, +- XmNbackground, &pix, +- NULL); ++ display = XtDisplay(gizmo); ++ XtVaGetValues(gizmo, XmNbackground, &pixel, NULL); ++ colormap = DefaultColormapOfScreen(XtScreen(gizmo)); + +- if (pix == BlackPixel(dpy, screen)) +- return; ++ color.pixel = pixel; ++ color.red = FLOAT2SHORT(r); ++ color.green = FLOAT2SHORT(g); ++ color.blue = FLOAT2SHORT(b); ++ color.flags = DoRed | DoGreen | DoBlue; + +- col.pixel = pix; +- col.red = FLOAT2SHORT(r); +- col.green = FLOAT2SHORT(g); +- col.blue = FLOAT2SHORT(b); +- col.flags = DoRed | DoGreen | DoBlue; +- XStoreColor(dpy, DefaultColormap(dpy, screen), &col); ++ XFreeColors(display, colormap, &pixel, 1, 0); ++ XAllocColor(display, colormap, &color); ++ XtVaSetValues(gizmo, XmNbackground, color.pixel, NULL); + } + + void +diff --git a/src/motogl/MotOGLDump.c b/src/motogl/MotOGLDump.c +index 54a4222..3bc25cc 100644 +--- a/src/motogl/MotOGLDump.c ++++ b/src/motogl/MotOGLDump.c +@@ -302,7 +302,7 @@ writeImg(void) + TIFFSetField(tif, TIFFTAG_BITSPERSAMPLE, 8); + + if (Quality < 100) +- TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_PACKBITS); ++ TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_LZW); + else + TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_NONE); + +diff --git a/src/os/CurrDir.c b/src/os/CurrDir.c +index edee778..7d2b242 100644 +--- a/src/os/CurrDir.c ++++ b/src/os/CurrDir.c +@@ -26,9 +26,9 @@ + #include <curr_dir.h> + + #include <stdlib.h> +-#ifdef WIN32 +-#include <direct.h> + #include <string.h> ++#ifdef WIN32 ++#include <direct.h> + #else + #include <unistd.h> + #include <errno.h> +@@ -36,43 +36,15 @@ + + static char *CurrDir = NULL; + ++void ++CurrDirSet(char *dir) ++{ ++ CurrDir = malloc(strlen(dir) + 1); ++ (void) strcpy(CurrDir, dir); ++} ++ + char * + CurrDirGet(void) + { +-#ifdef WIN32 +- int len, i; +-#else +- int size = 10; +-#endif +- +- if (CurrDir != NULL) +- return CurrDir; +- +-#ifdef WIN32 +- CurrDir = _getcwd(NULL, 0); +- if (CurrDir != NULL) { +- len = strlen(CurrDir); +- for (i = 0; i < len; i++) +- if (CurrDir[i] == '\\') +- CurrDir[i] = '/'; +- return CurrDir; +- } +-#else +- CurrDir = malloc(size); +- for (;;) { +- if (getcwd(CurrDir, size) != NULL) +- return CurrDir; +- if (errno != ERANGE) +- break; +- size *= 2; +- CurrDir = realloc(CurrDir, size); +- } +-#endif +- +- /* cannot get current directory, return root directory */ +- CurrDir = realloc(CurrDir, 2); +- CurrDir[0] = '/'; +- CurrDir[1] = '\0'; +- + return CurrDir; + } +diff --git a/src/os/ProgDir.c b/src/os/ProgDir.c +index 7abb08d..79ede45 100644 +--- a/src/os/ProgDir.c ++++ b/src/os/ProgDir.c +@@ -45,10 +45,6 @@ ProgDirSet(char *envVar, char *defVal) + dir = getenv(envVar); + if (dir == NULL) { + len = GetModuleFileName(NULL, exePath, sizeof(exePath)); +- if (len == 0) { +- ProgDir = defVal; +- return; +- } + len--; + while (len > 0 && exePath[len] != '\\') + len--; +@@ -65,9 +61,24 @@ ProgDirSet(char *envVar, char *defVal) + if (ProgDir[i] == '\\') + ProgDir[i] = '/'; + #else +- ProgDir = getenv(envVar); +- if (ProgDir == NULL) +- ProgDir = defVal; ++ char *dir; ++ char *exePath; ++ int len; ++ dir = getenv(envVar); ++ if (dir == NULL) { ++ exePath = defVal; ++ len = strlen(exePath); ++ len--; ++ while (len > 0 && exePath[len] != '/') ++ len--; ++ dir = exePath; ++ } else { ++ len = strlen(dir); ++ } ++ ++ ProgDir = malloc(len + 1); ++ (void) strncpy(ProgDir, dir, len); ++ + #endif + } + +diff --git a/src/win/WinDial.c b/src/win/WinDial.c +index 61d6432..e880559 100644 +--- a/src/win/WinDial.c ++++ b/src/win/WinDial.c +@@ -1072,148 +1072,143 @@ dialProc(HWND w, UINT msgKind, WPARAM wParam, LPARAM lParam) + childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA); + + switch (notifyCode) { +- case BN_CLICKED: +- if (childId < infoP->u.dial.childNo) { ++ case BN_CLICKED: ++ if (childId < infoP->u.dial.childNo) { + childP = (GizmoInfo *) GetWindowLong(GetFocus(), GWL_USERDATA); +- if (childP->type == GIZMO_TOGGLE) { +- boxP = childP->u.toggle.boxP; +- if (boxP->type == GIZMO_RADIO_BOX) { +- for (i = 0; i < infoP->u.dial.childNo; i++) { +- cP = infoP->u.dial.childPA[i]; +- if (cP->type != GIZMO_TOGGLE) +- continue; +- if (cP->u.toggle.boxP != boxP) +- continue; +- onOff = SendMessage(cP->w, BM_GETCHECK, 0, 0); +- if (onOff && cP != childP) { +- cP->u.toggle.onOff = FALSE; +- SendMessage(cP->w, BM_SETCHECK, FALSE, 0); +- selectStruc.onOff = FALSE; +- callCB(boxP, PU_CT_SELECT, cP->name, &selectStruc); +- break; +- } +- } +- if (cP != childP) { +- childP->u.toggle.onOff = TRUE; +- SendMessage(childP->w, BM_SETCHECK, TRUE, 0); +- selectStruc.onOff = TRUE; +- callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc); +- } +- } else { +- onOff = ! SendMessage(childP->w, BM_GETCHECK, 0, 0); +- childP->u.toggle.onOff = onOff; +- SendMessage(childP->w, BM_SETCHECK, onOff, 0); +- selectStruc.onOff = onOff; +- callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc); +- } +- } else { +- callCB(childP, PU_CT_ACTIVATE, childP->name, NULL); +- if (childP->type == GIZMO_TEXT_FIELD && +- childP->u.text.historySize > 0) +- childP->u.text.firstMod = TRUE; +- } +- } else { +- buttonI = childId - infoP->u.dial.childNo; +- callCB(infoP, BUTTON_FIRST + buttonI, ButtonLabelA[buttonI], NULL); +- } ++ if (childP->type == GIZMO_TOGGLE) { ++ boxP = childP->u.toggle.boxP; ++ if (boxP->type == GIZMO_RADIO_BOX) { ++ for (i = 0; i < infoP->u.dial.childNo; i++) { ++ cP = infoP->u.dial.childPA[i]; ++ if (cP->type != GIZMO_TOGGLE) continue; ++ if (cP->u.toggle.boxP != boxP) continue; ++ onOff = SendMessage(cP->w, BM_GETCHECK, 0, 0); ++ if (onOff && cP != childP) { ++ cP->u.toggle.onOff = FALSE; ++ SendMessage(cP->w, BM_SETCHECK, FALSE, 0); ++ selectStruc.onOff = FALSE; ++ callCB(boxP, PU_CT_SELECT, cP->name, &selectStruc); ++ break; ++ } ++ } ++ if (cP != childP) { ++ childP->u.toggle.onOff = TRUE; ++ SendMessage(childP->w, BM_SETCHECK, TRUE, 0); ++ selectStruc.onOff = TRUE; ++ callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc); ++ } ++ } else { ++ onOff = ! SendMessage(childP->w, BM_GETCHECK, 0, 0); ++ childP->u.toggle.onOff = onOff; ++ SendMessage(childP->w, BM_SETCHECK, onOff, 0); ++ selectStruc.onOff = onOff; ++ callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc); ++ } ++ } else { ++ callCB(childP, PU_CT_ACTIVATE, childP->name, NULL); ++ if (childP->type == GIZMO_TEXT_FIELD && childP->u.text.historySize > 0) childP->u.text.firstMod = TRUE; ++ } ++ } else { ++ buttonI = childId - infoP->u.dial.childNo; ++ callCB(infoP, BUTTON_FIRST + buttonI, ButtonLabelA[buttonI], NULL); ++ } + return TRUE; +- case EN_UPDATE: +- textEdit(childP); +- return TRUE; +- case LBN_SELCHANGE: +- for (i = 0; i < childP->u.list.entryNo; i++) +- if (SendMessage(childW, LB_GETSEL, i, 0) != +- childP->u.list.entryA[i].onOff) +- lastI = i; + +- for (i = 0; i < childP->u.list.entryNo; i++) { +- onOff = SendMessage(childW, LB_GETSEL, i, 0); +- if (onOff != childP->u.list.entryA[i].onOff) { +- if (! childP->u.list.autoDesel) ++ case EN_UPDATE: ++ textEdit(childP); ++ return TRUE; ++ ++ case LBN_SELCHANGE: ++ for (i = 0; i < childP->u.list.entryNo; i++) ++ if (SendMessage(childW, LB_GETSEL, i, 0) != childP->u.list.entryA[i].onOff) ++ lastI = i; ++ ++ for (i = 0; i < childP->u.list.entryNo; i++) { ++ onOff = SendMessage(childW, LB_GETSEL, i, 0); ++ if (onOff != childP->u.list.entryA[i].onOff) { ++ if (! childP->u.list.autoDesel) + childP->u.list.entryA[i].onOff = onOff; +- selectStruc.onOff = onOff; +- selectStruc.last = (i == lastI); +- callCB(childP, PU_CT_SELECT, +- childP->u.list.entryA[i].str, &selectStruc); +- } +- } +- +- if (childP->u.list.autoDesel) +- SendMessage(childW, LB_SETCURSEL, -1, 0); +- +- return TRUE; ++ selectStruc.onOff = onOff; ++ selectStruc.last = (i == lastI); ++ callCB(childP, PU_CT_SELECT, ++ childP->u.list.entryA[i].str, &selectStruc); ++ } ++ } ++ if (childP->u.list.autoDesel) ++ SendMessage(childW, LB_SETCURSEL, -1, 0); ++ return TRUE; + } ++ break; + +- break; +- case WM_VSCROLL: +- childW = (HWND) lParam; +- childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA); +- scrollCode = LOWORD(wParam); ++ case WM_VSCROLL: ++ childW = (HWND) lParam; ++ childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA); ++ scrollCode = LOWORD(wParam); + +- if (scrollCode == SB_LINEUP) { +- upHistory(childP->u.scroll.textP); +- } else if (scrollCode == SB_LINEDOWN) { +- downHistory(childP->u.scroll.textP); +- } else { +- return FALSE; +- } +- return TRUE; +- case WM_HSCROLL: +- scrollCode = LOWORD(wParam); +- if (scrollCode != SB_THUMBPOSITION && scrollCode != SB_THUMBTRACK) +- return FALSE; ++ if (scrollCode == SB_LINEUP) { ++ upHistory(childP->u.scroll.textP); ++ } else if (scrollCode == SB_LINEDOWN) { ++ downHistory(childP->u.scroll.textP); ++ } else { ++ return FALSE; ++ } ++ return TRUE; ++ case WM_HSCROLL: ++ scrollCode = LOWORD(wParam); ++ if (scrollCode != SB_THUMBPOSITION && scrollCode != SB_THUMBTRACK) ++ return FALSE; + +- scrollPos = (int)(short)HIWORD(wParam); +- childW = (HWND) lParam; +- childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA); ++ scrollPos = (int)(short)HIWORD(wParam); ++ childW = (HWND) lParam; ++ childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA); + +- floatStruc.oldVal = childP->u.slider.val; +- childP->u.slider.val = scrollPos / childP->u.slider.factor; +- SetScrollPos(childW, SB_CTL, +- (int) (childP->u.slider.val * childP->u.slider.factor), +- TRUE); ++ floatStruc.oldVal = childP->u.slider.val; ++ childP->u.slider.val = scrollPos / childP->u.slider.factor; ++ SetScrollPos(childW, SB_CTL, ++ (int) (childP->u.slider.val * childP->u.slider.factor), TRUE); + +- if (childP->u.slider.valuatorCB == NULL) { +- floatStruc.newVal = childP->u.slider.val; +- callCB(childP, PU_CT_MODIFY, childP->name, &floatStruc); +- } else { +- valStruc.act = PU_MA_ACTIVATE; +- valStruc.name = childP->name; +- valStruc.val = childP->u.slider.val; +- childP->u.slider.valuatorCB(childP, childP->u.slider.clientData, &valStruc); +- } ++ if (childP->u.slider.valuatorCB == NULL) { ++ floatStruc.newVal = childP->u.slider.val; ++ callCB(childP, PU_CT_MODIFY, childP->name, &floatStruc); ++ } else { ++ valStruc.act = PU_MA_ACTIVATE; ++ valStruc.name = childP->name; ++ valStruc.val = childP->u.slider.val; ++ childP->u.slider.valuatorCB(childP, childP->u.slider.clientData, &valStruc); ++ } ++ return TRUE; + +- return TRUE; +- case WM_PAINT: +- for (childId = 0; childId < infoP->u.dial.childNo; childId++) { +- childP = infoP->u.dial.childPA[childId]; +- if (childP->type == GIZMO_COLOR_FIELD) +- paintColor(childP->w, +- childP->u.color.r, childP->u.color.g, childP->u.color.b); +- } +- break; +- case WM_MOVE: +- if (infoP->u.dial.outside) { +- WinPlaceChanged(infoP->w); +- return TRUE; +- } +- break; +- case WM_CLOSE: +- buttonNo = 0; +- for (i = 0; i < BUTTON_NO; i++) +- if (infoP->u.dial.buttonSwitchA[i]) +- buttonNo++; +- if (buttonNo == 0) +- ShowWindow(infoP->w, SW_HIDE); +- return TRUE; +- case WM_DESTROY: +- WinRemoveDialog(w); +- for (childId = 0; childId < infoP->u.dial.childNo; childId++) +- freeInfo(infoP->u.dial.childPA[childId]); +- freeInfo(infoP); +- return TRUE; +- } ++ case WM_PAINT: ++ for (childId = 0; childId < infoP->u.dial.childNo; childId++) { ++ childP = infoP->u.dial.childPA[childId]; ++ if (childP->type == GIZMO_COLOR_FIELD) ++ paintColor(childP->w, ++ childP->u.color.r, childP->u.color.g, childP->u.color.b); ++ } ++ break; + ++ case WM_MOVE: ++ if (infoP->u.dial.outside) { ++ WinPlaceChanged(infoP->w); ++ return TRUE; ++ } ++ break; ++ case WM_CLOSE: ++ buttonNo = 0; ++ for (i = 0; i < BUTTON_NO; i++) { ++ if (infoP->u.dial.buttonSwitchA[i]) buttonNo++; ++ if (buttonNo == 0) { ++ ShowWindow(infoP->w, SW_HIDE); ++ } ++ } ++ return TRUE; ++ case WM_DESTROY: ++ WinRemoveDialog(w); ++ for (childId = 0; childId < infoP->u.dial.childNo; childId++) ++ freeInfo(infoP->u.dial.childPA[childId]); ++ freeInfo(infoP); ++ return TRUE; ++ } + return FALSE; + } + +diff --git a/src/winogl/WinOGLDump.c b/src/winogl/WinOGLDump.c +index 0a7d61a..a8ce850 100644 +--- a/src/winogl/WinOGLDump.c ++++ b/src/winogl/WinOGLDump.c +@@ -44,6 +44,7 @@ + #endif + #ifdef PNG_SUPPORT + #include <png.h> ++#include <pngpriv.h> + #endif + + #include "winogl_int.h" +@@ -251,7 +252,7 @@ static void + pngErrHand(png_structp pngStrucP, char *errMsg) + { + IORaiseError(errMsg); +- longjmp(pngStrucP->jmpbuf, 1); ++ longjmp(pngStrucP->longjmp_buffer, 1); + } + #endif + +@@ -314,7 +315,7 @@ writeImg(void) + TIFFSetField(tif, TIFFTAG_BITSPERSAMPLE, 8); + + if (Quality < 100) +- TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_PACKBITS); ++ TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_LZW); + else + TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_NONE); + +@@ -369,7 +370,7 @@ writeImg(void) + return IO_RES_ERR; + } + +- if (setjmp(pngStrucP->jmpbuf)) { ++ if (setjmp(pngStrucP->longjmp_buffer)) { + if (cBuf != NULL) + free(cBuf); + if (fBuf != NULL) diff --git a/sci-chemistry/molmol/metadata.xml b/sci-chemistry/molmol/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/molmol/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild new file mode 100644 index 000000000000..9fafb28a9e9f --- /dev/null +++ b/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild @@ -0,0 +1,79 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils multilib prefix toolchain-funcs + +MY_PV="${PV/_p/.}.0" +MY_P="${PN}-${MY_PV}" + +DESCRIPTION="Publication-quality molecular visualization package" +HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" +SRC_URI=" + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz" + +LICENSE="molmol" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND=" + || ( + ( media-libs/mesa + x11-libs/libGLw ) + media-libs/mesa[motif] ) + media-libs/libpng:0 + media-libs/tiff:0 + sys-libs/zlib + virtual/glu + virtual/jpeg + x11-libs/libXpm + x11-libs/motif:0 + x11-apps/xdpyinfo" +RDEPEND="${DEPEND}" + +S="${WORKDIR}" + +MAKEOPTS="${MAKEOPTS} -j1" + +pkg_setup() { + MMDIR="/usr/$(get_libdir)/molmol" +} + +src_prepare() { + rm -rf tiff* + # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided + epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff + + epatch "${FILESDIR}"/prefix.patch + eprefixify molmol + + epatch "${FILESDIR}"/ldflags.patch + + ln -s makedef.lnx "${S}"/makedef || die + + sed \ + -e "s:/bin/ksh:${EPREFIX}/bin/sh:" \ + -e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \ + -i "${S}"/molmol || die + sed \ + -e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -i "${S}"/makedef || die + + epatch "${FILESDIR}"/cast.patch + epatch "${FILESDIR}"/libpng15.patch +} + +src_install() { + dobin molmol + + exeinto ${MMDIR} + newexe src/main/molmol molmol.lnx + insinto ${MMDIR} + doins -r auxil help macros man setup tips + + dodoc HISTORY README +} diff --git a/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild new file mode 100644 index 000000000000..318269562f26 --- /dev/null +++ b/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils multilib prefix toolchain-funcs + +MY_PV="${PV/_p/.}.0" +MY_P="${PN}-${MY_PV}" + +DESCRIPTION="Publication-quality molecular visualization package" +HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" +SRC_URI=" + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz" + +LICENSE="molmol" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND=" + || ( + ( media-libs/mesa + x11-libs/libGLw ) + media-libs/mesa[motif] ) + media-libs/libpng:0 + media-libs/tiff:0 + sys-libs/zlib + virtual/glu + virtual/jpeg + x11-libs/libXpm + x11-libs/motif:0 + x11-apps/xdpyinfo" +RDEPEND="${DEPEND}" + +S="${WORKDIR}" + +MAKEOPTS="${MAKEOPTS} -j1" + +pkg_setup() { + MMDIR="/usr/$(get_libdir)/molmol" +} + +src_prepare() { + rm -rf tiff* + # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided + epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff + + epatch "${FILESDIR}"/prefix.patch + eprefixify molmol + + epatch "${FILESDIR}"/ldflags.patch + + ln -s makedef.lnx "${S}"/makedef || die + + sed \ + -e "s:/bin/ksh:${EPREFIX}/bin/sh:" \ + -e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \ + -i "${S}"/molmol || die + sed \ + -e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -i "${S}"/makedef || die + + epatch "${FILESDIR}"/cast.patch + epatch "${FILESDIR}"/libpng15.patch + + # patch from fink + # fixes numerous bad bracings and hopefully the OGL bug 429974 + epatch "${FILESDIR}"/${P}-fink.patch +} + +src_install() { + dobin molmol + + exeinto ${MMDIR} + newexe src/main/molmol molmol.lnx + insinto ${MMDIR} + doins -r auxil help macros man setup tips + + dodoc HISTORY README +} diff --git a/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild new file mode 100644 index 000000000000..d4034a9d63c5 --- /dev/null +++ b/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild @@ -0,0 +1,85 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils multilib prefix toolchain-funcs + +MY_PV="${PV/_p/.}.0" +MY_P="${PN}-${MY_PV}" + +DESCRIPTION="Publication-quality molecular visualization package" +HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" +SRC_URI=" + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz" + +LICENSE="molmol" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND=" + || ( + ( media-libs/mesa + x11-libs/libGLw ) + media-libs/mesa[motif] ) + media-libs/libpng:0 + media-libs/tiff:0 + sys-libs/zlib + virtual/glu + virtual/jpeg:0 + x11-libs/libXpm + x11-libs/motif:0 + x11-apps/xdpyinfo" +RDEPEND="${DEPEND}" + +S="${WORKDIR}" + +MAKEOPTS="${MAKEOPTS} -j1" + +pkg_setup() { + MMDIR="/usr/$(get_libdir)/molmol" +} + +src_prepare() { + rm -rf tiff* + # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided + epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff + + epatch "${FILESDIR}"/prefix.patch + eprefixify molmol + + epatch "${FILESDIR}"/ldflags.patch + + ln -s makedef.lnx "${S}"/makedef || die + + sed \ + -e "s:/bin/ksh:${EPREFIX}/bin/sh:" \ + -e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \ + -i "${S}"/molmol || die + sed \ + -e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -i "${S}"/makedef || die + + epatch "${FILESDIR}"/cast.patch + epatch "${FILESDIR}"/libpng15.patch + + # patch from fink + # fixes numerous bad bracings and hopefully the OGL bug 429974 + epatch "${FILESDIR}"/${P}-fink.patch + + tc-export AR +} + +src_install() { + dobin molmol + + exeinto ${MMDIR} + newexe src/main/molmol molmol.lnx + insinto ${MMDIR} + doins -r auxil help macros man setup tips + + dodoc HISTORY README +} diff --git a/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild new file mode 100644 index 000000000000..23720c5be51c --- /dev/null +++ b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild @@ -0,0 +1,84 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils multilib prefix toolchain-funcs + +MY_PV="${PV/_p/.}.0" +MY_P="${PN}-${MY_PV}" + +DESCRIPTION="Publication-quality molecular visualization package" +HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" +SRC_URI=" + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz" + +LICENSE="molmol" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND=" + || ( + ( media-libs/mesa + x11-libs/libGLw ) + media-libs/mesa[motif] ) + media-libs/libpng:0 + media-libs/tiff:0 + sys-libs/zlib + virtual/glu + virtual/jpeg:0 + x11-libs/libXpm + x11-libs/motif:0 + x11-apps/xdpyinfo" +RDEPEND="${DEPEND}" + +S="${WORKDIR}" + +MAKEOPTS="${MAKEOPTS} -j1" + +pkg_setup() { + MMDIR="/usr/$(get_libdir)/molmol" +} + +src_prepare() { + rm -rf tiff* + # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided + epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff + + epatch "${FILESDIR}"/ldflags.patch + epatch "${FILESDIR}"/opengl.patch + + ln -s makedef.lnx "${S}"/makedef || die + + sed \ + -e "s:ksh:sh:" \ + -e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR};MOLMOLDEV=\"Motif/OpenGL\":" \ + -i "${S}"/molmol || die + sed \ + -e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \ + -e "s:^CC.*:CC = $(tc-getCC):" \ + -i "${S}"/makedef || die + + epatch "${FILESDIR}"/cast.patch + epatch "${FILESDIR}"/libpng15.patch + + # patch from fink + # fixes numerous bad bracings and hopefully the OGL bug 429974 + epatch "${FILESDIR}"/${P}-fink.patch + + epatch "${FILESDIR}"/wild.patch + tc-export AR +} + +src_install() { + dobin molmol + + exeinto ${MMDIR} + doexe src/main/molmol + insinto ${MMDIR} + doins -r auxil help macros man setup tips + + dodoc HISTORY README +} diff --git a/sci-chemistry/molscript/Manifest b/sci-chemistry/molscript/Manifest new file mode 100644 index 000000000000..9e60a274b4e2 --- /dev/null +++ b/sci-chemistry/molscript/Manifest @@ -0,0 +1,10 @@ +AUX 2.1.2-ldflags.patch 818 SHA256 ef1f4079d7b11d69f8f9835266b7bf066fa74623ef2e34c1a5638125153771ab SHA512 0e14bbf2869357e19360a977941995f8610cf2c5c4fe272a30480725350705f4d8dfa83541b1eca441c78079ca926a6449d488854d3b6b7ee1c84e644d6c023a WHIRLPOOL eb0e1bdc1f88ca0e6bfc49ffdc61ce2bb77b461ac1beb6a3d4e8238298bd5d07f9bb0c29b32085b757340d4deac8ab3f1fd1d4d21156e6326ca5940501e3e0f0 +AUX 2.1.2-libpng15.patch 536 SHA256 46a9b1f08aabf4c6afe879a40241a4ffe3fb0e7489e73e074be1fec3bfa580de SHA512 29f929401478beb652e04ca2b043b8dd10497251c7fd7d6668479269f06791f1419db37f0535c173ec6e29cbeb44da26d68b3413593517641d6fe9ae63090f72 WHIRLPOOL eabf81779214d2a6e9d2626e9d858ab0a7c0e01931d29661bd4ce7b308cd141772ed2fe3f906c66b0ad8b1b6b2d87865719c9e24951385d6d43af63b9aa08bf1 +AUX 2.1.2-prll.patch 409 SHA256 23d968365bc5de71d43a9ef6bf2333dc749871b0ada84815f8687a82ca697364 SHA512 16b8566212cf06454a466678db61c2377c6080e8c72cd6e841b104f70f105fefa5d128ef96cb679f583a413d1d285a8f369dd2e757be347883d7e3e99bf88606 WHIRLPOOL 1eb32f1f7c6fd0debce8caadcd95f3146c2ad0e925adea6510a57738044727a80c4370a1ebcd520a0a24c9ef81b434f72cc62f93966deedf5c7469173f5a4bb3 +AUX fix-makefile-shared.patch 2051 SHA256 d692b236634d76f3f9d3482d3cc7b05451c0a116ad6edb8ade9075523e6b9bdf SHA512 0c12bd5aea0a6175b7647ed61ae139113329058c42cfb56105ee35af35bdab9f61adfe635a1c3322dbff00ddfcee06383bbd6bd048cc7ded1961f3997a527358 WHIRLPOOL 11d9a3e93cc3af9570a0a3e6863d4cea1a4ec8c9266dfe0c7bf2499ef211f52d714eed12e2986a06126162628ce75ae0e3933e60419d28e3a2c6976ea387df11 +AUX glutbitmap.h 845 SHA256 ba4caf7c2e7135e80385c2d33d7c780a28f5e9fc3ac557e297f65b70ce925a81 SHA512 a11e8c23472ed8950c8b56fdfd57ddd9c6539f427437ab26a2d3561ad388ca24a36029dee9ff6b8af759eeadf89fbd45dd10279d8089e6978eec07858624c7da WHIRLPOOL dc835c2604b33711ba26f5e846c40920eff7a26071560625f4fcd86f0a5c2d488b1adad0918d3e23ebf8775d08695caf17819608289f3fc87d35d72ee1144cbd +DIST molscript-2.1.2.tar.gz 412497 SHA256 01252931f5a3542d5659ddaa4ebceaed2e75becb8ed150dfa14b59da9a63ca01 SHA512 0f82936da3123770c0fdb703094dbb5289cc39e9f9ffd034d8dba563f8d615788f67040d38158ac2f203b480c5838a7d8e71ca07bc5098181c1e3cfea26703a4 WHIRLPOOL 1588f4dd47117f8da797a8bf62a2eba071106b1faca4f79b06e3093fe76092cae54476f1a0be995e3637173561ae6003fded264dd6d3a424d235488f95085a75 +EBUILD molscript-2.1.2-r2.ebuild 1407 SHA256 afa6d50b88a21b65122820067794f064a4a9493265e7081f416c8ab2faf3a825 SHA512 37358b677743c89b94c7960b3c5eaa458f8bd77494d412deb6cd4f583d59848bf8eadc10bb0d6bf7e3afdac24e2abb166b07d4d2143558147b29b847e1a746cc WHIRLPOOL 51856285ba80961113dff8b62c4f2137fa3422508abea80a51c2ede18d5961a0c07df013edec4832c24b65334787bf37734d0c4521b871ac7f2789005bb5a2f6 +MISC ChangeLog 2585 SHA256 5bcae4b20fc7d69c6e4258f995451717378f8463e99c6a7d929a36553692533a SHA512 fa629a8bb0ce755095cf909d68910d56033a433a54224e6595ef534104fb356dbec1e63c43240057eea887127e07155109015ebe41792d01ba1764b37ad7e243 WHIRLPOOL 2a331d868b484696bcd94a411b1726096d70f6641a3636e052d6ecc0aa59dfe0eab5a8b8eb16a886a0d89ed578afaccb171e03c9e99ec0b323ebd44a7715a0f4 +MISC ChangeLog-2015 3112 SHA256 7fad4b90086b3c09b9fe27c5efa3f86dc1868fdb63ba56d982cdec5d3ca3c7b7 SHA512 8fcb4f5d0cb61497fa7e18677fe693a0b2cb16964e1edf33d41c2ec179786929d44af7f910c19391073f982c98866be550891e8c57537369eacb81807ae317ba WHIRLPOOL 32371c32cd772d8faad416a98a795a5ca1cb4d7337187ef1c21fcb38a5b3c22b19e4230397a14fb360431a53a99b1e745a4f1c966dcf87585e3f0c1752c3b1b2 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/molscript/files/2.1.2-ldflags.patch b/sci-chemistry/molscript/files/2.1.2-ldflags.patch new file mode 100644 index 000000000000..8867bc10a6b5 --- /dev/null +++ b/sci-chemistry/molscript/files/2.1.2-ldflags.patch @@ -0,0 +1,22 @@ +diff --git a/Makefile.complete b/Makefile.complete +index 4ad535a..b565266 100644 +--- a/Makefile.complete ++++ b/Makefile.complete +@@ -91,7 +91,7 @@ clean: + + #------------------------------------------------------------ + molscript: $(OBJ) clib/clib.a +- $(CC) -o molscript $(COPT) $(OBJ) $(YLIB) clib/clib.a \ ++ $(CC) $(LDFLAGS) -o molscript $(COPT) $(OBJ) $(YLIB) clib/clib.a \ + $(GLUTLINK) $(JPEGLINK) $(PNGLINK) $(GIFLINK) $(ZLIBLINK) -lm + + molscript.tab.o: molscript.tab.c molscript.tab.h +@@ -147,7 +147,7 @@ gif_img.o: gif_img.c gif_img.h global.h graphics.h image.h opengl.h + + #------------------------------------------------------------ + molauto: molauto.o clib/clib.a +- $(CC) -o molauto molauto.o clib/clib.a -lm ++ $(CC) $(LDFLAGS) -o molauto molauto.o clib/clib.a -lm + + molauto.o: molauto.c + diff --git a/sci-chemistry/molscript/files/2.1.2-libpng15.patch b/sci-chemistry/molscript/files/2.1.2-libpng15.patch new file mode 100644 index 000000000000..9ed1b85909e8 --- /dev/null +++ b/sci-chemistry/molscript/files/2.1.2-libpng15.patch @@ -0,0 +1,19 @@ +--- png_img.c ++++ png_img.c +@@ -18,6 +18,7 @@ + + #include <GL/gl.h> + ++#include <zlib.h> + #include <png.h> + + #include "clib/str_utils.h" +@@ -69,7 +70,7 @@ + info_ptr = png_create_info_struct (png_ptr); + if (info_ptr == NULL) + yyerror ("png_img: could not create PNG info structure"); +- if (setjmp (png_ptr->jmpbuf)) yyerror ("png_img: could not setjmp"); ++ if (setjmp (png_jmpbuf(png_ptr))) yyerror ("png_img: could not setjmp"); + + png_init_io (png_ptr, outfile); + png_set_compression_level (png_ptr, compression_level); diff --git a/sci-chemistry/molscript/files/2.1.2-prll.patch b/sci-chemistry/molscript/files/2.1.2-prll.patch new file mode 100644 index 000000000000..e4c972a10533 --- /dev/null +++ b/sci-chemistry/molscript/files/2.1.2-prll.patch @@ -0,0 +1,10 @@ +diff --git a/Makefile.complete b/Makefile.complete +index 92ef20a..e3f68e3 100644 +--- a/Makefile.complete ++++ b/Makefile.complete +@@ -153,4 +153,4 @@ molauto.o: molauto.c + + #------------------------------------------------------------ + clib/clib.a: +- cd clib; make clib.a CFLAGS="-I. $(CFLAGS)" OPENGLCLIBOBJ="$(OPENGLCLIBOBJ)" ++ $(MAKE) -C clib clib.a CFLAGS="-I. $(CFLAGS)" OPENGLCLIBOBJ="$(OPENGLCLIBOBJ)" diff --git a/sci-chemistry/molscript/files/fix-makefile-shared.patch b/sci-chemistry/molscript/files/fix-makefile-shared.patch new file mode 100644 index 000000000000..a9947a61a665 --- /dev/null +++ b/sci-chemistry/molscript/files/fix-makefile-shared.patch @@ -0,0 +1,62 @@ +diff -urN molscript-2.1.2.orig/Makefile.complete molscript-2.1.2/Makefile.complete +--- molscript-2.1.2.orig/Makefile.complete 1998-11-25 01:04:39.000000000 -0800 ++++ molscript-2.1.2/Makefile.complete 2005-11-21 12:28:06.000000000 -0800 +@@ -23,9 +23,9 @@ + + # OpenGL and GLUT for X (UNIX). + # Must be modified for Windows 95/NT. <--- +-GLUTDIR = $(FREEWAREDIR)/glut +-GLUTLINK = $(GLUTDIR)/lib/glut/libglut.a -lGLU -lGL -lXmu -lXext -lX11 +-OPENGLFLAG = -DOPENGL_SUPPORT -I$(GLUTDIR)/include ++GLUTDIR = $(FREEWAREDIR) ++GLUTLINK = -lglut -lGLU -lGL -lXmu -lXext -lX11 ++OPENGLFLAG = -DOPENGL_SUPPORT -I$(GLUTDIR)/include/GL + OPENGLOBJ = opengl.o + OPENGLCLIBOBJ = ogl_utils.o ogl_body.o ogl_bitmap_character.o + +@@ -35,25 +35,25 @@ + + # JPEG image file format; requires the JPEG library. + # Comment out these lines if the JPEG library is not available. <--- +-JPEGDIR = $(FREEWAREDIR)/jpeg +-JPEGLINK = $(JPEGDIR)/libjpeg.a +-JPEGFLAG = -DJPEG_SUPPORT -I$(JPEGDIR) ++JPEGDIR = $(FREEWAREDIR) ++JPEGLINK = -ljpeg ++JPEGFLAG = -DJPEG_SUPPORT + JPEGOBJ = jpeg_img.o + + # PNG image file format; requires the PNG library and the zlib library. + # Comment out these lines if the PNG and zlib libraries are not available. <--- +-ZLIBDIR = $(FREEWAREDIR)/zlib +-ZLIBLINK = $(ZLIBDIR)/libz.a +-PNGDIR = $(FREEWAREDIR)/libpng +-PNGLINK = $(PNGDIR)/libpng.a +-PNGFLAG = -DPNG_SUPPORT -I$(PNGDIR) -I$(ZLIBDIR) ++ZLIBDIR = $(FREEWAREDIR) ++ZLIBLINK = -lz ++PNGDIR = $(FREEWAREDIR) ++PNGLINK = -lpng ++PNGFLAG = -DPNG_SUPPORT + PNGOBJ = png_img.o + + # GIF image file format; requires the gd 1.3 library. + # Comment out these lines if the gd 1.3 library is not available. <--- +-GIFDIR = $(FREEWAREDIR)/gd +-GIFLINK = $(GIFDIR)/libgd.a +-GIFFLAG = -DGIF_SUPPORT -I$(GIFDIR) ++GIFDIR = $(FREEWAREDIR) ++GIFLINK = -lgd ++GIFFLAG = -DGIF_SUPPORT + GIFOBJ = gif_img.o + + # SGI IRIX's C compiler. +@@ -62,7 +62,7 @@ + COPT = -O1 + # Correctness flags: + #CCHECK = -ansi -fullwarn -g -DSELECT_DEBUG +-CCHECK = -ansi -fullwarn ++CCHECK = -ansi + #CCHECK = -ansi -fullwarn -DNDEBUG + + # General cc compile flags. diff --git a/sci-chemistry/molscript/files/glutbitmap.h b/sci-chemistry/molscript/files/glutbitmap.h new file mode 100644 index 000000000000..9584bb129daa --- /dev/null +++ b/sci-chemistry/molscript/files/glutbitmap.h @@ -0,0 +1,32 @@ +#ifndef __glutbitmap_h__ +#define __glutbitmap_h__ + +/* Copyright (c) Mark J. Kilgard, 1994, 1998. */ + +/* This program is freely distributable without licensing fees + and is provided without guarantee or warrantee expressed or + implied. This program is -not- in the public domain. */ + +#define GLUT_NO_LIB_PRAGMA /* Avoid auto library linking when building + the GLUT library itself. */ +#include <GL/glut.h> + +typedef struct { + const GLsizei width; + const GLsizei height; + const GLfloat xorig; + const GLfloat yorig; + const GLfloat advance; + const GLubyte *bitmap; +} BitmapCharRec, *BitmapCharPtr; + +typedef struct { + const char *name; + const int num_chars; + const int first; + const BitmapCharRec * const *ch; +} BitmapFontRec, *BitmapFontPtr; + +typedef void *GLUTbitmapFont; + +#endif /* __glutbitmap_h__ */ diff --git a/sci-chemistry/molscript/metadata.xml b/sci-chemistry/molscript/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/molscript/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild b/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild new file mode 100644 index 000000000000..054edd99f7ff --- /dev/null +++ b/sci-chemistry/molscript/molscript-2.1.2-r2.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Display molecular 3D structures, such as proteins, in both schematic and detailed representations" +HOMEPAGE="http://www.avatar.se/molscript/" +SRC_URI="${P}.tar.gz" + +LICENSE="glut molscript" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND=" + media-libs/freeglut + media-libs/gd:2= + media-libs/libpng:0= + virtual/jpeg:0= + || ( + x11-libs/libXmu + x11-libs/libXext + x11-libs/libX11 + )" +RDEPEND="${DEPEND}" + +RESTRICT="fetch" + +pkg_nofetch() { + elog "Please visit ${HOMEPAGE}" + elog "and get ${A}." + elog "Place it in ${DISTDIR}" +} + +src_prepare() { + epatch \ + "${FILESDIR}"/fix-makefile-shared.patch \ + "${FILESDIR}"/${PV}-ldflags.patch \ + "${FILESDIR}"/${PV}-prll.patch \ + "${FILESDIR}"/${PV}-libpng15.patch + + # Provide glutbitmap.h, because freeglut doesn't have it + cp "${FILESDIR}"/glutbitmap.h "${S}"/clib/ || die + + # Stop an incredibly hacky include + sed \ + -e 's:<../lib/glut/glutbitmap.h>:"glutbitmap.h":g' \ + -i "${S}"/clib/ogl_bitmap_character.c || die +} + +src_compile() { + # Prefix of programs it links with + export FREEWAREDIR="${EPREFIX}/usr" + + ln -s Makefile.complete Makefile || die + + emake \ + CC="$(tc-getCC)" \ + COPT="${CFLAGS}" +} + +src_install() { + dobin molscript molauto + dohtml "${S}"/doc/*.html +} diff --git a/sci-chemistry/molsketch/Manifest b/sci-chemistry/molsketch/Manifest new file mode 100644 index 000000000000..32b1636db490 --- /dev/null +++ b/sci-chemistry/molsketch/Manifest @@ -0,0 +1,12 @@ +AUX molsketch-0.3.0-_DEFAULT_SOURCE.patch 661 SHA256 0ee57232a61e2ec9e44250b7a661bb2309f00f372ede8a6b1d9b51c139c90488 SHA512 9fd409ca55d5df0c61e84d3d9941f4855b7dcd32fd7521f24204570858dc6205c70ca4c645c5eee31bdc446a315e02081fa947677a4f22addce16ec4dad64c10 WHIRLPOOL bc1b6c740c22a866a375e08c002dcc39d3dae5e272dfaf531e79bee597a9d1053f7dbefd220bbb6911962f7651a1b1e9173eb28b33370bb3e3ee66480ad16b32 +AUX molsketch-0.3.0-desktop.patch 572 SHA256 6273aa20d8498ed522c3dbd5bcb966e7923e56f3497bff6441ff717a0f714486 SHA512 dbb074dd2bff41872ce9363241aa26bdc2537950c7635399c7a173845c30b8603de24bc6dcaf8a27a6eadbdc2c5249aa4cdd2bb63f059475d53f99b99acffd6a WHIRLPOOL 353f839287b5e58700cf25d788fb12b659bb345dbea714c59827957cd19c872660cec3b51619b90717fcc5755d21980258419f9de42586afdf5f1abd1ea6ce0a +AUX molsketch-0.3.0-no-quotes.patch 490 SHA256 3979e7020f559665692fdade6a4dca2e0d5c840866b88c2a5615f9e908263875 SHA512 cf5028b8b99c77543943f517eee6eafbe8bc8a590fe8dbb9840001e568866a74c852fd59653714f507b0a5a556ce7c40dd1768c29df92af9cb8ff4131ac48e35 WHIRLPOOL 3f2a0999a706e9ec5ebce4697aeba8ce1ea22ec9442c947369afe2292bd2415cf7faceb72e1fe0c8c7dbd9aa9b9ba77382e6fbee052448939e7e7df11802df54 +AUX molsketch-0.4.1-more-quotes.patch 478 SHA256 6cf71ad30457dc6dc6fc1b6f2d884cfd914304d6525faa5bc378c7de03933be8 SHA512 015344abb4aaa7f214e4e8a7eebe1a7a8f4d43b8a76a9c5f984fc4c5cf8da450430330543fe69d481ceec25c5a59ee332439654fd4ce82ce080aa4883cc1d113 WHIRLPOOL bb8a51964018cf50185e6d0e876ad7e2e255658c34b47a6292e7d157cc58b9b2759e2e17d1d3cfb88bab6b014247a09bc122790ba95cba2a63db89f360243ec2 +AUX molsketch-0.4.1-no-quotes.patch 545 SHA256 59a963c1720d39ed82ff3cd3178043c3188d168c79ca6a53ff31def8dfeef5cf SHA512 8bf7db168567f47980e9f7b3547c4359f3ed427187a6f5d3be60658214891362538caa9db9607fd791a34f99961baadfaf50cc07135669471740d77a3b715b6a WHIRLPOOL 128796460a931c6408928330feb05a31cbf6c9972ead3a4d0e14b496565df9752233d2a374999c8086b4469ad13411a695518ef999006ddf5f35ef139146b606 +DIST Molsketch-0.3.0-src.tar.gz 337388 SHA256 078b05bfd591930430bc1e5df802af27bdf40718b9218ba6435eadc209d4d1bc SHA512 405553c9d84f0ce9d70a237834f8273dd5010b95868434f9b1b9042fd626e2782c5d3da7d17d9485946210e48e86d0c2de8385d80667018dbc833c3928d076d4 WHIRLPOOL 659717039bf294072117a8e7dc1cb590c6804d3dbde625aa16451bfdb6371933c71f6241fee1e38cec696bdb89e19111c30cf6ed17810daf09b75272080fbb31 +DIST Molsketch-0.4.1-src.tar.gz 1499842 SHA256 6b183ed3ba92f89f1318879657a79c09d7135c99af28eee8758f46f131e05a30 SHA512 263b088c2b8d01c1f13802b18aea6f6784580fe1a806de45b0e1ecd9f29024350e01a611bdeed1891938acc733a42746203d345d3be13ebaf4c309413e86bf26 WHIRLPOOL 383e9fffd1cd2db195e962f58e97d0ffd858dc14353c99ed0bdd7e577413e5ac991ed18a41b5d4ee4b926887a6a2654fe30167f82759142b21b753c30e41cbd7 +EBUILD molsketch-0.3.0.ebuild 1352 SHA256 b7eae9694ea2ff18229e58b5e0060b6f5e0b8cd74a18ad93ee8a8f6273c27288 SHA512 d63d3a6ac76f071977d1708f072082a1e2ea3c7f02bb6cb37a28cdc62a9255eb2766257cf86b0a9c65ef9c7a0cf5828e7d1afc8616035c2cb93cb155fbbf72e0 WHIRLPOOL 4274d4095329e6ce6d3cf7a34817e9c6e70d3ba138eff52617a4faa2d8f977ad0b7f9c66ae35df2d29fa128f79f9bb6faa296e483c32d5203bca84fd53ca06ed +EBUILD molsketch-0.4.1-r1.ebuild 1359 SHA256 b757544dc82baa20480cfc96762d2b25b1c2ac68e5804f6552fcdeedc06e5710 SHA512 e1ecf0c0a0412cee651839204cd80039216a81bbd28cd37c23197a8270ce97e26b2df644b4b9144f139d7b8243b3437a2f13301c184152ad89fcf9778d6eaf82 WHIRLPOOL 8261ecef33ac730bbe54c174b6f36589749ac93258eccea088b1a5d71f5a9ab89eeb5c254fb1d4117ca4cc7cdbdc56d780f32870bd60bf24615fedad4e1049b5 +MISC ChangeLog 2816 SHA256 e78c58d727ebe8b65411864e63b95e353f29971ae992da2de36af559956a93e7 SHA512 3983064e72444fb53852a21148917b75954c9b52918382449aa8dfc2dbbb9882de0b5a9566a55402cbce835cec7d7e086765dc2d9ca95903ae6cd95fee0aabe2 WHIRLPOOL 0afd6960de30932d39bf2bb70fbebe30c42b319d4f7f79344e0fee81f127705ea75be5c90e50ae8a383fb27bbe78bf2ec5c11bc371a5c96d21eda8da32ed3ca7 +MISC ChangeLog-2015 1914 SHA256 6c5a568036ffbf415c7e20775fac372e1b58d991452ed26d508c49affaab5be3 SHA512 425528431c5f5024e126789276cdfd2c72a41eebb41fae603b3ecc17f8f37f78ac9ba9a6b648fe0343ebed13955f12996230112e4b89c954243d5e45ceb55697 WHIRLPOOL 66afd3262e5310709a7648482c0ac2b817dd05f6ad9d589483444ba8454780d590095a6fd717dcc5e23821b00f66d6eb62cd9f353b50c58a427adbe0c4aace37 +MISC metadata.xml 619 SHA256 de94cef511511dd22761e3d2f8c0bc071f7aca253618eb444768e6d846f5903a SHA512 a6b87cb6d49bbb2b4812d658b3b6b4259f2c3b838cf7eb7a96b2499a3becf4cb0ca14a764f3c84e684f5df8511b95a01bf9d48023854296848357e96bc98a906 WHIRLPOOL 820b6ff0f3d369788483f333de5254d4f919fe136e3853d6966ea81eed951a3d5b94eccc5890470615c03a69a36211d7970154b8e2fc3fbd90420f8106c0e1d9 diff --git a/sci-chemistry/molsketch/files/molsketch-0.3.0-_DEFAULT_SOURCE.patch b/sci-chemistry/molsketch/files/molsketch-0.3.0-_DEFAULT_SOURCE.patch new file mode 100644 index 000000000000..af3b5ceedac6 --- /dev/null +++ b/sci-chemistry/molsketch/files/molsketch-0.3.0-_DEFAULT_SOURCE.patch @@ -0,0 +1,16 @@ + CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index e3cd0fe..64c18a2 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -19,7 +19,7 @@ if (CMAKE_COMPILER_IS_GNUCXX) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wnon-virtual-dtor -Wno-long-long -ansi -Wundef -Wcast-align") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wchar-subscripts -Wall -W -Wpointer-arith -Wformat-security") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-exceptions -fno-check-new -fno-common") +- add_definitions(-D_BSD_SOURCE) ++ add_definitions(-D_DEFAULT_SOURCE) + endif (CMAKE_COMPILER_IS_GNUCXX) + + # Enable CPack diff --git a/sci-chemistry/molsketch/files/molsketch-0.3.0-desktop.patch b/sci-chemistry/molsketch/files/molsketch-0.3.0-desktop.patch new file mode 100644 index 000000000000..fd44e88c7870 --- /dev/null +++ b/sci-chemistry/molsketch/files/molsketch-0.3.0-desktop.patch @@ -0,0 +1,19 @@ + molsketch/src/molsketch.desktop | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/molsketch/src/molsketch.desktop b/molsketch/src/molsketch.desktop +index a4a5418..4e0a2ef 100644 +--- a/molsketch/src/molsketch.desktop ++++ b/molsketch/src/molsketch.desktop +@@ -5,9 +5,9 @@ Type=Application + Name=molsKetch + TryExec=molsketch + Exec=molsketch +-Icon=molsketch.png ++Icon=molsketch + DocPath=molsketch/index.html +-MimeType=chemical/x-cml ++MimeType=chemical/x-cml; + Terminal=false + Categories=Qt;Education;Science; + GenericName=2D molecular structures editor diff --git a/sci-chemistry/molsketch/files/molsketch-0.3.0-no-quotes.patch b/sci-chemistry/molsketch/files/molsketch-0.3.0-no-quotes.patch new file mode 100644 index 000000000000..db7be800e385 --- /dev/null +++ b/sci-chemistry/molsketch/files/molsketch-0.3.0-no-quotes.patch @@ -0,0 +1,16 @@ + CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 64c18a2..75c2fb7 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -97,7 +97,7 @@ endif(Qt5Core_FOUND AND Qt5Widgets_FOUND AND Qt5Gui_FOUND AND Qt5PrintSupport_FO + if(FORCEQt4) + add_definitions(-DQTVERSIONSUFFIX="") + else(FORCEQt4) +- add_definitions(-DQTVERSIONSUFFIX="\\\"-qt5\\\"") ++ add_definitions(-DQTVERSIONSUFFIX="-qt5") + endif(FORCEQt4) + + # and OpenBabel2 diff --git a/sci-chemistry/molsketch/files/molsketch-0.4.1-more-quotes.patch b/sci-chemistry/molsketch/files/molsketch-0.4.1-more-quotes.patch new file mode 100644 index 000000000000..c32b975778eb --- /dev/null +++ b/sci-chemistry/molsketch/files/molsketch-0.4.1-more-quotes.patch @@ -0,0 +1,11 @@ +--- a/libmolsketch/src/molscene.cpp ++++ b/libmolsketch/src/molscene.cpp +@@ -842,7 +842,7 @@ + void MolScene::dragEnterEvent(QGraphicsSceneDragDropEvent *event) + { + if (!event->mimeData() || !event->mimeData()->hasFormat(mimeType())) return; +- if (!event->proposedAction() == Qt::CopyAction) return; ++ if ((!event->proposedAction()) == Qt::CopyAction) return; + event->accept(); + for (genericAction* action : sceneActions()) + action->setChecked(false); diff --git a/sci-chemistry/molsketch/files/molsketch-0.4.1-no-quotes.patch b/sci-chemistry/molsketch/files/molsketch-0.4.1-no-quotes.patch new file mode 100644 index 000000000000..1b63ed51edec --- /dev/null +++ b/sci-chemistry/molsketch/files/molsketch-0.4.1-no-quotes.patch @@ -0,0 +1,16 @@ + CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 64c18a2..75c2fb7 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -97,7 +97,7 @@ endif(Qt5Core_FOUND AND Qt5Widgets_FOUND AND Qt5Gui_FOUND AND Qt5PrintSupport_FO + if(FORCEQt4) + add_definitions(-DQTVERSIONSUFFIX="") + else(FORCEQt4) +- add_definitions(-DQTVERSIONSUFFIX="\\\"-qt5\\\"") ++ add_definitions(-DQTVERSIONSUFFIX="-qt5") + endif(FORCEQt4) + + ################ Reading version and default paths diff --git a/sci-chemistry/molsketch/metadata.xml b/sci-chemistry/molsketch/metadata.xml new file mode 100644 index 000000000000..db8561869b3c --- /dev/null +++ b/sci-chemistry/molsketch/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription lang="en"> + Molsketch is a 2D molecular editing tool. Its goal is to help you draw + molecules quick and easily. Of course you're creation can be exported + afterwards in high quality in a number of vector and bitmap formats. +</longdescription> + <upstream> + <remote-id type="sourceforge">molsketch</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/molsketch/molsketch-0.3.0.ebuild b/sci-chemistry/molsketch/molsketch-0.3.0.ebuild new file mode 100644 index 000000000000..d9533bfed28c --- /dev/null +++ b/sci-chemistry/molsketch/molsketch-0.3.0.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +CMAKE_MAKEFILE_GENERATOR=ninja + +inherit cmake-utils multilib qmake-utils + +MY_P=${P/m/M}-src + +DESCRIPTION="A drawing tool for 2D molecular structures" +HOMEPAGE="http://molsketch.sourceforge.net/" +SRC_URI="mirror://sourceforge/project/${PN}/Molsketch/Lithium%20${PV}/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +DEPEND=" + >=sci-chemistry/openbabel-2.2 + dev-qt/qtcore:5 + dev-qt/qtgui:5 + dev-qt/qtprintsupport:5 + dev-qt/qtsvg:5 + dev-qt/qtwidgets:5 + " +RDEPEND="${DEPEND}" + +S=${WORKDIR}/${MY_P%%-src} + +PATCHES=( + "${FILESDIR}"/${P}-_DEFAULT_SOURCE.patch + "${FILESDIR}"/${P}-desktop.patch + "${FILESDIR}"/${P}-no-quotes.patch + ) + +src_prepare() { + sed -e "/LIBRARY DESTINATION/ s/lib/$(get_libdir)/g" \ + -i {obabeliface,libmolsketch/src}/CMakeLists.txt || die #351246 + sed -e "s:doc/molsketch:doc/${PF}:g" \ + -i molsketch/src/{CMakeLists.txt,mainwindow.cpp} || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DOPENBABEL2_INCLUDE_DIR="${EPREFIX}/usr/include/openbabel-2.0" + -DCMAKE_DISABLE_FIND_PACKAGE_KDE4=ON + -DENABLE_TESTS=$(usex test "ON" "OFF") + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + dosym ${PN}-qt5 /usr/bin/${PN} +} diff --git a/sci-chemistry/molsketch/molsketch-0.4.1-r1.ebuild b/sci-chemistry/molsketch/molsketch-0.4.1-r1.ebuild new file mode 100644 index 000000000000..c34e60a0106c --- /dev/null +++ b/sci-chemistry/molsketch/molsketch-0.4.1-r1.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR=ninja + +inherit cmake-utils multilib qmake-utils + +MY_P=${P/m/M}-src + +DESCRIPTION="A drawing tool for 2D molecular structures" +HOMEPAGE="http://molsketch.sourceforge.net/" +SRC_URI="mirror://sourceforge/project/${PN}/Molsketch/Beryllium-7%20${PV}/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +DEPEND=" + >=sci-chemistry/openbabel-2.2 + dev-qt/qtcore:5 + dev-qt/qtgui:5 + dev-qt/qtprintsupport:5 + dev-qt/qtsvg:5 + dev-qt/qtwidgets:5 + " +RDEPEND="${DEPEND}" + +S=${WORKDIR}/${MY_P%%-src} + +PATCHES=( + "${FILESDIR}"/${PN}-0.3.0-_DEFAULT_SOURCE.patch + "${FILESDIR}"/${P}-more-quotes.patch + ) + +src_prepare() { + sed -e "/LIBRARY DESTINATION/ s/lib/$(get_libdir)/g" \ + -i {obabeliface,libmolsketch/src}/CMakeLists.txt || die #351246 + sed -e "s:doc/molsketch:doc/${PF}:g" \ + -i molsketch/src/{CMakeLists.txt,mainwindow.cpp} || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DOPENBABEL2_INCLUDE_DIR="${EPREFIX}/usr/include/openbabel-2.0" + -DCMAKE_DISABLE_FIND_PACKAGE_KDE4=ON + -DENABLE_TESTS=$(usex test "ON" "OFF") + -DMSK_INSTALL_PREFIX=/usr + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + dosym ${PN}-qt5 /usr/bin/${PN} +} diff --git a/sci-chemistry/mongochem/Manifest b/sci-chemistry/mongochem/Manifest new file mode 100644 index 000000000000..05507f1b6457 --- /dev/null +++ b/sci-chemistry/mongochem/Manifest @@ -0,0 +1,5 @@ +DIST mongochem-0.7.0.tar.gz 448002 SHA256 a93f53e8d945f2e3b97efac8187cfaeae0a7e491265cd65d66d25e34577cf883 SHA512 076f79c9dbed372cc760c972d5529fc3a10ea23ba2a58bf1034b736c5394a9283223562c0d6d14a135cdf87786a222991ca613765484d5a36c31f65c2ccccb05 WHIRLPOOL 4b044e00e44b1333e3faec04e15eaf46e7b17eecd4c155099fc5f06dc9c62bde70adc8bb8a9793df9b305efc89f5e44bdea77eeaac1da3554c002cba117fe8c1 +EBUILD mongochem-0.7.0-r1.ebuild 746 SHA256 8c3072f989d778ac72fa9a37d16a205d62f5255c24b3171dd825e9f3494d0b43 SHA512 31f90a9923bec4da4f3596173e403fed9011fc9f9fd8ee888c4fd90688c57946cb58bd76ae73dd35e0e456774e1b1230449f269f26fdc53df769991dc63c177e WHIRLPOOL 138deaea5236542f4bc47e0a6acaa47c319aef3dbe66973e2c4f0212e9c7e99b4709917ce9583037daa2ac48aa1f02411bd1b33a799dc5a26f32c57660518756 +MISC ChangeLog 2791 SHA256 911a281ca04fa0e6b852ca342b17ef317059c1f98eceffe98d93f4938160dd9b SHA512 f525b7a4b9effaaf55f082b0ae8d252477fd48a91a4488f2467d42ee718fc3cc908647c5ae1ec4fbf3d1abf71d1e6398374cd1da3a972cd37ec5e43c8a363bab WHIRLPOOL d6b33dfaf614c27e1df2be6aff33b7cb30413b0057476368f8b5bc85ea64689662faa194cfc08c50b4aa83012865d595d47f125b9ecf6c43ffa74ffd67a7f6e1 +MISC ChangeLog-2015 367 SHA256 bd35844e6c36ceb60140cd9805ed39ca8914993d5a07bf2dc5d9f4d88d3fbe78 SHA512 92a979fe68deb8ad35cf99deee058fea621f8bb0e898b1e8a29a1addffed7bf15455aa62fc184fba745b2f0250ff6dc488facf9591a4e9dfc4ac901ffe98e9a0 WHIRLPOOL 97ebc096a8e679987753b81867f97ff63fa9a641f7e0b88a4eca68f7c30e3388dfcf6fdefb703663e0591468ca94bed6a189e343b8ca8700c462628efaeb17ca +MISC metadata.xml 363 SHA256 46955ab316d5f7d90b71812ffd4fe4c141a3ebf8626b71dbf17dc8eab7c2f346 SHA512 2b7123357c4bdcf41bdfc3744c0d4c7912127933eecca7024283e80cf318443fadc525c80cb340a7052fd12e96d5bb063f94dba2bdb5a722c19c1b7340f32255 WHIRLPOOL de3e6f2eb5b561013d068cf30abe9e41a797d0c57567c2c0f0966f96373d8f9a21d1af0e423c6ac8c292dc2be12ab769790c937a4141fbdee9d5271919fd4620 diff --git a/sci-chemistry/mongochem/metadata.xml b/sci-chemistry/mongochem/metadata.xml new file mode 100644 index 000000000000..dfefa021fbc3 --- /dev/null +++ b/sci-chemistry/mongochem/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="github">OpenChemistry/mongochem</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/mongochem/mongochem-0.7.0-r1.ebuild b/sci-chemistry/mongochem/mongochem-0.7.0-r1.ebuild new file mode 100644 index 000000000000..ad698d3c74d7 --- /dev/null +++ b/sci-chemistry/mongochem/mongochem-0.7.0-r1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit cmake-utils vcs-snapshot + +DESCRIPTION="Application for managing large collections of chemical data" +HOMEPAGE="http://www.openchemistry.org/" +#SRC_URI="http://openchemistry.org/files/v0.5/${P}.tar.gz" +SRC_URI="https://github.com/OpenChemistry/mongochem/archive/df36ebce92024dd4fd1c70eb37eb84e4c51120ff.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-libs/boost[threads] + dev-libs/mongo-cxx-driver + sci-libs/avogadrolibs[qt4] + sci-libs/chemkit + sci-libs/vtk[qt4,rendering] + sci-chemistry/molequeue +" +DEPEND="${RDEPEND}" diff --git a/sci-chemistry/mopac7/Manifest b/sci-chemistry/mopac7/Manifest new file mode 100644 index 000000000000..2f2554bd451d --- /dev/null +++ b/sci-chemistry/mopac7/Manifest @@ -0,0 +1,9 @@ +AUX Makefile 458 SHA256 5c44af6922cc7cadd7dafc7f26ee9f62c6614ccba2fbdedab365126d2ad8d742 SHA512 e127a839ea7363e0ad68e522311e953900d262c6712bd7fcb58d971ff0a80d0d587c8f9d43f698f2295b2ec218a31aad47259c4a42925064110b4ff46a6d62b5 WHIRLPOOL 8bf67d88814908c55bffc152c6a0d2cda3b6f59fc4318811e49857110174b1d4b354828cb30898d3513eb72a652233ad1e6b7c0c352b15385f8b7b30c52c6775 +DIST dcart.f 11044 SHA256 cdc4082b6b3811eca25eaf674e9345fcd37f58dfbdca3c5d72e9c4e88c47dec9 SHA512 788a184fd8419ff742e49c1a652d5ea093f9114dbe4f272665b8fb9eeac2afb7f7042628c288f2b81d0f54d8a7ef2f400490cd3aff39dda59a6d70a0deab5b80 WHIRLPOOL 399d7cf92d6fd27bb785c3f81eb24ec9615144b3e8605779d1f1f645ea16644a858428d8dfce44c102a495f984e1ae158fe7743ad0bef2b957ea10adc94ccb73 +DIST gmxmop.f 38956 SHA256 918bfac91b1dab65f7a8f759c3fd49e40be19bbddb6869d95f8e345830b93b67 SHA512 38bb2e5749c4d3c8c24f15682f72e40cb4edb6517c7916cecee1d21675b1870c0fe331ba2ec40312408dec473141e7742d1e155d4b64f1c2a25bfa4e11885194 WHIRLPOOL a0adaf3df1167d9675197f71ae2cd5a9a583eef4523b9a074d39291032dbfe0428349ebf78fabd88ed7e1deb5af093be319c9f19cab019deb52f0fb6e3924998 +DIST mopac7-1.15.tar.gz 764547 SHA256 6d7ac5d78522db70f7794fd816cea32829cfa9e93774202fe80ba5a54375fbaa SHA512 e0ccd643caa6dbd7e156867530d79e50e10243f5e3b5f8bc57781e68e1daf26f2a0e6987fff00afe07eb0fcb98cbd9f01e4cfa5d20acc0d8ab3cca632968636e WHIRLPOOL fe4d71e3900b8fe09697275c25bc239e8f94e97d2a570bf6df03c5bd59a3b2ab80bc7f255f739f09c0fc54037e9739b38cec205590ad3cb31ad58fe2067562d2 +EBUILD mopac7-1.15-r1.ebuild 1822 SHA256 9e8511e731fa73f3866c16a16e8c01e03c466a15c16bce431a567245fc9ccfb4 SHA512 123957aaa90f52b0007224fb8a11c8e195da2e0e2f26cc0e7f54b92fa5dead330688e01057c3523efadff3f1f12b0c2ae83ed5945046602c8d7c6c2cf6eb2e39 WHIRLPOOL 79554eaedf27e274881d6c39197ddf629015d24e4aeb06a004a2d250fff76cfba781e9b6e0c97f68d605c0d8c3ca5947a984576176b4549da060c64428c770ad +EBUILD mopac7-1.15.ebuild 2044 SHA256 94b481435365175f46b2321ffa805cd85185f043f4cdd5b727493d628368aa3f SHA512 55135a37436fc479539a769b8d0dd7a604cf9fe522243fe5105b4eed6862efaa9c333ede5cdf87b58e49110d41e4d445e80de2c991d38b28529bb610666cc8c7 WHIRLPOOL 488a2a36f0a7c8f565c25bff0699425c7eda91ca85ce80ee0b73281ab891caafa72a45e4d4d614ab84823e73df8e5ac87b2aa7da45a1c5e0c568f711f69f6f0d +MISC ChangeLog 3179 SHA256 2f154b386670c482379e459a9f6b26ff80f47cd8a5b90ef72b11e81e5886ed3e SHA512 f8d09c097c474617888d5599bbf4f616f490b51fbb1a93887755085e94735071d8eab5977dd156ce018c722139b598d72adde08d3b4367f411d0f28535610078 WHIRLPOOL 6e39ed837c5a62007d4a84a3b4a376132fd85e272c6aa72e09bc370753ba3b4018c57903677c6c202cd409297a45a31344bc4f633b9d2e1056e19137cacb3fc0 +MISC ChangeLog-2015 5059 SHA256 dfa188434b91d3d7918fca2b5dc2739f5bcf94f356c5042ceb826f595979244b SHA512 38e3a72438d7f7d29423b01c5f7df1e064f98ac14d42d497926b8e0b7abf595847f056b67ca42224fde259ba22469996a60b239af4bf19bf067d36e66b947c18 WHIRLPOOL fbbbeaf4ac7c47a454f5e71ede83fc7006ec912dbbbe5958286bfde3c12f62eb1acfcf967e2b3a38f58c5888143b7050a861734ef659044d491802db844cc24d +MISC metadata.xml 434 SHA256 356ea5a193e5a9c8a128c376f6154b251d2ece7c3a65f7c5f74872704e76b7e4 SHA512 77b3e0b69436a4f199c5ae3d9382c9b6cf2049ffd98144a2dc291495de9e8daa9deb6141d77b917f6e29902ad862c9044e7661ca7f0ae5e4fc68983857b3f6f2 WHIRLPOOL c80ed815123b6206214892b7745546219c1e8439963e225aa66716a481224f6832e39c47e3232ffc9e86caa329408a8f84809e6acdd7626d43e32d4285b8e5b8 diff --git a/sci-chemistry/mopac7/files/Makefile b/sci-chemistry/mopac7/files/Makefile new file mode 100644 index 000000000000..50370b3c2784 --- /dev/null +++ b/sci-chemistry/mopac7/files/Makefile @@ -0,0 +1,23 @@ +VERSION = GENTOOVERSION +MAJOR = 1 + +LIBS = -lgfortran -lf2c + +objects := $(patsubst %.f,%.o,$(wildcard *.f)) + +all: libgmxmopac7 + +clean: + rm -f moldat.*f deriv.* mopac7*.* compfg.* dcart.* + +%.o: %.f + $(FC) $(FFLAGS) -fPIC -c $< + +libgmxmopac7: $(objects) + $(FC) -shared $(LDFLAGS) -Wl,-soname,libgmxmopac7.so.$(MAJOR) -o $@.so.$(VERSION) $^ $(LIBS) + ln -sf $@.so.$(VERSION) libgmxmopac7.so + +static: $(objects) + ar rcv libgmxmopac7.a *.o + ranlib libgmxmopac7.a + diff --git a/sci-chemistry/mopac7/metadata.xml b/sci-chemistry/mopac7/metadata.xml new file mode 100644 index 000000000000..efd0c0d00e55 --- /dev/null +++ b/sci-chemistry/mopac7/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="gmxmopac7">Add support library for gromacs</flag> + </use> + <upstream> + <remote-id type="sourceforge">mopac7</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild b/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild new file mode 100644 index 000000000000..2a6b04bc3bba --- /dev/null +++ b/sci-chemistry/mopac7/mopac7-1.15-r1.ebuild @@ -0,0 +1,65 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools fortran-2 flag-o-matic toolchain-funcs + +DESCRIPTION="Autotooled, updated version of a powerful, fast semi-empirical package" +HOMEPAGE="https://sourceforge.net/projects/mopac7/" +SRC_URI=" + http://www.bioinformatics.org/ghemical/download/current/${P}.tar.gz + http://wwwuser.gwdg.de/~ggroenh/qmmm/mopac/dcart.f + http://wwwuser.gwdg.de/~ggroenh/qmmm/mopac/gmxmop.f" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux" +IUSE="gmxmopac7 static-libs" + +DEPEND="dev-libs/libf2c" +RDEPEND="${DEPEND}" + +src_prepare() { + # Install the executable + sed -i \ + -e "s:noinst_PROGRAMS = mopac7:bin_PROGRAMS = mopac7:g" \ + fortran/Makefile.am \ + || die "sed failed: install mopac7" + # Install the script to run the executable + sed -i \ + -e "s:EXTRA_DIST = autogen.sh run_mopac7:bin_SCRIPTS = run_mopac7:g" \ + Makefile.am \ + || die "sed failed: install run_mopac7" + + eautoreconf + append-fflags -std=legacy -fno-automatic +} + +src_compile() { + emake + if use gmxmopac7; then + einfo "Making mopac7 lib for gromacs" + mkdir "${S}"/fortran/libgmxmopac7 && cd "${S}"/fortran/libgmxmopac7 + cp -f ../SIZES ../*.f "${FILESDIR}"/Makefile . || die + emake clean + cp -f "${DISTDIR}"/gmxmop.f "${DISTDIR}"/dcart.f . || die + sed "s:GENTOOVERSION:${PV}:g" -i Makefile + emake FC=$(tc-getFC) + use static-libs && emake static + fi +} + +src_install() { + # A correct fix would have a run_mopac7.in with @bindir@ that gets + # replaced by configure, and run_mopac7 added to AC_OUTPUT in configure.ac + sed -i "s:./fortran/mopac7:mopac7:g" run_mopac7 || die + + default + + if use gmxmopac7; then + cd "${S}"/fortran/libgmxmopac7 + dolib.so libgmxmopac7.so* + use static-libs && dolib.a libgmxmopac7.a + fi +} diff --git a/sci-chemistry/mopac7/mopac7-1.15.ebuild b/sci-chemistry/mopac7/mopac7-1.15.ebuild new file mode 100644 index 000000000000..9ee026f0d21b --- /dev/null +++ b/sci-chemistry/mopac7/mopac7-1.15.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit autotools fortran-2 toolchain-funcs + +DESCRIPTION="Autotooled, updated version of a powerful, fast semi-empirical package" +HOMEPAGE="https://sourceforge.net/projects/mopac7/" +SRC_URI=" + http://www.bioinformatics.org/ghemical/download/current/${P}.tar.gz + http://wwwuser.gwdg.de/~ggroenh/qmmm/mopac/dcart.f + http://wwwuser.gwdg.de/~ggroenh/qmmm/mopac/gmxmop.f" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux" +IUSE="gmxmopac7 static-libs" + +DEPEND="dev-libs/libf2c" +RDEPEND="${DEPEND}" + +src_prepare() { + # Install the executable + sed -i \ + -e "s:noinst_PROGRAMS = mopac7:bin_PROGRAMS = mopac7:g" \ + fortran/Makefile.am \ + || die "sed failed: install mopac7" + # Install the script to run the executable + sed -i \ + -e "s:EXTRA_DIST = autogen.sh run_mopac7:bin_SCRIPTS = run_mopac7:g" \ + Makefile.am \ + || die "sed failed: install run_mopac7" + + eautoreconf +} + +src_configure() { + #set -std=legacy -fno-automatic according to + #http://www.bioinformatics.org/pipermail/ghemical-devel/2008-August/000763.html + FFLAGS="${FFLAGS} -std=legacy -fno-automatic" econf +} + +src_compile() { + emake + if use gmxmopac7; then + einfo "Making mopac7 lib for gromacs" + mkdir "${S}"/fortran/libgmxmopac7 && cd "${S}"/fortran/libgmxmopac7 + cp -f ../SIZES ../*.f "${FILESDIR}"/Makefile . || die + emake clean + cp -f "${DISTDIR}"/gmxmop.f "${DISTDIR}"/dcart.f . || die + sed "s:GENTOOVERSION:${PV}:g" -i Makefile + emake FC=$(tc-getFC) + if use static-libs; then + emake static + fi + fi +} + +src_install() { + # A correct fix would have a run_mopac7.in with @bindir@ that gets + # replaced by configure, and run_mopac7 added to AC_OUTPUT in configure.ac + sed -i "s:./fortran/mopac7:mopac7:g" run_mopac7 + + make DESTDIR="${D}" install || die + dodoc AUTHORS README ChangeLog + if use gmxmopac7; then + cd "${S}"/fortran/libgmxmopac7 + dolib.so libgmxmopac7.so* + if use static-libs; then + dolib.a libgmxmopac7.a + fi + fi +} diff --git a/sci-chemistry/mpqc/Manifest b/sci-chemistry/mpqc/Manifest new file mode 100644 index 000000000000..9b9a19f04580 --- /dev/null +++ b/sci-chemistry/mpqc/Manifest @@ -0,0 +1,13 @@ +AUX mpqc-2.3.1-as-needed.patch 6101 SHA256 5ed64fad86561612bf03678f6f3e780099f5bd393f0b5c20622fa7789ac23845 SHA512 b5e0398ebd3528059eff4c477a39cb8f76933cb0ab3ed3a4a054ab595d8fb171f9962e49601588eb880c4b418b0e91bfd25341a075f6e36328277a9ca9a68142 WHIRLPOOL fbb6a0264edfeb8828b4b37ae9bd4584a3bc183da10c6f71f72f33d0c79154d4a236189f061c28eaf4fe599d37ce49b66a6902909500dbb72eea32b7ea8641d6 +AUX mpqc-2.3.1-blas.patch 1917 SHA256 aa378d4baf693fa28260ade19a0ec6b583692b9735ac43f4357168a2c9f18c52 SHA512 33000fbd0d9ea2ddbfcfee997f27e71c43fb4128c5e9f5ae79cb7c5fc9ed3bd787a86b0e9efbb1842d6f962b643deadb8fa8498b870bef6268cddc5455d8fb07 WHIRLPOOL dac2f253a6742f0ddddac32fc0478229f7e6e43a916373823499b22d0d830315992dd2ed1a16bd664b4ba90f2c37bf28015e44ae7db60af766b37a928eef9438 +AUX mpqc-2.3.1-respect-ldflags.patch 666 SHA256 3f50b2e3a0038b7d4fc8f98eb375f794f37164a69edf6d7a767b0146e20481ca SHA512 84618392ab07884a09ec197a86c6ca26c298bb73d9c5a8a4f641a875d61f77a7d05494a7d0f4c8eef8cac742e5e4f1ebef99c333066a2fe8bd23e467f7918b56 WHIRLPOOL 4eb8cbbee7f77d438c0fe411030d04fbf55b266619154c3028810bd4daa27389f84a535a1ec0eeffeb8f7bc826b6e7346a899c561c2f42092b266764a3f2d613 +AUX mpqc-2.3.1-test-failure-hack.patch 543 SHA256 af5ae5f76916cbfe1a94981f94a30b373188de60ea19cc3d677d82c71412e503 SHA512 ae626fd6b723f6089b4cf6c2866863ab622aded5636735475cc2d85450b3753bc1cd3168ae1dcb49a579c4a15103cc64256c96eb12b52fcf0599e12bbdacfbc9 WHIRLPOOL 805f603220dd5a1fb8b2a59fe3fe543bbee028503e218e9be031b06657825e103ec19514681803e2a9945547190b4903d8fb6b683fa79858ec93bb751a51dae7 +AUX mpqc-2.3.1-wformat-security.patch 2284 SHA256 06bd711b6826a7005f35413b8686692d163fdaa16d4d93105e178ca7cdde61cb SHA512 22b30cc10f64ff96d027d2727643a3f3bfb08315f33996dfd8b9a28e0dcb9bee2d07cf1d8eead0df22be3117206737a52e350e7dfcfa07d381086610a6b94595 WHIRLPOOL 3d5f5349c16fb41ece48d4f308d9b8b9256276004296539c536ac20eb098c85063284c53626dcd6c94db18038b976020779b8439080a12c4e91f46ceb0b58b67 +DIST mpqc-2.3.1.tar.bz2 2521392 SHA256 18f162ca9cb8b3b05372b0ec3d02b4b8a4a7aabfc7b2abead350ddef8f048ecc SHA512 34f24f72c6c0024e72d47c7fd17927ca2a88020b30d22a791954fbc933f67ed6dd6741ee8a80ddd4fdb007f1a357b5f5ea7fc284cab85474bf60e9f29aaaa747 WHIRLPOOL 504e5be36673b85494866b8a09588964dd9b352208c4d08a1365cbc06b39dfe91dc6050a0e16cbd713b43b3e92d86cbe40f53a44a644f224e84340dd065e54ab +EBUILD mpqc-2.3.1-r1.ebuild 2267 SHA256 6506dbdef23964ea9f24a2e156164e85298c1874f987b8e246a39a535e5d071f SHA512 4b191021570bd3f29e58e76fdd63a0c25a6eed87160df189d8fbe202b4fb1f0dc4c63aba0c5500e87ab39c8a018eefda25252560bf6e1acd4ad29fe3a2c504e1 WHIRLPOOL 0cc3689c01ed2b3cbaeeb4ae84ce89f5ee89fdd71b3e9ff28cbedf346621ed04f1e5fbfb9ab4cc32b970ed1795e0e5a2c24eaf9051d95bb97e58e21838e73528 +EBUILD mpqc-2.3.1-r2.ebuild 2471 SHA256 efff831c662c454a9636fe0d5f78c0d170432095d3596ce7f07deb278bbf4ed6 SHA512 c87973d00b02822c0966151fc61c113430ed51ce4f9c048173163b77928fbc4ca4f664ad46d48455c33c7307835173ce1609197286441d4ff329dcdbacab4f16 WHIRLPOOL 8013ec8e71cc02106de3d0a208a675fc7b92dc08a8d8751f846d9c1ba5baf3f335238f3c2b661c55a429b5b7eb310111ffa58f681f07c2adb062924117311d41 +EBUILD mpqc-2.3.1-r3.ebuild 2481 SHA256 2497afa68929a74fdca3a52072160aa5a3a9aa5fb809776ffb3875f948dc8589 SHA512 e169bc991e917b036ae715d2a08c8ee013c585a4607f16c70edaf8910ff577a3b8325b10d8ae0d59bf653ecee2a1c897364338c7da925683c1b30f8e50b87826 WHIRLPOOL c86a28ed32255564a2358b7b2b2cb45baecd407a71b3ae7bba504417f6548e3438d3f90b0c4767c75e611de48bdb4c7ec6210ebf1d7e89bae90723358984f19a +EBUILD mpqc-2.3.1-r4.ebuild 2418 SHA256 8cd6442e69e1cd62f72a4a0a972fd8a58b0e838d4426a93583472861a075b4b4 SHA512 41e91bcdc68613f53a712cb9235c3b0783f3d841395594c8f7bc90211cb80d30981b9d0c4290906cee52269e3486560576b5f09a836ccf5ccb96cc2bae7db512 WHIRLPOOL db015cca4a425cec85a4d2540be31651ab6b8815dd3f2093f442e44ba244624726c2e756b06027c4345c4de19628fa524e23805a945a00c8487cee5c180a6488 +MISC ChangeLog 2952 SHA256 6e66605b423223a440402845c8147aa2ebaad03e0193d8738ce1f074c88d79ec SHA512 5c6de88602f63c761449d183287e438da3de499b385f911605f64016e89be03b3ec1f063b164876b3c70deacfa8ac16f49e0bb39d091f28cf6f4b1d3e85f23ea WHIRLPOOL 50fa63b4ebdd65317cef8dd13dbb114fe812cad88ffcece584a69dfbd03311de99bb0788e255178906eb9e866320a8b2891fc18ce4c83caca82ef990c57188e2 +MISC ChangeLog-2015 6335 SHA256 9fe0fb0fad3594ee2b41da0110f535bb393eb2e0f129d81782dfe8b3e6dead46 SHA512 e149639826e0ff880451cb491a32bab0658e7533ba87d7a741129387fc9acb4ba1e29293a30c4422543682ad9fc36b54154d74ac8b19d137cc10f781ba268e1a WHIRLPOOL 7fac8b7a397bf67bc89cf9bcae07e9c298445b28acc2c476142dab596217528d4d07dee502a6ea602faf4e336b8c41bd3ad3c7612711c515a67d0763d5dd2ba4 +MISC metadata.xml 349 SHA256 90739186c623452754368d506945352b925a4caa6b847262d074fe0d1ab61358 SHA512 4cdfca1b779b107326bdc77fd120008a4daa7da9b93ed3f783e95637796545b95c04477786633856f3d3e1656339db042953d3b2644a18cc25a2b1dc91dc80c6 WHIRLPOOL af33ef21a05f9d9e120fd32b7108a17f70378cde85f4eceb476112681bebb0578fd12896329408207974904f7342bc4ea30da3aabdee0e17ba289a4f4ed1dd84 diff --git a/sci-chemistry/mpqc/files/mpqc-2.3.1-as-needed.patch b/sci-chemistry/mpqc/files/mpqc-2.3.1-as-needed.patch new file mode 100644 index 000000000000..a917c0aaff70 --- /dev/null +++ b/sci-chemistry/mpqc/files/mpqc-2.3.1-as-needed.patch @@ -0,0 +1,163 @@ +--- mpqc-2.3.1.orig/src/lib/chemistry/molecule/Makefile 2005-05-26 08:00:29.000000000 +0200 ++++ mpqc-2.3.1/src/lib/chemistry/molecule/Makefile 2010-02-13 14:28:46.514285918 +0100 +@@ -66,6 +66,12 @@ + interface:: $(DEPENDINCLUDE) + + LIBS = $(shell $(LISTLIBS) $(INCLUDE) $(SRCDIR)/LIBS.h) ++LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCcontainer.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCclass.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCkeyval.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCoptimize.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCscmat.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCsymmetry.la + + LD = $(CXX) + +--- mpqc-2.3.1.orig/src/lib/chemistry/qc/wfn/Makefile 2004-06-12 06:50:35.000000000 +0200 ++++ mpqc-2.3.1/src/lib/chemistry/qc/wfn/Makefile 2010-02-13 14:20:06.911896080 +0100 +@@ -48,6 +48,12 @@ + + LIBS = $(shell $(LISTLIBS) $(INCLUDE) $(SRCDIR)/../dft/LIBS.h) + ++LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCisosurf.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCsolvent.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCbasis.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCdft.la \ ++ $(SRCDIR)/$(TOPDIR)/lib/libSCintv3.la ++ + wfntest:: wfntest.$(OBJSUF) $(LIBS) + $(LTLINK) $(CXX) $(LDFLAGS) -o wfntest $^ $(SYSLIBS) $(LTLINKBINOPTS) + +--- mpqc-2.3.1.orig/src/lib/chemistry/qc/intv3/Makefile 2002-04-04 01:08:04.000000000 +0200 ++++ mpqc-2.3.1/src/lib/chemistry/qc/intv3/Makefile 2010-02-13 14:04:15.393432311 +0100 +@@ -52,6 +52,8 @@ + LIBOBJ = $(LIBSRC:%.c=%.$(OBJSUF)) + LIBOBJ := $(LIBOBJ:%.cc=%.$(OBJSUF)) + ++LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCoint3.la ++ + DISTFILES = $(TESTCSRC) $(INC) atoms.sgen Makefile LIBS.h + + DEPENDINCLUDE = $(INC) $(GENINC) $(SGENINC) +--- mpqc-2.3.1.orig/src/lib/chemistry/qc/mbpt/Makefile 2005-07-07 17:54:05.000000000 +0200 ++++ mpqc-2.3.1/src/lib/chemistry/qc/mbpt/Makefile 2010-02-13 14:12:38.975370147 +0100 +@@ -44,6 +44,7 @@ + CSRCS = bzerofast.c + + LIBOBJ= $(CXXSRCS:%.cc=%.$(OBJSUF)) $(CSRCS:%.c=%.$(OBJSUF)) ++LIBADD= $(SRCDIR)/$(TOPDIR)/lib/libSCsymmetry.la + + default:: $(DEPENDINCLUDE) + +--- mpqc-2.3.1.orig/src/lib/chemistry/qc/basis/Makefile 2004-02-11 01:24:43.000000000 +0100 ++++ mpqc-2.3.1/src/lib/chemistry/qc/basis/Makefile 2010-02-13 14:04:15.395432868 +0100 +@@ -59,6 +59,7 @@ + DISTFILES = $(CXXSRC) $(INC) Makefile $(TESTSRC) $(TESTFILES) + + LIBOBJ= $(CXXSRC:%.cc=%.$(OBJSUF)) ++LIBADD = $(SYSLIBS) + + default:: $(DEPENDINCLUDE) + +--- mpqc-2.3.1.orig/src/lib/math/scmat/Makefile 2003-09-16 17:07:03.000000000 +0200 ++++ mpqc-2.3.1/src/lib/math/scmat/Makefile 2010-02-13 14:27:36.028370446 +0100 +@@ -75,6 +75,8 @@ + DISTFILES = $(CXXSRC) $(INC) scmat.h $(WEBSRC) Makefile LIBS.h \ + $(TESTSRC) $(TESTFILES) + ++LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCgroup.la $(SYSLIBS) ++ + LIBS = $(shell $(LISTLIBS) $(INCLUDE) $(SRCDIR)/LIBS.h) + + matrixtest: +--- mpqc-2.3.1.orig/src/lib/util/class/Makefile 2005-05-26 08:00:49.000000000 +0200 ++++ mpqc-2.3.1/src/lib/util/class/Makefile 2010-02-13 14:04:15.396433004 +0100 +@@ -41,6 +41,7 @@ + + BIN_OR_LIB = LIB + TARGET_TO_MAKE = libSCclass ++LIBADD = $(SYSLIBS) + + TESTCXXSRC = classtest.cc scextest.cc + DISTFILES = $(CXXSRC) $(INC) Makefile LIBS.h $(TESTCXXSRC) +--- mpqc-2.3.1.orig/src/lib/util/state/Makefile 2005-05-26 08:00:51.000000000 +0200 ++++ mpqc-2.3.1/src/lib/util/state/Makefile 2010-02-13 14:22:06.302369965 +0100 +@@ -50,6 +50,7 @@ + + BIN_OR_LIB = LIB + TARGET_TO_MAKE = libSCstate ++LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCkeyval.la + + default:: $(DEPENDINCLUDE) + +--- mpqc-2.3.1.orig/src/lib/util/group/Makefile 2005-07-30 02:30:18.000000000 +0200 ++++ mpqc-2.3.1/src/lib/util/group/Makefile 2010-02-13 14:21:38.582370124 +0100 +@@ -61,6 +61,7 @@ + + BIN_OR_LIB = LIB + TARGET_TO_MAKE = libSCgroup ++LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCkeyval.la + + TESTCXXSRC = pooltest.cc messtest.cc rnglocktest.cc thrtest.cc prttest.cc + DISTFILES = $(REQUIREDCXXSRC) $(OPTIONALCXXSRC) $(INC) \ +--- mpqc-2.3.1.orig/src/lib/util/Makefile 2001-08-07 00:29:56.000000000 +0200 ++++ mpqc-2.3.1/src/lib/util/Makefile 2010-02-13 14:40:23.611369920 +0100 +@@ -5,7 +5,7 @@ + + include $(SRCDIR)/$(TOPDIR)/lib/GlobalMakefile + +-SUBDIRS = options ref container class state misc keyval group render ++SUBDIRS = options keyval ref container class state misc group render + + include $(SRCDIR)/$(TOPDIR)/lib/GlobalSubDirs + +--- mpqc-2.3.1.orig/lib/GlobalRules 2010-02-13 19:47:19.019432588 +0100 ++++ mpqc-2.3.1/lib/GlobalRules 2010-02-13 19:47:57.760370198 +0100 +@@ -75,7 +75,7 @@ + $(RANLIB) $@ + + $(TOPDIR)/lib/$(TARGET_TO_MAKE).la: $(LIBOBJ) +- $(LTLINK) $(CXX) -o $@ $^ $(wildcard $(TMPLREPO)/*.o) $(LTLINKLIBOPTS) ++ $(LTLINK) $(CXX) $(LDFLAGS) -o $@ $^ $(wildcard $(TMPLREPO)/*.o) $(LTLINKLIBOPTS) $(LIBADD) + + else + +@@ -104,7 +104,7 @@ + endif + + $(TOPDIR)/lib/$(TARGET_TO_MAKE).la: $(LIBOBJ) +- $(LTLINK) $(CXX) -o $@ $^ $(LTLINKLIBOPTS) ++ $(LTLINK) $(CXX) $(LDFLAGS) -o $@ $^ $(LTLINKLIBOPTS) $(LIBADD) + + endif + +--- mpqc-2.3.1.orig/doc/devsamp/Makefile 2004-04-28 22:45:14.000000000 +0200 ++++ mpqc-2.3.1/doc/devsamp/Makefile 2010-02-13 19:58:56.958452043 +0100 +@@ -9,4 +9,4 @@ + LTLINKBINOPTS := $(shell $(SCCONFIG) --ltlinkbinopts) + + mp2: mp2.o +- $(LTLINK) $(CXX) $(CXXFLAGS) -o $@ $^ -L$(LIBDIR) -lmpqc $(LIBS) $(LTLINKBINOPTS) ++ $(LTLINK) $(CXX) $(LDFLAGS) $(CXXFLAGS) -o $@ $^ -L$(LIBDIR) -lmpqc $(LIBS) $(LTLINKBINOPTS) +--- mpqc-2.3.1.orig/src/bin/mpqc/Makefile 2005-07-28 18:57:47.000000000 +0200 ++++ mpqc-2.3.1/src/bin/mpqc/Makefile 2010-02-13 19:57:40.484216235 +0100 +@@ -82,7 +82,7 @@ + $(RANLIB) $@ + + $(TOPDIR)/lib/libmpqc.la: $(BINOBJ) +- $(LTLINK) $(CXX) -o $@ $^ $(LTLINKLIBOPTS) ++ $(LTLINK) $(CXX) $(LDFLAGS) -o $@ $^ $(LTLINKLIBOPTS) + + install_devel:: $(TOPDIR)/lib/libmpqc.$(LIBSUF) + $(INSTALL) $(INSTALLDIROPT) $(installroot)$(libdir) +--- mpqc-2.3.1.orig/src/lib/chemistry/qc/Makefile.orig 2010-06-18 18:09:58.192621760 +0000 ++++ mpqc-2.3.1/src/lib/chemistry/qc/Makefile 2010-06-18 18:10:10.350261767 +0000 +@@ -33,7 +33,7 @@ + include $(SRCDIR)/$(TOPDIR)/lib/GlobalMakefile + include $(TOPDIR)/lib/Makedirlist + +-SUBDIRS = basis oint3 intv3 wfn scf dft mbpt ++SUBDIRS = basis oint3 intv3 dft wfn scf mbpt + ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_QC_PSI),yes) + SUBDIRS := $(SUBDIRS) psi + endif diff --git a/sci-chemistry/mpqc/files/mpqc-2.3.1-blas.patch b/sci-chemistry/mpqc/files/mpqc-2.3.1-blas.patch new file mode 100644 index 000000000000..b99c82fb71da --- /dev/null +++ b/sci-chemistry/mpqc/files/mpqc-2.3.1-blas.patch @@ -0,0 +1,55 @@ + configure.in | 36 +++--------------------------------- + 1 files changed, 3 insertions(+), 33 deletions(-) + +diff --git a/configure.in b/configure.in +index ee82977..caae1f9 100644 +--- a/configure.in ++++ b/configure.in +@@ -1487,44 +1487,14 @@ AC_LANG_CPLUSPLUS + LIBSSAV="$LIBS" + LIBS="$LIBSSAV $FLIBS" + +-LIBBLAS="" +-F77_DGEMM=`$PERL $srcdir/bin/mkf77sym.pl.in -method $F77_SYMBOLS DAXPY` +-AC_CHECK_FUNC($F77_DGEMM,HAVE_BLAS=yes,[ +- AC_CHECK_LIB(essl,$F77_DGEMM,[HAVE_BLAS=yes;LIBBLAS="-lessl"], +- AC_CHECK_LIB(blas,$F77_DGEMM,[HAVE_BLAS=yes;LIBBLAS="-lblas"]) +- )] +-) +-if test X$HAVE_BLAS != Xyes; then +- LIBSSAV2="$LIBS" +- LIBS="-latlas $LIBS" +- AC_CHECK_LIB(f77blas,$F77_DGEMM,[HAVE_BLAS=yes;LIBBLAS="-lf77blas -latlas"], +- LIBS="$LIBSSAV2") +-fi +-AC_SUBST(HAVE_BLAS) +-if test X$HAVE_BLAS != Xyes; then +- echo "WARNING: Could not link to the BLAS library. It can be obtained at" +- echo "http://www.netlib.org/blas. Use --with-libdirs and/or --with-libs" +- echo "to specify the name of the library." +- AC_MSG_ERROR([BLAS is required to complete the build]) +-fi ++PKG_CHECK_MODULES([BLAS], [blas], [LIBBLAS="${BLAS_LIBS}"]) + + LIBS="$LIBSSAV $LIBBLAS $FLIBS" + +-LIBLAPACK="" +-F77_DGESVD=`$PERL $srcdir/bin/mkf77sym.pl.in -method $F77_SYMBOLS DGESVD` +-AC_CHECK_FUNC($F77_DGESVD,HAVE_LAPACK=yes,[ +- AC_CHECK_LIB(lapack,$F77_DGESVD,[HAVE_LAPACK=yes;LIBLAPACK="-llapack"] +- )] +-) +-AC_SUBST(HAVE_LAPACK) +-if test X$HAVE_LAPACK != Xyes; then +- echo "Could not link to the LAPACK library. It can be obtained at" +- echo "http://www.netlib.org/lapack. Use --with-libdirs and/or --with-libs" +- echo "to specify the name of the library." +- AC_MSG_ERROR([LAPACK is required to complete the build]) +-fi ++PKG_CHECK_MODULES([LAPACK], [lapack], [LIBLAPACK="${LAPACK_LIBS}"]) + + FLIBS="$LIBLAPACK $LIBBLAS $FLIBS" ++ + AC_LANG_RESTORE + + dnl ----------- check for Scalable BLAS library -------------- diff --git a/sci-chemistry/mpqc/files/mpqc-2.3.1-respect-ldflags.patch b/sci-chemistry/mpqc/files/mpqc-2.3.1-respect-ldflags.patch new file mode 100644 index 000000000000..c38c9579ddde --- /dev/null +++ b/sci-chemistry/mpqc/files/mpqc-2.3.1-respect-ldflags.patch @@ -0,0 +1,25 @@ +--- mpqc-2.3.1.orig/configure.in 2006-03-22 19:04:54.000000000 +0100 ++++ mpqc-2.3.1/configure.in 2010-02-13 17:46:19.545557872 +0100 +@@ -10,6 +10,8 @@ + AC_CONFIG_HEADER(src/lib/scconfig.h) + AC_CONFIG_AUX_DIR(bin) + ++m4_include([lib/autoconf/cca.m4]) ++m4_include([lib/autoconf/acinclude.m4]) + AC_CANONICAL_SYSTEM + + AC_DEFINE_UNQUOTED(HOST_ARCH, "$host") +@@ -473,12 +473,10 @@ + echo Using FORTRAN runtime libraries: $withval + ) + +-LDFLAGS= +-LIBDIRS= + AC_ARG_WITH(libdirs, + [ --with-libdirs Specifies library directories (-Ldir1 -Ldir2).], + LIBDIRS=$withval +-LDFLAGS=$withval ++LDFLAGS="$LDFLAGS $withval" + echo Using extra library directories: $withval + ) + diff --git a/sci-chemistry/mpqc/files/mpqc-2.3.1-test-failure-hack.patch b/sci-chemistry/mpqc/files/mpqc-2.3.1-test-failure-hack.patch new file mode 100644 index 000000000000..91fcc30d0d90 --- /dev/null +++ b/sci-chemistry/mpqc/files/mpqc-2.3.1-test-failure-hack.patch @@ -0,0 +1,11 @@ +--- mpqc-2.3.1.orig/src/bin/mpqc/validate/Makefile 2006-03-22 19:03:51.000000000 +0100 ++++ mpqc-2.3.1/src/bin/mpqc/validate/Makefile 2010-02-13 20:26:12.496370219 +0100 +@@ -52,7 +52,7 @@ + # Also need to see if --mpqc was specified. If not, then add + # --mpqc ../../mpqc. + ifeq ($(filter --mpqc%, $(ALL_MPQCRUN_ARGS)),) +-ALL_MPQCRUN_ARGS:=--mpqc ../../mpqc $(ALL_MPQCRUN_ARGS) ++ALL_MPQCRUN_ARGS:=--mpqc "LD_LIBRARY_PATH=\"../../../../../lib/.libs/\" ../../mpqc" $(ALL_MPQCRUN_ARGS) + endif + + ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_QC_MBPTR12),yes) diff --git a/sci-chemistry/mpqc/files/mpqc-2.3.1-wformat-security.patch b/sci-chemistry/mpqc/files/mpqc-2.3.1-wformat-security.patch new file mode 100644 index 000000000000..7f25a92ad891 --- /dev/null +++ b/sci-chemistry/mpqc/files/mpqc-2.3.1-wformat-security.patch @@ -0,0 +1,71 @@ +Fix -Werror=format-security errors +https://bugs.gentoo.org/show_bug.cgi?id=542278 + +--- mpqc-2.3.1/src/lib/chemistry/molecule/atominfo.cc ++++ mpqc-2.3.1/src/lib/chemistry/molecule/atominfo.cc +@@ -493,7 +493,7 @@ + if (iname != symbol_to_Z_.end()) return iname->second; + + if (allow_exceptions) { +- ExEnv::err0() << sprintf("AtomInfo: invalid name: %s\n",name.c_str()); ++ ExEnv::err0() << fprintf(stderr, "AtomInfo: invalid name: %s\n",name.c_str()); + throw std::runtime_error("invalid atom name"); + } + +--- mpqc-2.3.1/src/lib/chemistry/molecule/atominfo.h ++++ mpqc-2.3.1/src/lib/chemistry/molecule/atominfo.h +@@ -49,8 +49,8 @@ + struct atom + { + int Z; +- char *name; +- char *symbol; ++ const char *name; ++ const char *symbol; + }; + + static struct atom elements_[Nelement]; +--- mpqc-2.3.1/src/lib/chemistry/molecule/simple.cc ++++ mpqc-2.3.1/src/lib/chemistry/molecule/simple.cc +@@ -214,7 +214,7 @@ + os << scprintf(" %4d", atoms[i]); + + if (mol.nonnull()) { +- char *separator = " "; ++ const char *separator = " "; + os << " "; + for (i=0; i<(4-natoms()); i++) { + os << " "; +--- mpqc-2.3.1/src/lib/chemistry/qc/psi/psiexenv.cc ++++ mpqc-2.3.1/src/lib/chemistry/qc/psi/psiexenv.cc +@@ -147,7 +147,7 @@ + return 0; + } + +-int PsiExEnv::run_psi_module(char *module) ++int PsiExEnv::run_psi_module(const char *module) + { + int errcod; + char *module_cmd = new char[2*cwd_.size()+strlen(module)+psiprefix_.size()+fileprefix_.size()+stdout_.size()+stderr_.size()+40]; +--- mpqc-2.3.1/src/lib/chemistry/qc/psi/psiexenv.h ++++ mpqc-2.3.1/src/lib/chemistry/qc/psi/psiexenv.h +@@ -57,7 +57,7 @@ + /// Executes Psi input+driver + int run_psi(); + /// Executes a Psi module +- int run_psi_module(char *); ++ int run_psi_module(const char *); + + /// Returns current working directory + string get_cwd() const { return cwd_;}; +--- mpqc-2.3.1/src/lib/chemistry/qc/psi/psiwfn.cc ++++ mpqc-2.3.1/src/lib/chemistry/qc/psi/psiwfn.cc +@@ -44,7 +44,7 @@ + bytes = 2000000; + int bytes_str_len = (int)ceil(log10((long double)bytes)); + memory_ = new char[bytes_str_len+5]; +- sprintf(memory_,"(%ld B)",bytes); ++ sprintf(memory_,"(%d B)",bytes); + } + + PsiWavefunction::~PsiWavefunction() diff --git a/sci-chemistry/mpqc/metadata.xml b/sci-chemistry/mpqc/metadata.xml new file mode 100644 index 000000000000..2a8e4866597f --- /dev/null +++ b/sci-chemistry/mpqc/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">mpqc</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/mpqc/mpqc-2.3.1-r1.ebuild b/sci-chemistry/mpqc/mpqc-2.3.1-r1.ebuild new file mode 100644 index 000000000000..794008aa31d9 --- /dev/null +++ b/sci-chemistry/mpqc/mpqc-2.3.1-r1.ebuild @@ -0,0 +1,92 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +DESCRIPTION="The Massively Parallel Quantum Chemistry Program" +HOMEPAGE="http://www.mpqc.org/" +SRC_URI="mirror://sourceforge/mpqc/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc ppc64 x86" +IUSE="doc threads tk" + +RDEPEND=" + virtual/blas + virtual/lapack + tk? ( dev-lang/tk )" +DEPEND="${RDEPEND} + dev-lang/perl + sys-devel/flex + sys-apps/sed + virtual/pkgconfig + doc? ( + app-doc/doxygen + media-gfx/graphviz )" + +src_unpack() { + unpack ${A} + cd "${S}" + + # do not install tkmolrender if not requested + if ! use tk; then + sed \ + -e "s:.*/bin/molrender/tkmolrender.*::" \ + -e "s:.*\$(INSTALLBINOPT) tkmolrender.*::" \ + -e "s:/bin/rm -f tkmolrender::" \ + -i "./src/bin/molrender/Makefile" \ + || die "failed to disable tkmolrender" + fi +} + +src_compile() { + # Only shared will work on ppc64 - bug #62124 + # But we always want shared libraries + econf \ + $(use_enable threads) \ + --enable-shared \ + ${myconf} + + sed \ + -e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS}:" \ + -e "s:^FFLAGS =.*$:FFLAGS=${FFLAGS:- -O2}:" \ + -e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS}:" \ + lib/LocalMakefile + emake || die "emake failed" +} + +src_test() { + cd "${S}"/src/bin/mpqc/validate + + # we'll only run the small test set, since the + # medium and large ones take >10h and >24h on my + # 1.8Ghz P4M + emake -j1 check0 || die "failed in test routines" +} + +src_install() { + emake -j1 installroot="${D}" install install_devel install_inc \ + || die "install failed" + + dodoc CHANGES CITATION README || die "failed to install docs" + + # make extended docs + if use doc; then + cd "${S}"/doc + emake -j1 all || die "failed to generate documentation" + doman man/man1/* man/man3/* || \ + die "failed to install man pages" + dohtml -r html/ + fi +} + +pkg_postinst() { + echo + einfo "MPQC can be picky with regard to compilation flags." + einfo "If during mpqc runs you have trouble converging or " + einfo "experience oscillations during SCF interations, " + einfo "consider recompiling with less aggressive CFLAGS/CXXFLAGS." + einfo "Particularly, replacing -march=pentium4 by -march=pentium3" + einfo "might help if you encounter problems with correlation " + einfo "consistent basis sets." + echo +} diff --git a/sci-chemistry/mpqc/mpqc-2.3.1-r2.ebuild b/sci-chemistry/mpqc/mpqc-2.3.1-r2.ebuild new file mode 100644 index 000000000000..c2776b711a1d --- /dev/null +++ b/sci-chemistry/mpqc/mpqc-2.3.1-r2.ebuild @@ -0,0 +1,102 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=2 + +inherit autotools eutils toolchain-funcs + +DESCRIPTION="The Massively Parallel Quantum Chemistry Program" +HOMEPAGE="http://www.mpqc.org/" +SRC_URI="mirror://sourceforge/mpqc/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 x86" +IUSE="doc mpi threads tk" + +RDEPEND=" + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[cxx] ) + tk? ( dev-lang/tk )" +DEPEND="${RDEPEND} + dev-lang/perl + sys-devel/flex + sys-apps/sed + virtual/pkgconfig + doc? ( + app-doc/doxygen + media-gfx/graphviz )" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-as-needed.patch \ + "${FILESDIR}"/${P}-respect-ldflags.patch \ + "${FILESDIR}"/${P}-test-failure-hack.patch + # do not install tkmolrender if not requested + if ! use tk; then + sed \ + -e "s:.*/bin/molrender/tkmolrender.*::" \ + -e "s:.*\$(INSTALLBINOPT) tkmolrender.*::" \ + -e "s:/bin/rm -f tkmolrender::" \ + -i "./src/bin/molrender/Makefile" \ + || die "failed to disable tkmolrender" + fi + eautoreconf +} + +src_configure() { + tc-export CC CXX + if use mpi; then + export CC=mpicc + export CXX=mpicxx + fi + econf \ + $(use_enable threads) \ + $(use_enable mpi parallel) \ + --enable-shared \ + ${myconf} + + sed \ + -e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS}:" \ + -e "s:^FFLAGS =.*$:FFLAGS=${FFLAGS:- -O2}:" \ + -e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS}:" \ + lib/LocalMakefile +} + +src_test() { + cd "${S}"/src/bin/mpqc/validate + + # we'll only run the small test set, since the + # medium and large ones take >10h and >24h on my + # 1.8Ghz P4M + emake -j1 check0 || die "failed in test routines" +} + +src_install() { + emake installroot="${D}" install install_devel install_inc \ + || die "install failed" + + dodoc CHANGES CITATION README || die "failed to install docs" + + # make extended docs + if use doc; then + cd "${S}"/doc + emake -j1 all || die "failed to generate documentation" + doman man/man1/* man/man3/* || \ + die "failed to install man pages" + dohtml -r html/ + fi +} + +pkg_postinst() { + echo + einfo "MPQC can be picky with regard to compilation flags." + einfo "If during mpqc runs you have trouble converging or " + einfo "experience oscillations during SCF interations, " + einfo "consider recompiling with less aggressive CFLAGS/CXXFLAGS." + einfo "Particularly, replacing -march=pentium4 by -march=pentium3" + einfo "might help if you encounter problems with correlation " + einfo "consistent basis sets." + echo +} diff --git a/sci-chemistry/mpqc/mpqc-2.3.1-r3.ebuild b/sci-chemistry/mpqc/mpqc-2.3.1-r3.ebuild new file mode 100644 index 000000000000..b53abbdc26cb --- /dev/null +++ b/sci-chemistry/mpqc/mpqc-2.3.1-r3.ebuild @@ -0,0 +1,106 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils toolchain-funcs + +DESCRIPTION="The Massively Parallel Quantum Chemistry Program" +HOMEPAGE="http://www.mpqc.org/" +SRC_URI="mirror://sourceforge/mpqc/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc ppc64 x86" +IUSE="doc mpi threads static-libs tk" + +RDEPEND=" + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[cxx] ) + tk? ( dev-lang/tk )" +DEPEND="${RDEPEND} + dev-lang/perl + sys-devel/flex + sys-apps/sed + virtual/pkgconfig + doc? ( + app-doc/doxygen + media-gfx/graphviz )" + +PATCHES=( + "${FILESDIR}"/${P}-as-needed.patch + "${FILESDIR}"/${P}-respect-ldflags.patch + "${FILESDIR}"/${P}-test-failure-hack.patch + "${FILESDIR}"/${P}-blas.patch + ) + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +DOCS=(CHANGES CITATION README) + +src_prepare() { + # do not install tkmolrender if not requested + if ! use tk; then + sed \ + -e "s:.*/bin/molrender/tkmolrender.*::" \ + -e "s:.*\$(INSTALLBINOPT) tkmolrender.*::" \ + -e "s:/bin/rm -f tkmolrender::" \ + -i "./src/bin/molrender/Makefile" \ + || die "failed to disable tkmolrender" + fi + autotools-utils_src_prepare +} + +src_configure() { + tc-export CC CXX + if use mpi; then + export CC=mpicc + export CXX=mpicxx + fi + local myeconfargs=( + $(use_enable threads) + $(use_enable mpi parallel) ) + + autotools-utils_src_configure + sed \ + -e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS}:" \ + -e "s:^FFLAGS =.*$:FFLAGS=${FFLAGS:- -O2}:" \ + -e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS}:" \ + -i lib/LocalMakefile || die +} + +src_test() { + cd "${AUTOTOOLS_BUILD_DIR}"/src/bin/mpqc/validate + + # we'll only run the small test set, since the + # medium and large ones take >10h and >24h on my + # 1.8Ghz P4M + emake -j1 check1 +} + +src_install() { + autotools-utils_src_install installroot="${D}" install install_devel install_inc + + # make extended docs + if use doc; then + cd "${AUTOTOOLS_BUILD_DIR}"/doc + emake -j1 all + doman man/man1/* man/man3/* + dohtml -r html + fi +} + +pkg_postinst() { + echo + einfo "MPQC can be picky with regard to compilation flags." + einfo "If during mpqc runs you have trouble converging or " + einfo "experience oscillations during SCF interations, " + einfo "consider recompiling with less aggressive CFLAGS/CXXFLAGS." + einfo "Particularly, replacing -march=pentium4 by -march=pentium3" + einfo "might help if you encounter problems with correlation " + einfo "consistent basis sets." + echo +} diff --git a/sci-chemistry/mpqc/mpqc-2.3.1-r4.ebuild b/sci-chemistry/mpqc/mpqc-2.3.1-r4.ebuild new file mode 100644 index 000000000000..bdf7bcdcce0a --- /dev/null +++ b/sci-chemistry/mpqc/mpqc-2.3.1-r4.ebuild @@ -0,0 +1,105 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools toolchain-funcs + +DESCRIPTION="The Massively Parallel Quantum Chemistry Program" +HOMEPAGE="http://www.mpqc.org/" +SRC_URI="mirror://sourceforge/mpqc/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86" +IUSE="doc mpi threads static-libs tk" + +RDEPEND=" + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[cxx] ) + tk? ( dev-lang/tk:0 )" +DEPEND="${RDEPEND} + dev-lang/perl + sys-devel/flex + sys-apps/sed + virtual/pkgconfig + doc? ( + app-doc/doxygen + media-gfx/graphviz )" + +PATCHES=( + "${FILESDIR}/${P}-as-needed.patch" + "${FILESDIR}/${P}-respect-ldflags.patch" + "${FILESDIR}/${P}-test-failure-hack.patch" + "${FILESDIR}/${P}-blas.patch" + "${FILESDIR}/${P}-wformat-security.patch" +) +DOCS=(CHANGES CITATION README) + +src_prepare() { + # do not install tkmolrender if not requested + if ! use tk; then + sed \ + -e "s:.*/bin/molrender/tkmolrender.*::" \ + -e "s:.*\$(INSTALLBINOPT) tkmolrender.*::" \ + -e "s:/bin/rm -f tkmolrender::" \ + -i "./src/bin/molrender/Makefile" \ + || die "failed to disable tkmolrender" + fi + default + mv configure.{in,ac} || die + eautoreconf +} + +src_configure() { + tc-export CC CXX + if use mpi; then + export CC=mpicc + export CXX=mpicxx + fi + + econf \ + $(use_enable threads) \ + $(use_enable mpi parallel) \ + $(use_enable static-libs static) + + sed \ + -e "s:^CFLAGS =.*$:CFLAGS=${CFLAGS}:" \ + -e "s:^FFLAGS =.*$:FFLAGS=${FFLAGS:- -O2}:" \ + -e "s:^CXXFLAGS =.*$:CXXFLAGS=${CXXFLAGS}:" \ + -i lib/LocalMakefile || die +} + +src_test() { + cd src/bin/mpqc/validate || die + + # we'll only run the small test set, since the + # medium and large ones take >10h and >24h on my + # 1.8Ghz P4M + emake -j1 check1 +} + +src_install() { + emake installroot="${D}" install install_devel install_inc + + # make extended docs + if use doc; then + cd doc || die + emake all + doman man/man1/* man/man3/* + dodoc -r html/ + fi +} + +pkg_postinst() { + echo + einfo "MPQC can be picky with regard to compilation flags." + einfo "If during mpqc runs you have trouble converging or " + einfo "experience oscillations during SCF interations, " + einfo "consider recompiling with less aggressive CFLAGS/CXXFLAGS." + einfo "Particularly, replacing -march=pentium4 by -march=pentium3" + einfo "might help if you encounter problems with correlation " + einfo "consistent basis sets." + echo +} diff --git a/sci-chemistry/msms-bin/Manifest b/sci-chemistry/msms-bin/Manifest new file mode 100644 index 000000000000..952587810d5d --- /dev/null +++ b/sci-chemistry/msms-bin/Manifest @@ -0,0 +1,6 @@ +DIST msms_i86Linux2_2.6.1.tar.gz 112762 SHA256 ab4f9e60df6fe18a5ac05550bf074b287792638a818a047697ead049d8737caf SHA512 814a5b5fa760b57c773f6900d42cacc5b68a2bf16d8792aa63cfa779aeabdab4e05064b86de6fb2551194543db925d83e07cf4ef74be8c08935ef5ecc8dcfe73 WHIRLPOOL dab6bfd4e8dca59939cd9d0fd6638a3304314dec023b684a09a34eb9bf90fcdc348091af4ea0676a4bf246e30b685a97e1750e0ccfbfccc8e9a90c1cf8445994 +DIST msms_i86_64Linux2_2.6.1.tar.gz 593147 SHA256 5f0ca50360b5938e74c538e0399d582abc4a40ef4cf410e66f31a1f91e6e3e1f SHA512 630da1ae57b2d8d072247b650636a71e5ef6f07a245c8c4d07b26e20618d9c5dbaffcff563d0504b9b899ca263ba5f3458447f0e649bbfb895aea34305c1c8f8 WHIRLPOOL dff76b55ff1cd53770a4b0fc91d9c7c4f2ae7422008f1081a630965858718bd5cbb2b8e5167809f5957123fb55909e0042c9ca469596eecea7c44cb1c587f085 +EBUILD msms-bin-2.6.1-r1.ebuild 1063 SHA256 da70b208116b7cccec4fdcda0e82e5df95584e138c6f21694f80c971d229fffa SHA512 e0041ed3ffab683b8be0456cfa216124d04447c9a5640e3637bfb1443bf8cebaea196c95b97bb01bd32ec22dd2c9e951564149a25fc74aa45e079a59e86abbce WHIRLPOOL 0947186e713d9b75a40680a140fd60529b1d399a31992b1d213adf92de8256cd696be6ed7e7c5eb690255c025df978968d3c11ed19bd6bd0b587c340425bb14b +MISC ChangeLog 2441 SHA256 ae4d009a3bd7b7041e6c65c32d1e94f7341bfeef4299d498b536ada6a3fc6d25 SHA512 2075e1080db41f5d937a7aef170e71f69f294015e4ed8607ff905c5a765e78e96ef84b468624869d294c667f4661d394c1a6a8fc5033e77aa854910d90f03452 WHIRLPOOL e998e5860a28bb889ed6c7e6e99db3480c94e6972a4055ac9796afad008db5624b1d10170393bd605d080264b85a7eb991ddce8b44374dd531c73c6cb3094638 +MISC ChangeLog-2015 1428 SHA256 e1aec089408724fa6878b8783f7715330870266e1219e957a6360ff3cb520737 SHA512 24e642558412281b97d5d60eac775d243c54216ef9fcac70b1d18a04fe4ed032d73291395361bd2c9f22cc8e17e6e440e98045e0bc143c4d379c968e713d02b8 WHIRLPOOL 8f6a43811becc33a944daf63c8148ff8402fa9f84d99dce2bcd67761c3d9981039dc5cd805849ea6aef68174afb7d9d852a0be127670dd9668a41ed0faa0c6a8 +MISC metadata.xml 342 SHA256 6e74575656406b91602694e2d9ae391bbdcfe25efd3ac8a16bcf0e1a454199ba SHA512 2dbd8b2bdf37d4a2d4127cb373db2c6ff8fc4de6bf294e4518f1d424115860c0b083d538935a8b1a54543b396b968985e46a7ca293367ee1a0b462d11639b7ab WHIRLPOOL 9feb232502b198a4a6c820aaf6a54af0daee5d32be0ad3afa030a9a9109579012fa6784f12feb7c2286171f240735f204e121f21a54c7b59d3985e41a43f8f9f diff --git a/sci-chemistry/msms-bin/metadata.xml b/sci-chemistry/msms-bin/metadata.xml new file mode 100644 index 000000000000..ba21fec241dd --- /dev/null +++ b/sci-chemistry/msms-bin/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexxy@gentoo.org</email> + </maintainer> +<maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild b/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild new file mode 100644 index 000000000000..75e928623167 --- /dev/null +++ b/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +DESCRIPTION="MSMS allows to compute very efficiently triangulations of Solvent Excluded Surfaces" +HOMEPAGE="http://mgl.scripps.edu/people/sanner/html/msms_home.html" +SRC_URI=" + amd64? ( msms_i86_64Linux2_2.6.1.tar.gz ) + x86? ( msms_i86Linux2_2.6.1.tar.gz ) +" + +LICENSE="MSMS" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RESTRICT="fetch" + +S="${WORKDIR}" + +QA_PREBUILT="${EROOT#/}opt/bin/.*" + +pkg_nofetch() { + einfo "Please download ${A} from http://mgltools.scripps.edu/downloads#msms and place it to ${DISTDIR}" +} + +src_install() { + doman msms.1 + dodoc README msms.html ReleaseNotes + exeinto /opt/bin + if use amd64; then + newexe ${PN%-bin}.x86_64Linux2.${PV} msms + elif use x86; then + newexe ${PN%-bin}.i86Linux2.${PV} msms + fi + insinto /usr/share/${PN}/ + doins atmtypenumbers + sed \ + -e 's:nawk:awk:g' \ + -e "s:./atmtypenumbers:${EPREFIX}/usr/share/${PN}/atmtypenumbers:g" \ + -i pdb_to_xyz* || die + dobin pdb_to_xyz* +} diff --git a/sci-chemistry/mustang/Manifest b/sci-chemistry/mustang/Manifest new file mode 100644 index 000000000000..291893d652f0 --- /dev/null +++ b/sci-chemistry/mustang/Manifest @@ -0,0 +1,8 @@ +AUX mustang-3.2.1-gcc-4.7.patch 477 SHA256 9dc8e18c3f4eb904196836a644807a0c168ff8055ffd6f0a4b1ad10b390bffb8 SHA512 169e68335093d3400c3294a38246d5e9264f77bbaeab7c047318f8db5934cfed24ae5f0f421f2483e2c9fe8df1db40b8ab48c0dac1c20867f4119011b3e4f52e WHIRLPOOL 36ae5826fcd9b324ac42aa1ee091f0d2e766fa67c38ba0ae354377e4d3a451efcffbceb01fe4495cdfaf432efeab510bf975799203a2b1dc46b9fb4f0650b134 +DIST mustang_v3.2.1.tgz 161216 SHA256 38f8ec10f15466a42ade770eb6c3ed0ed2449bb070a53b5e8d3125f2596b1556 SHA512 aee37bb77edbdc601cdc735db8602d0a3804065200df1b36b6956e74dfd5f85b554a655be1bfbe673aada1abd5e1aee1c0f59fb2ff0380bfcb725e38439d41ff WHIRLPOOL 521edce7648c28c067dae4462e432c8b5f2b9a60be4248ba78280067254fdfb9f584c18ce9afc5c99927f6227e1e650989cd7d65df1b3c6e7494d617b89a74fe +DIST mustang_v3.2.2.tgz 141940 SHA256 6fe274a93b54ba3c46e262fc6d7114bad239d1cbd2dadec8a92a7194328373a2 SHA512 cb862f860f3cdb3349743c6005a29acc14cde5269df9d61f1100ffdc9a22c1d8e3dd46771371557b823724e79783f8fcb7356c63c6f0c0a09aac09bee407a26d WHIRLPOOL 63e7b6f881274c20df59e85699b1f1a07506f0dd20082e898001c163fb02b60336c0ee6b629bf19f773f86b3479f4ae1344cf1ea6b7f6052d1407db3f05910bb +EBUILD mustang-3.2.1.ebuild 1052 SHA256 605845ee81cc020bdc19c233587f78ab558272c6fba2db4312b1bff1eeb54904 SHA512 3d39237989798c26ecfb5f398fdc9fd10c9199af5c9e443e780dbf5474b4c825e3beefb099755eefe79190301317a24928e9f8450521dbc13c10c11efe2b562c WHIRLPOOL 425d4820c0d03be25323be4f52ac99e271fad3d48608703c3db8bf4014e622366b251af713417dd033874d90bc6faa5a8ffd08f7d0c71a0041260029f7835dd6 +EBUILD mustang-3.2.2.ebuild 1108 SHA256 1ab809b4d8b4fcbf0b4361f392dab29c0b0b05983dc54c56845b4aefdb86902a SHA512 33ed04c0c7cdb999a17921b189b9bb41973334a65085b6bc9655dedbd7e125b838a0833d398c5da31b7b36e21ab4cdcded7329c56d58b1de1067f6faa54a0301 WHIRLPOOL 7201deec46f56812bb00f6a589183b9a9553e7c58a021c4f9c55c989f3effa002415baf4b3347f0218eb18eaf27ec59efa74d3b37737af5c471a138d42fd0beb +MISC ChangeLog 2732 SHA256 7a2965c669ff70d068fc74cf4cd1a0ebf0b7b2667e4df986eadf5bd9101bf42e SHA512 6ac0a4663dee32c455d5526a7cdeb3f06d032fb47cf2bacd799227535f121585a7f2868c0e7fecee13b2087f8a34d2b6ee62d3ff4daaf94b0ff587b5c430109a WHIRLPOOL 55dff48e10ef09fdf028e9debb586b1d4f79e3f81c2a9d0093c377476e2f3095675c4eff240731d0e32a44315ec11ea3581f50146835980492fe7c6fcc8f352e +MISC ChangeLog-2015 1808 SHA256 05377da2fdd7f1b6915bdfa608f92cc6944b064011d0871efb2195174e6d35dc SHA512 7228727ad9a0985eb37002c9fd3a1f30660494a98a95e4c51a013937faebc3ec00277d75b7ed4c2fc54209e1249ab0448bcba34637e613f42de6758952c71f5b WHIRLPOOL ac3891d5931eac563e69b85eedb5a2c415f9e09f25b3a31aa7128a076ad730518f722bcc66d2b9fed8be4deba16c9076557deb7c10cbd3ea95a3bf51019c8e8c +MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d diff --git a/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch b/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch new file mode 100644 index 000000000000..9e5dea85afeb --- /dev/null +++ b/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch @@ -0,0 +1,16 @@ + src/superpose_on_core_2.cpp | 2 ++ + 1 files changed, 2 insertions(+), 0 deletions(-) + +diff --git a/src/superpose_on_core_2.cpp b/src/superpose_on_core_2.cpp +index ae137de..059dfe3 100644 +--- a/src/superpose_on_core_2.cpp ++++ b/src/superpose_on_core_2.cpp +@@ -55,6 +55,8 @@ using std::ofstream ; + #include "multiple_superposition.h" + #include "3D_manip_functions.h" + ++#include <unistd.h> ++ + int **core_columns ; + int *core_columns_2 , NCORE = 0 ; + int **algn_to_seq_hash ; diff --git a/sci-chemistry/mustang/metadata.xml b/sci-chemistry/mustang/metadata.xml new file mode 100644 index 000000000000..da36ecbfcd6a --- /dev/null +++ b/sci-chemistry/mustang/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/mustang/mustang-3.2.1.ebuild b/sci-chemistry/mustang/mustang-3.2.1.ebuild new file mode 100644 index 000000000000..47e67a964a4a --- /dev/null +++ b/sci-chemistry/mustang/mustang-3.2.1.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +MY_PN="MUSTANG" +SRC_P="${PN}_v${PV}" +MY_P="${MY_PN}_v${PV}" + +DESCRIPTION="MUltiple STructural AligNment AlGorithm" +HOMEPAGE="http://www.csse.monash.edu.au/~karun/Site/mustang.html" +SRC_URI="http://www.csse.unimelb.edu.au/~arun/${PN}/${SRC_P}.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-gcc-4.7.patch +} + +src_compile() { + emake \ + CPP=$(tc-getCXX) \ + CPPFLAGS="${CXXFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_test() { + ./bin/${P} -f ./data/test/test_zf-CCHH || die +} + +src_install() { + newbin bin/${P} mustang + doman man/${PN}.1 + dodoc README +} + +pkg_postinst() { + elog "If you use this program for an academic paper, please cite:" + elog "Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey, and Arthur M. Lesk" + elog "Proteins: Structure, Function, and Bioinformatics. 64(3):559-574, Aug. 2006" +} diff --git a/sci-chemistry/mustang/mustang-3.2.2.ebuild b/sci-chemistry/mustang/mustang-3.2.2.ebuild new file mode 100644 index 000000000000..9bbd00dc51c9 --- /dev/null +++ b/sci-chemistry/mustang/mustang-3.2.2.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +MY_PN="MUSTANG" +SRC_P="${PN}_v${PV}" +MY_P="${MY_PN}_v${PV}" + +DESCRIPTION="MUltiple STructural AligNment AlGorithm" +HOMEPAGE="http://www.csse.monash.edu.au/~karun/Site/mustang.html" +SRC_URI="http://www.csse.monash.edu.au/~karun/${PN}/${PN}_v${PV}.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-3.2.1-gcc-4.7.patch + sed -e 's:3.2.1:3.2.2:g' -i Makefile || die +} + +src_compile() { + emake \ + CPP=$(tc-getCXX) \ + CPPFLAGS="${CXXFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_test() { + ./bin/${P} -f ./data/test/test_zf-CCHH || die +} + +src_install() { + newbin bin/${P} ${PN} + doman man/${PN}.1 + dodoc README +} + +pkg_postinst() { + elog "If you use this program for an academic paper, please cite:" + elog "Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey, and Arthur M. Lesk" + elog "Proteins: Structure, Function, and Bioinformatics. 64(3):559-574, Aug. 2006" +} diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest new file mode 100644 index 000000000000..e6e7c423d7b3 --- /dev/null +++ b/sci-chemistry/namd/Manifest @@ -0,0 +1,10 @@ +AUX namd-2.10-gentoo.patch 4636 SHA256 2bee11bb1bfa086c12acf84abf94e35c7bcba8dc269d80ce6aa20490b9ef6a0c SHA512 28ffbedb05d24a74e05a4f65424a25a4598e2172b7b4ab07fe84570e3162373e4e018f66077636bb097c6e0687666ac81dbb8b925a195f23c269829ebb9234c8 WHIRLPOOL 3616c28a38b92fe1d376fa413c6f565bd5727edfa821c98682c1cbc3834e95d1c1093c43ba99cb26904637d661c31a893c3f6e7a838b07c696c2bd3689795ab9 +AUX namd-2.7-iml-dec.patch 520 SHA256 6be7d0a3b4dff7fa39246e7ce49afb82ff508456ebbe3983e2def1202ebb3024 SHA512 50ddf91bcb0e370a98d6fe5329f00ec9a8016f0178e342b086f4b9d4130a41e525ed9d960e92dc83b4372f135ce9d454bef836d3e215fb6ac7933999278efa37 WHIRLPOOL f68a4f6bd2df6b8d031ca8709bdb66e6ab558b520ea3ad9bef4ea949e24be6380717c3da9840e8daa9b65cfa8b007d37c36ea0e33f7b4c39ab08f93a4e0ecade +AUX namd-2.9-gentoo.patch 5480 SHA256 ff76fceaadbd267023eb30cf256a44aff2b7cd567c8bcf1362afbfec6ca2b26f SHA512 e59a01fe0b65fe9df6b47e962f776eea650b55071081210d0e1269dd76e4da4bca8faef11398bd0cb1f8acc883c8ebf6b37d7fdab066602fd251aae82cb87264 WHIRLPOOL 2b9fee1f2c8a872665b77275b32b45cbd0965aedae5cdaf08024f317add12d57ac93c1f8fc2d91cfb2c8b209cd7fa26e020e2c1a109e667d5b765d79aabcbf26 +DIST NAMD_2.10_Source.tar.gz 9200234 SHA256 a5282c172524c2fbe6b9ba56f2de8c84f1093405c914ffbc70442dd0dd4e4289 SHA512 3712a03841fad76c502ac4e41469162ff78e6152560d0f6855d61d2b5583241a661e2a3e7446029b56a6f6f1100f25cb51b2c3df6571542397961d3bb625bc92 WHIRLPOOL b97e47c1d73d505620c26a2eca2e2e91807ebeff19e8820d9be7ea6ddd84c59cd5839846a18a2615ae993a1a6fc22b90e5080cf9d8a72aa412f6b81354e0f284 +DIST NAMD_2.9_Source.tar.gz 8814042 SHA256 9ba6a1f87d4600a62847728d7c223295be214f9a72b5bb62552f74d644108424 SHA512 0644814a2799b560d9dcf807ba0047325bc9f0a26e3831b0465d95180784f038d69595e036daac85d59cd919c92d11a0343031975d99deb1fa3052c8a649bdd6 WHIRLPOOL 5494ccb2ee2f2792fe52ad7dcfe6da9d11453f0a9b0859d30698dea56b00d92fae73465967f82bd708abee5cd4ff50b0a6ffde86451e859e2f515af203e09286 +EBUILD namd-2.10.ebuild 2532 SHA256 63bed8d35a44b082087d50e664bc41cef5ca280a92207350acd61180f52fc275 SHA512 24bcf70033603527cbf3369358cad093bc3a7cc3336a8ccd2363d0caa801dd9d57da39e8cf184c12183d1b93916af758dd980cbfe59569ec7f499b78719304f3 WHIRLPOOL 449913ddbbb8805fd521b4588645221e297ef9b16e8a25d22643c543daf54df6453452f44d255b68deafa293ef3e92e2591e00338485e105c38836a8fed57c5e +EBUILD namd-2.9-r1.ebuild 2523 SHA256 fda6cdb358c2c82ce066aaa6800a3afd76630af31dcef454b8c8f2973c398ced SHA512 1c53db643c5cd3224f434d6c1867d986d2242bc461f6cf32061188663f07e611ef04f149657256b308fff69b72e7b636a571357fd8afc0e3d0704dc336220bee WHIRLPOOL f528ea13af06a0528bfef097c80cbcd47378ba0f800c8760aa6e11371337ca9bfbf9409f544bafde89759a7244d48284a5860e9596827ad8a1c26915355c1e9d +MISC ChangeLog 2842 SHA256 577f86031e7ff99a932610518ecd8e97f83e56aa572f14e8cd6879bfb0774b60 SHA512 57e21a7aed4809a15eb6ede1f64a55247e32437a1874e13a5c0a4589ea134dd6736d781312a773cb53d2506a4c4fa805719d46c8eee2b383243ab2fe55bea56c WHIRLPOOL 2f91a6d7218d4c1a8c611af0bf27fe36d7c84ea7f876dd85bd5386f32129e965f3a05838c966e1db414a296ea462cd49a4526d16222aea243ff73eb19d0b0b30 +MISC ChangeLog-2015 4105 SHA256 f31ef3545a40677d74ca01ad76197a208ae08c6845bb7155d53b23884a8c958e SHA512 fb88713f37db829157bb655d8c6fc4b7ee23cb45c61d524d9d184652cb6fa2509464ede903a07c063e00d06d31ea3c71333e48e248f9f46d0f3da410a5346515 WHIRLPOOL ce68c3389ba1d2995c22d66989612cb0f67ef3086e19af142d62feed2d1b79e240a55dba524a4df0e3a2f236c8c1b77a3f08cbe24568c61424a3369cedc90ac8 +MISC metadata.xml 375 SHA256 7bdb54390a98284020aeb6a9495820a59da7671c5caa59b10c25a69ab0d3c3a0 SHA512 da64c8ba453ccf6ba5997af7c60bb4873f6f5e0379fc0c3787e77dd46fef945d3c4bd5d06d62a071526324ed6b3e1b7287d9f2e68f141042d12a469ef4e46757 WHIRLPOOL 0ca7348323b8cc2076a66ec1ff17fbd1c226143ba5eb56b85442c1c72d4d618e2d6feb7957006660cca5f6ab4bf7ad7c0c784dda9c32a15ae6d6d2e9274c4c2e diff --git a/sci-chemistry/namd/files/namd-2.10-gentoo.patch b/sci-chemistry/namd/files/namd-2.10-gentoo.patch new file mode 100644 index 000000000000..e578c131c36d --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.10-gentoo.patch @@ -0,0 +1,124 @@ +diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw NAMD_2.10_Source/arch/Linux-x86_64.fftw +--- NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw 2015-03-06 17:53:44.170416075 -0700 ++++ NAMD_2.10_Source/arch/Linux-x86_64.fftw 2015-03-06 17:54:46.641162629 -0700 +@@ -1,7 +1,7 @@ + +-FFTDIR=/Projects/namd2/fftw/linux-x86_64 ++FFTDIR=/usr + FFTINCL=-I$(FFTDIR)/include +-FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw ++FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw + FFTFLAGS=-DNAMD_FFTW + FFT=$(FFTINCL) $(FFTFLAGS) + +diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl NAMD_2.10_Source/arch/Linux-x86_64.tcl +--- NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl 2015-03-06 17:53:44.170416075 -0700 ++++ NAMD_2.10_Source/arch/Linux-x86_64.tcl 2015-03-06 17:54:46.641162629 -0700 +@@ -1,9 +1,9 @@ + + #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64 +-TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded ++TCLDIR=/usr + TCLINCL=-I$(TCLDIR)/include + #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl +-TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread ++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread + TCLFLAGS=-DNAMD_TCL + TCL=$(TCLINCL) $(TCLFLAGS) + +diff -Naur NAMD_2.10_Source.orig/Makefile NAMD_2.10_Source/Makefile +--- NAMD_2.10_Source.orig/Makefile 2015-03-06 17:53:44.170416075 -0700 ++++ NAMD_2.10_Source/Makefile 2015-03-06 18:01:32.645966590 -0700 +@@ -389,10 +389,10 @@ + $(DSTDIR)/stringhash.o + + # definitions for Charm routines +-CHARMC = $(CHARM)/bin/charmc +-CHARMXI = $(CHARM)/bin/charmc +-CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 +-CHARMLIB = $(CHARM)/lib ++CHARMC = /usr/bin/charmc ++CHARMXI = /usr/bin/charmc ++CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1 ++CHARMLIB = /usr/gentoo-libdir + CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -module CkMulticast + #CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB + #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB +@@ -418,7 +418,7 @@ + + # Add new executables here. + +-BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb charmrun ++BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb + + # This should be rebuilt at every compile, but not on Win32. + BUILDINFO = $(DSTDIR)/buildinfo +@@ -434,7 +434,7 @@ + + namd2: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) + $(MAKEBUILDINFO) +- $(CHARMC) -verbose -ld++-option \ ++ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \ + '$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS) $(CXXMICOPTS)' \ + "$(CHARM_MODULES)" -language charm++ \ + $(BUILDINFO).o \ +@@ -484,11 +484,8 @@ + charmd_faceless.exe: + $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe + +-charmrun.exe: +- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe +- + psfgen: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) +- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm ++ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm + + psfgen.exe: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL) + $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm +@@ -506,7 +503,7 @@ + $(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -lm + + flipdcd: $(SRCDIR)/flipdcd.c +- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ + echo "#!/bin/sh\necho unavailable on this platform" > $@; \ + chmod +x $@ + +@@ -516,7 +513,7 @@ + chmod +x $@ + + fixdcd: $(SRCDIR)/fixdcd.c +- $(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c + + dumpdcd: $(SRCDIR)/dumpdcd.c + $(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c +@@ -711,9 +708,7 @@ + + DOC_FILES = README.txt announce.txt license.txt notes.txt + +-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2 +- +-WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL) ++RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2 + + release: all + $(ECHO) Creating release $(RELEASE_DIR_NAME) +@@ -724,17 +719,9 @@ + for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \ + /bin/rm -rf $$f; \ + done +- if [ -r $(CHARM)/bin/charmd ]; then \ +- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ +- fi +- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ +- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ +- fi + chmod -R a+rX $(RELEASE_DIR_NAME) + tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) + gzip $(RELEASE_DIR_NAME).tar +- echo $(CHARM) +- ls -l $(CHARM)/lib + -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done + + winrelease: winall diff --git a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch new file mode 100644 index 000000000000..e5ee3bd6c818 --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch @@ -0,0 +1,24 @@ +diff --git a/src/flipbinpdb.c b/src/flipbinpdb.c +index 94b71ba..01a2529 100644 +--- a/src/flipbinpdb.c ++++ b/src/flipbinpdb.c +@@ -9,6 +9,7 @@ + #include <sys/mman.h> + #include <fcntl.h> + #include <stdio.h> ++#include <stdlib.h> + + #ifndef MAP_FILE + #define MAP_FILE 0 +diff --git a/src/flipdcd.c b/src/flipdcd.c +index 8ec85b7..1c23433 100644 +--- a/src/flipdcd.c ++++ b/src/flipdcd.c +@@ -13,6 +13,7 @@ + #include <sys/mman.h> + #include <fcntl.h> + #include <stdio.h> ++#include <stdlib.h> + + #ifndef MAP_FILE + #define MAP_FILE 0 diff --git a/sci-chemistry/namd/files/namd-2.9-gentoo.patch b/sci-chemistry/namd/files/namd-2.9-gentoo.patch new file mode 100644 index 000000000000..583cc52645df --- /dev/null +++ b/sci-chemistry/namd/files/namd-2.9-gentoo.patch @@ -0,0 +1,151 @@ +diff -Naur NAMD_2.9_Source.original/Make.charm NAMD_2.9_Source/Make.charm +--- NAMD_2.9_Source.original/Make.charm 2012-02-29 19:12:11.000000000 -0700 ++++ NAMD_2.9_Source/Make.charm 2013-09-13 21:23:26.000000000 -0600 +@@ -2,5 +2,5 @@ + # The config script will override this setting if there is a directory + # called charm-6.4.0 or charm in the NAMD base directory. + +-CHARMBASE = /Projects/namd2/charm-6.4.0 ++CHARMBASE = /usr/include/charm-6.4.0 + +diff -Naur NAMD_2.9_Source.original/Makefile NAMD_2.9_Source/Makefile +--- NAMD_2.9_Source.original/Makefile 2012-04-27 09:53:24.000000000 -0600 ++++ NAMD_2.9_Source/Makefile 2013-09-13 21:30:15.000000000 -0600 +@@ -344,10 +344,10 @@ + $(DSTDIR)/stringhash.o + + # definitions for Charm routines +-CHARMC = $(CHARM)/bin/charmc +-CHARMXI = $(CHARM)/bin/charmc +-CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 +-CHARMLIB = $(CHARM)/lib ++CHARMC = /usr/bin/charmc ++CHARMXI = /usr/bin/charmc ++CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1 ++CHARMLIB = /usr/gentoo-libdir + CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB + #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB + #MSA = -DCHARM_HAS_MSA +@@ -370,7 +370,7 @@ + + # Add new executables here. + +-BINARIES = namd2 psfgen sortreplicas charmrun flipdcd flipbinpdb ++BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb + + # This should be rebuilt at every compile, but not on Win32. + BUILDINFO = $(DSTDIR)/buildinfo +@@ -386,7 +386,7 @@ + + namd2: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) + $(MAKEBUILDINFO) +- $(CHARMC) -verbose -ld++-option \ ++ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \ + "$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \ + "$(CHARM_MODULES)" -language charm++ \ + $(BUILDINFO).o \ +@@ -402,16 +402,9 @@ + $(EXTRALINKLIBS) \ + -lm -o namd2 + +-charmrun: $(CHARM)/bin/charmrun # XXX +- $(COPY) $(CHARM)/bin/charmrun $@ +- + $(LIBCUDARTSO): + $(COPY) $(CUDASODIR)/$(LIBCUDARTSO) $@; + +-WINDOWSBINARIES = namd2.exe psfgen.exe sortreplicas.exe +-# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe +-windowsbinaries: $(WINDOWSBINARIES) +- + namd2.exe: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) $(TCLDLL) + $(MAKEBUILDINFO) + $(CHARMC) -verbose \ +@@ -434,11 +427,8 @@ + charmd_faceless.exe: + $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe + +-charmrun.exe: +- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe +- + psfgen: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) +- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm ++ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm + + psfgen.exe: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL) + $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm +@@ -456,7 +446,7 @@ + $(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -lm + + flipdcd: $(SRCDIR)/flipdcd.c +- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ + echo "#!/bin/sh\necho unavailable on this platform" > $@; \ + chmod +x $@ + +@@ -466,7 +456,7 @@ + chmod +x $@ + + fixdcd: $(SRCDIR)/fixdcd.c +- $(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c + + dumpdcd: $(SRCDIR)/dumpdcd.c + $(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c +@@ -665,9 +655,7 @@ + + DOC_FILES = README.txt announce.txt license.txt notes.txt + +-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2 +- +-WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL) ++RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2 + + release: all + $(ECHO) Creating release $(RELEASE_DIR_NAME) +@@ -678,17 +666,9 @@ + for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \ + /bin/rm -rf $$f; \ + done +- if [ -r $(CHARM)/bin/charmd ]; then \ +- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ +- fi +- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ +- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ +- fi + chmod -R a+rX $(RELEASE_DIR_NAME) + tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) + gzip $(RELEASE_DIR_NAME).tar +- echo $(CHARM) +- ls -l $(CHARM)/lib + -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done + + winrelease: winall +diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.fftw NAMD_2.9_Source/arch/Linux-x86_64.fftw +--- NAMD_2.9_Source.original/arch/Linux-x86_64.fftw 2009-02-21 21:16:04.000000000 -0700 ++++ NAMD_2.9_Source/arch/Linux-x86_64.fftw 2013-09-13 20:55:02.000000000 -0600 +@@ -1,7 +1,7 @@ + +-FFTDIR=/Projects/namd2/fftw/linux-x86_64 ++FFTDIR=/usr + FFTINCL=-I$(FFTDIR)/include +-FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw ++FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw + FFTFLAGS=-DNAMD_FFTW + FFT=$(FFTINCL) $(FFTFLAGS) + +diff -Naur NAMD_2.9_Source.original/arch/Linux-x86_64.tcl NAMD_2.9_Source/arch/Linux-x86_64.tcl +--- NAMD_2.9_Source.original/arch/Linux-x86_64.tcl 2011-06-17 14:38:43.000000000 -0600 ++++ NAMD_2.9_Source/arch/Linux-x86_64.tcl 2013-09-13 20:56:30.000000000 -0600 +@@ -1,9 +1,9 @@ + + #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64 +-TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded ++TCLDIR=/usr + TCLINCL=-I$(TCLDIR)/include + #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl +-TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread ++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread + TCLFLAGS=-DNAMD_TCL + TCL=$(TCLINCL) $(TCLFLAGS) + diff --git a/sci-chemistry/namd/metadata.xml b/sci-chemistry/namd/metadata.xml new file mode 100644 index 000000000000..dc42d24f9afb --- /dev/null +++ b/sci-chemistry/namd/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>nicolasbock@gentoo.org</email> + <name>Nicolas Bock</name> + </maintainer> +<maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/namd/namd-2.10.ebuild b/sci-chemistry/namd/namd-2.10.ebuild new file mode 100644 index 000000000000..d67280b8d0f1 --- /dev/null +++ b/sci-chemistry/namd/namd-2.10.ebuild @@ -0,0 +1,104 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils multilib toolchain-funcs flag-o-matic + +DESCRIPTION="A powerful and highly parallelized molecular dynamics code" +LICENSE="namd" +HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/" + +MY_PN="NAMD" + +SRC_URI="${MY_PN}_${PV}_Source.tar.gz" + +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +RESTRICT="fetch" + +RDEPEND=" + >=sys-cluster/charm-6.5.1-r2 + sci-libs/fftw:3.0 + dev-lang/tcl:0=" + +DEPEND="${RDEPEND} + app-shells/tcsh" + +NAMD_ARCH="Linux-x86_64-g++" + +NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD" + +S="${WORKDIR}/${MY_PN}_${PV}_Source" + +pkg_nofetch() { + echo + einfo "Please download ${MY_PN}_${PV}_Source.tar.gz from" + einfo "${NAMD_DOWNLOAD}" + einfo "after agreeing to the license and then move it to" + einfo "${DISTDIR}" + einfo "Be sure to select the ${PV} version!" + echo +} + +src_prepare() { + CHARM_VERSION=$(best_version sys-cluster/charm | cut -d- -f3) + + # apply a few small fixes to make NAMD compile and + # link to the proper libraries + epatch "${FILESDIR}"/namd-2.10-gentoo.patch + epatch "${FILESDIR}"/namd-2.7-iml-dec.patch + sed \ + -e "/CHARMBASE =/s:= .*:= /usr/bin/charm-${CHARM_VERSION}:" \ + -i Make.charm || die + + # Remove charm distribution. We don't need it. + rm -f charm-*.tar + + # proper compiler and cflags + sed \ + -e "s/g++.*/$(tc-getCXX)/" \ + -e "s/gcc.*/$(tc-getCC)/" \ + -e "s/CXXOPTS = .*/CXXOPTS = ${CXXFLAGS} ${LDFLAGS}/" \ + -e "s/COPTS = .*/COPTS = ${CFLAGS} ${LDFLAGS}/" \ + -i arch/${NAMD_ARCH}.arch || die + + sed \ + -e "s/gentoo-libdir/$(get_libdir)/g" \ + -e "s/gentoo-charm/charm-${CHARM_VERSION}/g" \ + -i Makefile || die "Failed gentooizing Makefile." + sed -e "s@/lib@/$(get_libdir)@g" -e '/FFTDIR=/s@=.*@=/usr@' -i arch/Linux-x86_64.fftw3 || die + sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die +} + +src_configure() { + # configure + ./config ${NAMD_ARCH} --with-fftw3 --charm-arch . || die +} + +src_compile() { + # build namd + cd "${S}/${NAMD_ARCH}" + emake +} + +src_install() { + dodoc announce.txt license.txt notes.txt + cd "${S}/${NAMD_ARCH}" + + # the binaries + dobin ${PN}2 psfgen flipbinpdb flipdcd +} + +pkg_postinst() { + echo + einfo "For detailed instructions on how to run and configure" + einfo "NAMD please consults the extensive documentation at" + einfo "http://www.ks.uiuc.edu/Research/namd/" + einfo "and the NAMD tutorials available at" + einfo "http://www.ks.uiuc.edu/Training/Tutorials/" + einfo "Have fun :)" + echo +} diff --git a/sci-chemistry/namd/namd-2.9-r1.ebuild b/sci-chemistry/namd/namd-2.9-r1.ebuild new file mode 100644 index 000000000000..869c1ec2f182 --- /dev/null +++ b/sci-chemistry/namd/namd-2.9-r1.ebuild @@ -0,0 +1,104 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils multilib toolchain-funcs flag-o-matic + +DESCRIPTION="A powerful and highly parallelized molecular dynamics code" +LICENSE="namd" +HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/" + +MY_PN="NAMD" + +SRC_URI="${MY_PN}_${PV}_Source.tar.gz" + +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +RESTRICT="fetch" + +RDEPEND=" + >=sys-cluster/charm-6.5.1-r2 + sci-libs/fftw:3.0 + dev-lang/tcl:0=" + +DEPEND="${RDEPEND} + app-shells/tcsh" + +NAMD_ARCH="Linux-x86_64-g++" + +NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD" + +S="${WORKDIR}/${MY_PN}_${PV}_Source" + +pkg_nofetch() { + echo + einfo "Please download ${MY_PN}_${PV}_Source.tar.gz from" + einfo "${NAMD_DOWNLOAD}" + einfo "after agreeing to the license and then move it to" + einfo "${DISTDIR}" + einfo "Be sure to select the ${PV} version!" + echo +} + +src_prepare() { + CHARM_VERSION=$(best_version sys-cluster/charm | cut -d- -f3) + + # apply a few small fixes to make NAMD compile and + # link to the proper libraries + epatch "${FILESDIR}"/namd-2.9-gentoo.patch + epatch "${FILESDIR}"/namd-2.7-iml-dec.patch + sed \ + -e "s:charm-.\+:charm-${CHARM_VERSION}:" \ + -i Make.charm || die + + # Remove charm distribution. We don't need it. + rm -f charm-6.4.0.tar || die + + # proper compiler and cflags + sed \ + -e "s/g++.*/$(tc-getCXX)/" \ + -e "s/gcc.*/$(tc-getCC)/" \ + -e "s/CXXOPTS = .*/CXXOPTS = ${CXXFLAGS} ${LDFLAGS}/" \ + -e "s/COPTS = .*/COPTS = ${CFLAGS} ${LDFLAGS}/" \ + -i arch/${NAMD_ARCH}.arch || die + + sed \ + -e "s/gentoo-libdir/$(get_libdir)/g" \ + -e "s/gentoo-charm/charm-${CHARM_VERSION}/g" \ + -i Makefile || die "Failed gentooizing Makefile." + sed -e "s@/lib@/$(get_libdir)@g" -e '/FFTDIR=/s@=.*@=/usr@' -i arch/Linux-x86_64.fftw3 || die + sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die +} + +src_configure() { + # configure + ./config ${NAMD_ARCH} --with-fftw3 --charm-arch . || die +} + +src_compile() { + # build namd + cd "${S}/${NAMD_ARCH}" + emake +} + +src_install() { + dodoc announce.txt license.txt notes.txt + cd "${S}/${NAMD_ARCH}" + + # the binaries + dobin ${PN}2 psfgen flipbinpdb flipdcd +} + +pkg_postinst() { + echo + einfo "For detailed instructions on how to run and configure" + einfo "NAMD please consults the extensive documentation at" + einfo "http://www.ks.uiuc.edu/Research/namd/" + einfo "and the NAMD tutorials available at" + einfo "http://www.ks.uiuc.edu/Training/Tutorials/" + einfo "Have fun :)" + echo +} diff --git a/sci-chemistry/nmrglue/Manifest b/sci-chemistry/nmrglue/Manifest new file mode 100644 index 000000000000..fdbace82d4de --- /dev/null +++ b/sci-chemistry/nmrglue/Manifest @@ -0,0 +1,6 @@ +AUX nmrglue-0.5-nohyper.patch 1408 SHA256 96ad150a0d6f01a135c20a30c022fa80fef9c56a02122467e19fb91819294a0c SHA512 f68ea345f2692123e24fc41335001a0a8418b84003d864e9d673935d4a517aa82353e08f4f554b33ddc18cea96c9442827715cdabad6303dc60f5dd18cd103dd WHIRLPOOL f373fc8912b073aa8012bcf612691a7b45514e613fbe7f448a3d9cf70aec42a2cceaed705c1d1e65a81a2ae692c18dce2b8f297a0baf07a3a6febd0f285b1032 +DIST nmrglue-0.5.tar.gz 142604 SHA256 a05c880bd0d5f0b388156409e18a5618742f829f2532d19970d05b11bfcc6103 SHA512 2a4b94eb6bae966000bfdee4dd16f4e312568915fb5f19f59f84c6deff690703f54f76366d3f9299f7ec187192ff64f2bf62836617a424d4c5c895c67d819af2 WHIRLPOOL 78f9d094a2ab1ebc01f452717fdc1cdeccc27951195c9dd6e97069a575722acf25442009b4ccede03ad728b0767fced4a2220a8072ccc1d604a9f62e9c45af4a +EBUILD nmrglue-0.5-r1.ebuild 731 SHA256 8f832d11ad367640d71ab63e939ead804a9520dbb468061d5637df94c586fe09 SHA512 22d3bae493423dc2e3fa3a3c5a5e9a110f68ada07b0a9d30176c350f4705d0e5a96697c3a4864241ee8b9c428313b8f47fee70850fcfabfac3a971c0346ca51f WHIRLPOOL 6075e70b8dad7083e3503966cc3a17f06a7ba15459c54a236ae6b98e98bcaa8688085acd8f256b1ddf2eebbae0483d06b22becdfa92d48a10d6c5113f83ad660 +MISC ChangeLog 3013 SHA256 0b9b8c10a0cb9043bb7c2a2972adba6faa8308e0215dd89651e9c473ffcc784e SHA512 a43ad6398854e7d9c35b6523ed46a7f7ed18d1c5b51f46c97dc044f5048d9a5841eb919dcc18b13a6fcabd717a9513fcd3f6abb7291988f053bb7ac8cbb8fcd1 WHIRLPOOL 033b185e10956e706b1159ecfde8f39e696ee98d5b611d98f67f2910a62995f65380b4b732418acfb81124da35ddddaab575eff997cdf8804dced22bf7856a9f +MISC ChangeLog-2015 689 SHA256 26d93992a39ef4db578883a615b7fbce1285e1e8fddc5cf04a4173563c18f131 SHA512 70d1328005577e4eb76ddec29f84ace2bdcafe8e9219ebd203be0e2aa15ee4f77d7de2d688000edf83c6fb20325ec79ad6c99a2b55c70fc15cc91086844ad054 WHIRLPOOL 12d264ee1a48880d27f85ea5ece5c2c52768785bcebc3c31b5f25dad3c1e147ead8d2934ab3c97ee7e95393cde8381195dc0dc22cd25bc65aa50d638459ab9fd +MISC metadata.xml 1338 SHA256 0714c426b85786c120b47cfbc8b40f2d678dc144447a01c899dd5482203d3e3e SHA512 7defa016b2c5f51327f282ef8dbb5f99767e554112baf10d72a6c86462d86bf7bd3129226340bbdb00f9e95b2349fc3594b6d0d8cd0175457bbb5f034e31aa7c WHIRLPOOL a5b90cf56e472f26409d11452ebc17d0a53c63e1074ed359a6da47950d58340c5649cfe1f94b319e947fc2adc9bed8b25fc27717ed412d0a121e8669c464904e diff --git a/sci-chemistry/nmrglue/files/nmrglue-0.5-nohyper.patch b/sci-chemistry/nmrglue/files/nmrglue-0.5-nohyper.patch new file mode 100644 index 000000000000..103f5b154d0b --- /dev/null +++ b/sci-chemistry/nmrglue/files/nmrglue-0.5-nohyper.patch @@ -0,0 +1,33 @@ +From ba1eee9e71623110511545c058afe2a92e139aa5 Mon Sep 17 00:00:00 2001 +From: Jonathan Helmus <jjhelmus@gmail.com> +Date: Tue, 3 Mar 2015 19:47:05 -0600 +Subject: [PATCH] pipe_proc.py tp function correctly sets FDSIZE. + +Fixes issue #27 +--- + nmrglue/process/pipe_proc.py | 7 +++++-- + 1 file changed, 5 insertions(+), 2 deletions(-) + +diff --git a/nmrglue/process/pipe_proc.py b/nmrglue/process/pipe_proc.py +index 79b6303..8c1271c 100644 +--- a/nmrglue/process/pipe_proc.py ++++ b/nmrglue/process/pipe_proc.py +@@ -1527,13 +1527,16 @@ def tp(dic, data, hyper=False, nohyper=False, auto=False, nohdr=False): + data = np.array(p.tp_hyper(data), dtype="complex64") + else: + data = p.tp(data) +- if dic[fn2 + "QUADFLAG"] != 1 and nohyper is not True: ++ if dic[fn2 + "QUADFLAG"] != 1 and nohyper is False: + # unpack complex as needed + data = np.array(p.c2ri(data), dtype="complex64") + + # update the dimentionality and order + dic["FDSLICECOUNT"] = data.shape[0] +- if data.dtype == 'float32': ++ if (data.dtype == 'float32') and (nohyper is True): ++ # when nohyper is True and the new last dimension was complex ++ # prior to transposing then FDSIZE is set as if the dimension was ++ # converted to complex data, that is half the actual size. + dic["FDSIZE"] = data.shape[1] / 2 + else: + dic["FDSIZE"] = data.shape[1] diff --git a/sci-chemistry/nmrglue/metadata.xml b/sci-chemistry/nmrglue/metadata.xml new file mode 100644 index 000000000000..55fa34fcbc44 --- /dev/null +++ b/sci-chemistry/nmrglue/metadata.xml @@ -0,0 +1,29 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +Nmrglue has the ability to read, write and convert between a number of NMR file +formats including Agilent/Varian, Bruker, NMRPipe, Sparky, SIMPSON, Rowland NMR +Toolkit files. The files, which are represented in Python as dictionaries of +spectral parameters and NumPy ndarray objects, can be easily examined, modified +and processed as desired. + +Nmrglue provides a number of functions for processing NMR data such as +apodization, spectral shifting, Fourier and other transformations, baseline +smoothing and flattening, and linear prediction modeling and extrapolation. +In addition new processing schemes can be implemented easily using the nmrglue +provided functions and the multitude of numerical routines provided by the NumPy +and SciPy packages. + +When used in conjunction with the matplotlib (or other) python plotting library +nmrglue can be used to create publication quality figures of NMR spectrum or +examine data interactively. +</longdescription> + <upstream> + <remote-id type="github">jjhelmus/nmrglue</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild new file mode 100644 index 000000000000..9f1cae764afb --- /dev/null +++ b/sci-chemistry/nmrglue/nmrglue-0.5-r1.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) + +inherit distutils-r1 + +DESCRIPTION="A module for working with NMR data in Python" +HOMEPAGE="http://nmrglue.com/" +SRC_URI="https://github.com/jjhelmus/nmrglue/releases/download/v${PV}/${P}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}]" +DEPEND=" + test? ( + ${RDEPEND} + dev-python/nose[${PYTHON_USEDEP}] + ) +" + +PATCHES=( "${FILESDIR}"/${P}-nohyper.patch ) + +python_test() { + nosetests --verbosity=3 || die +} diff --git a/sci-chemistry/numbat/Manifest b/sci-chemistry/numbat/Manifest new file mode 100644 index 000000000000..d02a8970421c --- /dev/null +++ b/sci-chemistry/numbat/Manifest @@ -0,0 +1,6 @@ +AUX numbat-0.999-gnuplot.patch 2048 SHA256 689e9690e92f531ffbbdfbb7620c5ba4f9f2cb2531c6b3267aac502bd541e5aa SHA512 dd646e8f6652a63cb4e1c97830a755629e45d20fa13431f628b66fe8a5062b7bd7ebacddb3dbcca5aeeac3ae0d89f59c61036c1a3639d25fe0426ada77a888bb WHIRLPOOL 18248ba1654f499af5c4ba22e9a03ba010b3d3c359976014bf1a0e3a584f424e61e5be868a941b1e0dd842d20ee671634c67d661114258467ff2d6492dd67b6a +DIST Numbat-0.999.tar.gz 1791471 SHA256 aef72903f262c5a25e542429f3cc7aca4d2dbc920c08b59847d5cb325855e9ab SHA512 0887f77905bbb476b0d12a7015d5d5745023740acc974ea9cd452de7d38a75a92e6090015127588b38ba62353d38c2be20f57be5df3011b51050c4934dfd206c WHIRLPOOL 8282bf5481a93d17a833f809c28d927d681d6d5016552a07b9267bdb78e99fc568370321567d7d6a87a84f31eea8fae9494c1ae8c0109157fca779c7c06805d9 +EBUILD numbat-0.999-r1.ebuild 1075 SHA256 43ffd2cfb44d6ccfa0efe6d0ee874d7493bd8cf07c59e26dbbea9795409882bf SHA512 28df0153d08c7656c59212ced742ab2d6c8e3eaefaa96c5f62d44beb2e56e39cc60d51a8dc284187e90b3eb57322f7352137908294508b53b13e79e7e0719a30 WHIRLPOOL d97c4042f3163e15d2b0970056bf1fea02732d9d7804c25acc504916e31d489e1e03a239235f6e84034e766ba983fee440cc675aebdae85da9367b47e5d9600c +MISC ChangeLog 2610 SHA256 356de4f5f73d5180dcb84f3edf86fe38a24241a536b20265008ee605d05aa83e SHA512 742eea54775960ebd7b6f0ec66ebc6214cb53375e953bed1e17c602bb88bae18643deac578459f3c99fa60369b2865c441f32a0c9e1d77e77cb3fe7e33f9428b WHIRLPOOL a5c4324a0cd0fe606bfc700340b632fdd09641d7260705df3cd3b900f6481611d7999c7a6399972a9e7c8cdd70ea5ea85f5812450e4314747e1dec0b0622b500 +MISC ChangeLog-2015 695 SHA256 7a057f9001163360fe83457617413cca318326a1b6a704d6d58fbec64d58dcb7 SHA512 8eb3d41d769d0be4f2b8fc8d49c58ed682b81e615535c5bce482165aecf910b3434d7009fb55d26375a0c78b20dc534e0a5ac9367dbd8ac8c76a93cfe858b8ba WHIRLPOOL f33a3a491ed15f04491bc30328ac563a78ea017806aa0f6c70ce1929b9c3304fe21d644fa3ab9ee7ca27e5b04a2ba2702c3a4ddaaa5fcd655237addfd487aa12 +MISC metadata.xml 852 SHA256 00c4cc1301e237e514595470acd436d91c2c5095b972c40e1ac25c9f4b139e37 SHA512 64e5552a677fc7370f68f7f811734ac17144fcb95e23503c962b678a1678dccf22a2d19991eb69dcdf8d4c1c97448d35d7f34654245ebe3fee8b30a0a8fa586c WHIRLPOOL 99bc5bfa27a4c358c8c4df4671651256907cdd50e63e9051551191a8be5be8844ddb5c1866de819e4b5fdf1353635c894dc9cf7b0c0c49d5a05d9bd98b0e5148 diff --git a/sci-chemistry/numbat/files/numbat-0.999-gnuplot.patch b/sci-chemistry/numbat/files/numbat-0.999-gnuplot.patch new file mode 100644 index 000000000000..942f5871e50b --- /dev/null +++ b/sci-chemistry/numbat/files/numbat-0.999-gnuplot.patch @@ -0,0 +1,42 @@ + src/error_analysis.c | 20 ++++++++++---------- + 1 file changed, 10 insertions(+), 10 deletions(-) + +diff --git a/src/error_analysis.c b/src/error_analysis.c +index eb86a6f..c0edf5f 100644 +--- a/src/error_analysis.c ++++ b/src/error_analysis.c +@@ -848,11 +848,11 @@ void write_sanson_mac(FILE * F, char * name_plot, char * name_world, int number_ + } + + fprintf(F, "reset\n"); +- fprintf(F, "set noxtics\n"); +- fprintf(F, "set noytics\n"); ++ fprintf(F, "unset xtics\n"); ++ fprintf(F, "unset ytics\n"); + fprintf(F, "set angles degrees\n"); +- fprintf(F, "set nogrid\n"); +- fprintf(F, "set noborder\n"); ++ fprintf(F, "unset grid\n"); ++ fprintf(F, "unset border\n"); + //fprintf(F, "width=40\n"); + //fprintf(F, "height=width*(3./4.)\n"); + //fprintf(F, "set xrange [-width : width]\n"); +@@ -867,12 +867,12 @@ void write_sanson_mac(FILE * F, char * name_plot, char * name_world, int number_ + fprintf(F, "YC(lat,lon)=(lon-long0)*cos(lat)\n"); + fprintf(F, "plot '%s' using (YC($2,$1)):(XC($2,$1)) t '' with lines lw 0.1 lt -1", name_world); + for(i = 0; i < number_of_tensor; i++){ +- fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points %d", name_plot, +- 6*i+2, 6*i+1, 6*i+2, 6*i+1, 3*i+1); +- fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points %d", name_plot, +- 6*i+4, 6*i+3, 6*i+4, 6*i+3, 3*i+2); +- fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points %d", name_plot, +- 6*i+6, 6*i+5, 6*i+6, 6*i+5, 3*i+3); ++ fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points", name_plot, ++ 6*i+2, 6*i+1, 6*i+2, 6*i+1); ++ fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points", name_plot, ++ 6*i+4, 6*i+3, 6*i+4, 6*i+3); ++ fprintf(F, ", '%s' using (YC($%d,$%d)):(XC($%d,$%d)) t '' with points", name_plot, ++ 6*i+6, 6*i+5, 6*i+6, 6*i+5); + } + fprintf(F, "\n"); + //fprintf(F, "pause 2\n"); diff --git a/sci-chemistry/numbat/metadata.xml b/sci-chemistry/numbat/metadata.xml new file mode 100644 index 000000000000..0f4399d7df6d --- /dev/null +++ b/sci-chemistry/numbat/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +Numbat is a user friendly software that fits dX-tensor to a set of PCS +measurements and a structure from a PDB file. It has also been designed to +assist in the semi automatic process of PCS assignment. A detailed description +of the software can be found in this publication: + +Christophe Schmitz, Mitchell J. Stanton-Cook, Xun-Cheng Su, Gottfried Otting, +and Thomas Huber (2008). Numbat: an interactive software tool for fitting +Δχ-tensors to molecular coordinates using pseudocontact shifts. Journal of +Biomolecular NMR. 41:179-189. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/numbat/numbat-0.999-r1.ebuild b/sci-chemistry/numbat/numbat-0.999-r1.ebuild new file mode 100644 index 000000000000..66f5b2ae0652 --- /dev/null +++ b/sci-chemistry/numbat/numbat-0.999-r1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +MY_PN="Numbat" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="new user-friendly method built for automatic dX-tensor determination" +HOMEPAGE="http://www.nmr.chem.uu.nl/~christophe/numbat.html" +SRC_URI="http://comp-bio.anu.edu.au/private/downloads/Numbat/${MY_P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +CDEPEND=" + gnome-base/libglade:2.0 + sci-libs/gsl + x11-libs/gtk+:2" +DEPEND="${CDEPEND} + virtual/pkgconfig" +RDEPEND="${CDEPEND} + sci-chemistry/molmol + sci-chemistry/pymol + sci-visualization/gnuplot" + +S="${WORKDIR}"/${MY_P} + +PATCHES=( +# "${FILESDIR}"/${P}-glade.patch + "${FILESDIR}"/${P}-gnuplot.patch ) + +src_prepare() { + sed \ + -e '/COPYING/d' \ + -e "s:doc/numbat:share/doc/${PF}:g" \ + -i Makefile.am src/common.h || die + rm missing + emake distclean + autotools-utils_src_prepare +} + +src_install() { + docompress -x /usr/share/doc/${PF} + autotools-utils_src_install +} diff --git a/sci-chemistry/openbabel-perl/Manifest b/sci-chemistry/openbabel-perl/Manifest new file mode 100644 index 000000000000..430fc44ecbdd --- /dev/null +++ b/sci-chemistry/openbabel-perl/Manifest @@ -0,0 +1,10 @@ +AUX openbabel-perl-2.3.2-bindings_only.patch 4557 SHA256 5ccb04d28bcbaf190275581fb66729b6a06c59b2e4a10e288bd90251f06f66a5 SHA512 475600513f188f2e3dee711ab2073954511b7d71c0af222dc9fe121bcbd4821d0ab32934d5035452ad4820d0dd750899995696c20504769b25cad7ef2d27aa5e WHIRLPOOL c573a123b43c67324b04a1283b2b567ed589f619dc2a22c1f4937edab82a2da40d74f56e52cb2d9418477c7713fd1f450dfd2f6b4563f745717a5a417a67975b +AUX openbabel-perl-2.3.2-gcc-6_and_7-backport.patch 635 SHA256 49f9fc47d1c864d501a266c4d1d7251d5921ce64f1de33a7679d369938bd8490 SHA512 e1b4402f34d01ced5b4caaa184b4e5544cf47893cfe7958054052b05a57dc34b4d44239a212c7d909f29b9366b83b6df74993f844a20f23748c01272ec093081 WHIRLPOOL 8789037e71722ee28d8769eadc574edf2d7d80e8e01f6a8475b18fd4ed0314757bd02854eacf375f7c23ca20b9ec8cc9a40797b51ad3fe64921440549a49cd3d +AUX openbabel-perl-2.3.2-trunk_cmake.patch 2335 SHA256 20692e07e436c610b0d18f6a28ebaef342b43053b3b1dd57cc23b0c87fe5dedf SHA512 9f42cb3c8aff7eb765790fd3a7f259d8076ebce11f3c2e324a9568a94d948583455db90a8714cdcbd6b6a74087167ada9ec19261862233823d0792bc79302f30 WHIRLPOOL 766f7f1eec840021cc7fe29e94a45a839966bb4726578c72d341dcb9047bb71eec50df72de1072888d158b4ff69b7ee2c8c88a97e1569fb4f4024c8de3d26213 +DIST openbabel-2.3.2.tar.gz 20509105 SHA256 4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188 SHA512 d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919 WHIRLPOOL 74eff18b73d24c8f702e5573a58ba6afba8402e9ce8782de95dc0568575a7d2d632dbc8e8a98b3cd25efdfa7379494f7dcd449342c81ddf73f42a387bce77aaa +DIST openbabel-2.4.1.tar.gz 11618304 SHA256 204136582cdfe51d792000b20202de8950218d617fd9c6e18cee36706a376dfc SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6 WHIRLPOOL 88e333b47118449e1edba2b164af77ac7fac9c60e2965b5d6657ba8cf981845f49f6bac9427515ebbdf62668fddf38ae2422c4e107b98df46922c5bba860b216 +EBUILD openbabel-perl-2.3.2.ebuild 1637 SHA256 e17a865b1f898e8df9b5257072b17218b3bd5652fdfa06e17e861e2669b72070 SHA512 1e6337cf0e5838b85250b8ffd2c1492591a88c4ba975084092065d379a76b356bf558b1b546bc294b486a9b4475f19ebcc2c4a23695c823946476090c16bf8a1 WHIRLPOOL 450d0348bcd1a8a0af335d5c457d20f6728ac55c0bce81d16e2721fea8f4aa34bcafbc6517d7bd46dea7273f4aa73b6e24d3c83d2bb0b96eaa299d0c4a753ab7 +EBUILD openbabel-perl-2.4.1.ebuild 1567 SHA256 ab3943a279de596ef26ecf2e8b84486cb418e7a53daca8e7b5b5889b3cf2740d SHA512 46b6bb68dea80fc17625850ca66f4e90af334099f6d724ea28def4950ff400653212476d79d52d9e8b037f611bca751793695ffa530289ec68384139c98ca72d WHIRLPOOL 09c0cbc8f55c7bae87282f5b2be2506ebaca172a6cb0689f372a621496fb40871df7b9e2939f15b628022aa1ddc87a5cc3f05a618a1aaecfee896dbba91957ad +MISC ChangeLog 2902 SHA256 0623acf0c451c7a2d370588dbd9bf47b1f855bf1f65b0880e83e3d32081fdba5 SHA512 e595628bce359fd2a109f3b9f67fcf01e6bdef9369eb9842678fbe1c9393185d0cf81cda78645c4fb0acbe0e82d377ff1db8ef8ddb294101d027f9f22d8760a8 WHIRLPOOL b7247336838319b4b80ede05e03c268f54e76812245f3b4dd66135e0da7b4e46426ca4f5df4c0cc7e698bbddfa8366a9f7a57bca63bd20002ead12f0bbddc480 +MISC ChangeLog-2015 2484 SHA256 e3be062bded30d8606a8fc3a1177b635885a53ec93a89069e520787d03075a74 SHA512 f06d9c71a1221e54151d9139487b76a6aee21e28fcff852cd2137595973bb335e76c3e21269fc9ae832f18acffd99c8a2a47ad92487c6b613fdd3793a25f6ecd WHIRLPOOL e4586a3b3fda10ddac9d5e743a593c8b929a85846e0182c2593e17f9be9a9a10d08c655d7741f974da55f1cd7c7a908f890a1f4249cfc88599de5205f2e4394f +MISC metadata.xml 735 SHA256 ac781461bfe74b655f72b911700b3e3281c836b5dce045c774d94688cb49cea6 SHA512 62052b0e677a52adba98961185e5b83525c652e260ebad1b820ed19b071a1f6476cca550ec0c570a5faf0cbad7189cadb78ac8d6de077fbf15e346b7c66e4cf7 WHIRLPOOL 05a0c16c873dea1dd9a39c013a195da0a1adc4886e67ab9628dceddef0ebf86183d404bba4042286be6b9f55988c4fce7d15f85b71baf391e8f49087e8eaac96 diff --git a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-bindings_only.patch b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-bindings_only.patch new file mode 100644 index 000000000000..92e126a77d86 --- /dev/null +++ b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-bindings_only.patch @@ -0,0 +1,108 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 449f4b4..1c9ad00 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -252,7 +252,8 @@ if(NOT MSVC) + } + " SCANDIR_NEEDS_CONST) + +- set(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}") ++ set(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}" ++ CACHE PATH "Set to system install for bindings only build") + add_definitions(-DOB_MODULE_PATH="\\"${OB_MODULE_PATH}\\"") + + # Add some visibility support when using GCC +@@ -380,7 +381,8 @@ if(UNIX AND BUILD_SHARED) + if(APPLE) + set(CMAKE_INSTALL_NAME_DIR ${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}) + else() +- set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}") ++ set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}" ++ CACHE PATH "Set sane rpath") + set(CMAKE_SKIP_BUILD_RPATH FALSE) + set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) + set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) +@@ -477,6 +479,13 @@ endif() + # Should the language bindings be regenereted? + option(RUN_SWIG "Generate language bindings with SWIG" OFF) + ++# Build bindings only ++option(BINDINGS_ONLY "Build bindings only" OFF) ++ ++# Point to library if building bindings only ++set(BABEL_SYSTEM_LIBRARY ${BABEL_LIBRARY} ++ CACHE PATH "Point to openbabel library if building bindings only") ++ + # Should all bindings be built? + option(ALL_BINDINGS "Build all languages bindings" OFF) + +diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt +index 16e9000..8f92e91 100644 +--- a/scripts/CMakeLists.txt ++++ b/scripts/CMakeLists.txt +@@ -92,16 +92,30 @@ if (DO_PYTHON_BINDINGS) + endif(RUN_SWIG) + + add_library(bindings_python MODULE ${openbabel_SOURCE_DIR}/scripts/python/openbabel-python.cpp) +- target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_LIBRARY}) ++ if(BINDINGS_ONLY) ++ target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_SYSTEM_LIBRARY}) ++ else() ++ target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_LIBRARY}) ++ endif() ++ + if(NOT WIN32) + set_target_properties(bindings_python PROPERTIES + OUTPUT_NAME _openbabel + PREFIX "" + SUFFIX .so ) +- add_dependencies(bindings_python openbabel) +- install(TARGETS bindings_python LIBRARY DESTINATION ${LIB_INSTALL_DIR}) +- install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py DESTINATION ${LIB_INSTALL_DIR}) +- install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py DESTINATION ${LIB_INSTALL_DIR}) ++ if(NOT BINDINGS_ONLY) ++ add_dependencies(bindings_python openbabel) ++ endif() ++ ++ install(TARGETS bindings_python ++ LIBRARY DESTINATION ${LIB_INSTALL_DIR} ++ COMPONENT bindings_python) ++ install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py ++ DESTINATION ${LIB_INSTALL_DIR} ++ COMPONENT bindings_python) ++ install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py ++ DESTINATION ${LIB_INSTALL_DIR} ++ COMPONENT bindings_python) + else(NOT WIN32) + set_target_properties(bindings_python PROPERTIES + OUTPUT_NAME _openbabel +@@ -231,13 +245,25 @@ if (DO_PERL_BINDINGS) + endif (RUN_SWIG) + + add_library(bindings_perl MODULE ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp) +- target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_LIBRARY} ${PERL_EXTRA_LINK_FLAGS}) ++ if(BINDINGS_ONLY) ++ target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_SYSTEM_LIBRARY} ${PERL_EXTRA_LINK_FLAGS}) ++ else() ++ target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_LIBRARY} ${PERL_EXTRA_LINK_FLAGS}) ++ endif() ++ + set_target_properties(bindings_perl PROPERTIES + PREFIX "" + OUTPUT_NAME OpenBabel) +- add_dependencies(bindings_perl openbabel) +- install(TARGETS bindings_perl LIBRARY DESTINATION ${LIB_INSTALL_DIR}) +- install(FILES ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm DESTINATION ${LIB_INSTALL_DIR}) ++ if(NOT BINDINGS_ONLY) ++ add_dependencies(bindings_perl openbabel) ++ endif() ++ ++ install(TARGETS bindings_perl ++ LIBRARY DESTINATION ${LIB_INSTALL_DIR}/auto/Chemistry/OpenBabel/ ++ COMPONENT bindings_perl) ++ install(FILES ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm ++ DESTINATION ${LIB_INSTALL_DIR}/Chemistry/ ++ COMPONENT bindings_perl) + + endif (DO_PERL_BINDINGS) + diff --git a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-gcc-6_and_7-backport.patch b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-gcc-6_and_7-backport.patch new file mode 100644 index 000000000000..e23dc6020ee5 --- /dev/null +++ b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-gcc-6_and_7-backport.patch @@ -0,0 +1,13 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 0ee545cf..7f4b944e 100755 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -239,7 +239,7 @@ check_type_size(clock_t CLOCK_T) + # Get the GCC version - from KDE4 cmake files + if(CMAKE_COMPILER_IS_GNUCXX) + exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info) +- string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}") ++ string(REGEX MATCH "[34567]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}") + # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the + # patch level, handle this here: + if (NOT _gcc_version) diff --git a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-trunk_cmake.patch b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-trunk_cmake.patch new file mode 100644 index 000000000000..b72a622a3afb --- /dev/null +++ b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-trunk_cmake.patch @@ -0,0 +1,41 @@ +diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt +index e7298ce..16e9000 100644 +--- a/scripts/CMakeLists.txt ++++ b/scripts/CMakeLists.txt +@@ -231,36 +239,6 @@ if (DO_PERL_BINDINGS) + install(TARGETS bindings_perl LIBRARY DESTINATION ${LIB_INSTALL_DIR}) + install(FILES ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm DESTINATION ${LIB_INSTALL_DIR}) + +- set(PERL_INSTALLDIRS_TEXT "") +- if (OBPERL_INSTALLDIRS) +- set(PERL_INSTALLDIRS_TEXT "INSTALLDIRS=${OBPERL_INSTALLDIRS}") +- endif (OBPERL_INSTALLDIRS) +- +- if (NOT MSVC) +- add_custom_target(pre_bindings_perl ALL +- # Create the scripts/perl directory; we cannot do this inside +- # bindings_perl as the WORKING_DIRECTORY needs to already exist! +- COMMAND ${CMAKE_COMMAND} -E make_directory ${openbabel_BINARY_DIR}/scripts/perl +- ) +- add_custom_target(bindings_perl ALL +- COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/perl/Makefile.PL ${openbabel_BINARY_DIR}/scripts/perl +- COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm ${openbabel_BINARY_DIR}/scripts/perl +- COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp ${openbabel_BINARY_DIR}/scripts/perl +- COMMAND PERL5LIB=${openbabel_SOURCE_DIR}/scripts/perl/inc SRC_DIR=${openbabel_SOURCE_DIR} OBJ_DIR=${openbabel_BINARY_DIR} ${PERL_EXECUTABLE} ${openbabel_BINARY_DIR}/scripts/perl/Makefile.PL ${PERL_PREFIX_TEXT} ${PERL_INSTALLDIRS_TEXT} +- COMMAND PERL5LIB=${openbabel_SOURCE_DIR}/scripts/perl/inc make +- DEPENDS openbabel ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp +- WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl +- ) +- add_dependencies(bindings_perl pre_bindings_perl openbabel) +- install(CODE "execute_process(COMMAND make install DESTDIR=\$ENV{DESTDIR} WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl)") +- +- else (NOT MSVC) +- add_library(bindings_perl MODULE ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp) +- target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_LIBRARY}) +- set_target_properties(bindings_perl PROPERTIES +- OUTPUT_NAME openbabel_perl ) +- endif(NOT MSVC) +- + endif (DO_PERL_BINDINGS) + + ################### diff --git a/sci-chemistry/openbabel-perl/metadata.xml b/sci-chemistry/openbabel-perl/metadata.xml new file mode 100644 index 000000000000..e549fb694ab7 --- /dev/null +++ b/sci-chemistry/openbabel-perl/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +OpenBabel is a chemical toolbox designed to speak the many languages of +chemical data. It's an open, collaborative project allowing anyone to +search, convert, analyze, or store data from molecular modeling, chemistry, +solid-state materials, biochemistry, or related areas. +This package enables to access OpenBabel library from Perl programs. +</longdescription> + <upstream> + <remote-id type="sourceforge">openbabel</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild b/sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild new file mode 100644 index 000000000000..1f6b5d8005a2 --- /dev/null +++ b/sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils eutils perl-module + +DESCRIPTION="Perl bindings for OpenBabel" +HOMEPAGE="http://openbabel.sourceforge.net/" +SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz" + +KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux" +SLOT="0" +LICENSE="GPL-2" +IUSE="" + +RDEPEND=" + dev-lang/perl:= + ~sci-chemistry/openbabel-${PV}" +DEPEND="${RDEPEND} + >=dev-util/cmake-2.4.8 + >=dev-lang/swig-2" + +S="${WORKDIR}/openbabel-${PV}" + +PATCHES=( + "${FILESDIR}"/${P}-trunk_cmake.patch + "${FILESDIR}"/${P}-bindings_only.patch + "${FILESDIR}"/${P}-gcc-6_and_7-backport.patch +) + +src_prepare() { + sed \ + -e '/__GNUC__/s:== 4:>= 4:g' \ + -i include/openbabel/shared_ptr.h || die + epatch "${PATCHES[@]}" + perl_set_version +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_INSTALL_RPATH= + -DBINDINGS_ONLY=ON + -DBABEL_SYSTEM_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libopenbabel.so" + -DOB_MODULE_PATH="${EPREFIX}/usr/$(get_libdir)/openbabel/${PV}" + -DLIB_INSTALL_DIR="${D}/${VENDOR_ARCH}" + -DPERL_BINDINGS=ON + -DRUN_SWIG=ON + ) + + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile bindings_perl +} + +src_test() { + mkdir "${CMAKE_BUILD_DIR}/$(get_libdir)/Chemistry" + cp \ + "${CMAKE_USE_DIR}/scripts/perl/OpenBabel.pm" \ + "${CMAKE_BUILD_DIR}/$(get_libdir)/Chemistry/" + for i in "${CMAKE_USE_DIR}"/scripts/perl/t/*; do + einfo "Running test: ${i}" + perl -I"${CMAKE_BUILD_DIR}/$(get_libdir)" "${i}" || die + done +} + +src_install() { + cd "${CMAKE_BUILD_DIR}" + cmake -DCOMPONENT=bindings_perl -P cmake_install.cmake +} diff --git a/sci-chemistry/openbabel-perl/openbabel-perl-2.4.1.ebuild b/sci-chemistry/openbabel-perl/openbabel-perl-2.4.1.ebuild new file mode 100644 index 000000000000..1e01e9007b7b --- /dev/null +++ b/sci-chemistry/openbabel-perl/openbabel-perl-2.4.1.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils perl-module + +DESCRIPTION="Perl bindings for OpenBabel" +HOMEPAGE="http://openbabel.sourceforge.net/" +SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz" + +KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux" +SLOT="0/5" +LICENSE="GPL-2" +IUSE="" + +RDEPEND=" + dev-lang/perl:= + ~sci-chemistry/openbabel-${PV}" +DEPEND="${RDEPEND} + >=dev-util/cmake-2.4.8 + >=dev-lang/swig-2" + +S="${WORKDIR}/openbabel-${PV}" + +PATCHES=( + "${FILESDIR}"/${PN}-2.3.2-gcc-6_and_7-backport.patch +) + +src_prepare() { + sed \ + -e '/__GNUC__/s:== 4:>= 4:g' \ + -i include/openbabel/shared_ptr.h || die + default + perl_set_version +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_INSTALL_RPATH= + -DBINDINGS_ONLY=ON + -DBABEL_SYSTEM_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libopenbabel.so" + -DOB_MODULE_PATH="${EPREFIX}/usr/$(get_libdir)/openbabel/${PV}" + -DLIB_INSTALL_DIR="${D}/${VENDOR_ARCH}" + -DPERL_BINDINGS=ON + -DRUN_SWIG=ON + ) + + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile bindings_perl +} + +src_test() { + mkdir "${CMAKE_BUILD_DIR}/$(get_libdir)/Chemistry" || die + cp \ + "${CMAKE_USE_DIR}/scripts/perl/OpenBabel.pm" \ + "${CMAKE_BUILD_DIR}/$(get_libdir)/Chemistry/" || die + for i in "${CMAKE_USE_DIR}"/scripts/perl/t/*; do + einfo "Running test: ${i}" + perl -I"${CMAKE_BUILD_DIR}/$(get_libdir)" "${i}" || die + done +} + +src_install() { + cd "${CMAKE_BUILD_DIR}" || die + cmake -DCOMPONENT=bindings_perl -P cmake_install.cmake +} diff --git a/sci-chemistry/openbabel-python/Manifest b/sci-chemistry/openbabel-python/Manifest new file mode 100644 index 000000000000..725c5dbc48dc --- /dev/null +++ b/sci-chemistry/openbabel-python/Manifest @@ -0,0 +1,11 @@ +AUX openbabel-python-2.3.2-bindings_only.patch 8843 SHA256 dc6eec80f84e851a7dabad19c32a69179ccb747ddf7de3ba321a2ac40216105f SHA512 c933ac9f0c2370ceb305ebb831ab81e3d66dc9233d175f2b31f0e6ca0cc91dce591c46478ef5d5ccc118cfa8f6d82459331d5e7885bffa904ad486215c657333 WHIRLPOOL addaba85bee01eaa5342fbc55c8dde5ce27fb126b2e07f0a16d3b8ababc3593f7f5ba4d679b0112a6d13cf69a80b3f98f4dbff16badcb95a6c6650f289b6e17e +AUX openbabel-python-2.3.2-gcc-6_and_7-backport.patch 635 SHA256 49f9fc47d1c864d501a266c4d1d7251d5921ce64f1de33a7679d369938bd8490 SHA512 e1b4402f34d01ced5b4caaa184b4e5544cf47893cfe7958054052b05a57dc34b4d44239a212c7d909f29b9366b83b6df74993f844a20f23748c01272ec093081 WHIRLPOOL 8789037e71722ee28d8769eadc574edf2d7d80e8e01f6a8475b18fd4ed0314757bd02854eacf375f7c23ca20b9ec8cc9a40797b51ad3fe64921440549a49cd3d +AUX openbabel-python-2.3.2-swig-3.0.3.patch 4138 SHA256 d4aa44552155f16d43fb086c2cd35a944d5d9ff35ae97bb6e632d9772566bfe8 SHA512 ac454d8f8a8e6d8942d493ee648ad190e275d616bea99cc16bede97e00733d4aa6522cf43a80707b3aa59a78ba68731ccdf748beb76fb2b69267b3b060a5e96f WHIRLPOOL 1a758196daad39b1ebb01d13a26256ccfdefee086676b476e4812206aa65a32fb494fe91b0f6cc64ba3233ccdf747752f97786c261d8f679c9472a4fd4f898cd +AUX openbabel-python-2.3.2-testpybel.patch 1105 SHA256 d39e2530c31f074aa2860f0dea4845acbb3731004491e409169d0c3689682114 SHA512 65df0351fc626ba9d88c06c7f9e84e5707585f302baea4b4885faa3b190c29483b0016d7390e23c2d2444e83c39ad525ba52d7b8d22faed89d82beb480c5b469 WHIRLPOOL 34be3e8bf7322f1c03b4c55d87b4b46d51603ace4a6f1a1524394c115b8ff731125ed0c55132248029718a0519d7d9a96ff8fb56db430d9ca3bc95014d7915a1 +DIST openbabel-2.3.2.tar.gz 20509105 SHA256 4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188 SHA512 d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919 WHIRLPOOL 74eff18b73d24c8f702e5573a58ba6afba8402e9ce8782de95dc0568575a7d2d632dbc8e8a98b3cd25efdfa7379494f7dcd449342c81ddf73f42a387bce77aaa +DIST openbabel-2.4.1.tar.gz 11618304 SHA256 204136582cdfe51d792000b20202de8950218d617fd9c6e18cee36706a376dfc SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6 WHIRLPOOL 88e333b47118449e1edba2b164af77ac7fac9c60e2965b5d6657ba8cf981845f49f6bac9427515ebbdf62668fddf38ae2422c4e107b98df46922c5bba860b216 +EBUILD openbabel-python-2.3.2.ebuild 2249 SHA256 e5ffb874d14e0d8a8f663b0989849c42bd7e2ed54d6f13e40a73080858444c11 SHA512 5cda71fe2a54d46eb8d7d68e03c0791866172466a54769a032a03e3ab7327ad3c5dac96a937416dd576635528f6b1c0602f753fc13a3f44e8d79579620279fe7 WHIRLPOOL d4d6ca8a48024d5e905c0ff0a06da7c9687843184f414bc4e1338fb6168dd4abf7c451e09a6c926271269b08881747623105e6a43bb3c637ca253e6fac91467b +EBUILD openbabel-python-2.4.1-r1.ebuild 2175 SHA256 d496dabb0855ae8de3e3cbcff4e50c0fb6672b38f777580b4ddda24642e244ee SHA512 a4174ac5fabedd91719a7adba9bfac803ca231e223243a32eff6bfd98a95d6d21e0ab7c9ac0457f43b064866bb5876fb684449f6389764afa2365a83aa749ae2 WHIRLPOOL f3f09cc9f56ca936c6125d72bb623ff1f7351ebec91387df3feb43e1211d5e9eb40ab758f08c2ea504dc0c8d7e0ce41bc320453614466cc61bf988f19aa14c69 +MISC ChangeLog 3304 SHA256 09a73e802e749856c8ae4f694d330bb08f74c5028688e251fdc3e3ae379d4916 SHA512 72f3630b79ebed432388c9b60e3f547b64b4dc5e3716bc5281c3e4ca155540d796a5218dff38059fe2b6f9c79688fbe78a7b534cdd48d882170da274fde99b72 WHIRLPOOL 1a1fb6ac98ea62a630fc799aadd66d4a8ddb264855ce8fd48c9abb43f7db6e6d48a71f0ab6e1362d7d5e8b2a866fc1ece189b46913222806b4ddfbd5b0480bc4 +MISC ChangeLog-2015 4216 SHA256 93e5ef940fc808b25b5225faab8e21f4e37f53dd71a0446062e0bf7db9e8ed9c SHA512 46fe186c7e5f4d5155d7dcc3953c1db2e6fa6c8fc8731b1cc18333f1bd9ddd90c00b6449aa858b2aa82449246a71ae9abc78b329f4644afdafe5f4b7b7e74868 WHIRLPOOL 21239983513f5f6b68a5eff420742d15079e4c6c1c8983195eb8fd0b35d7d1fbfde180c63165b70c11e9f0bd83ab5aa6bdb88c0dca01b5681e5988e386ece91f +MISC metadata.xml 737 SHA256 a0d128cb29b316c9a99d6ae6e1a5a1ff153d957514619f375cceb37fda483cb4 SHA512 7ff97ef3f6752a8fed578676aa2cb9706b7d68e31ee22d26e90d4bbb01c10ff410b66da20a91b078293add3bcb3a3711ad180d5174368e0d588ea718ad297d7e WHIRLPOOL 39cf569c8e097bff03a0d2aa32690203db72c13b913fcf40b1f7d1e87fb7c15d5a326bb7930812e7c8a79fae5c5a96a5685264de9ffab3df7c1d6705c4a173ab diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch new file mode 100644 index 000000000000..2e776b4029ec --- /dev/null +++ b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch @@ -0,0 +1,209 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 449f4b4..1c9ad00 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -252,7 +252,8 @@ if(NOT MSVC) + } + " SCANDIR_NEEDS_CONST) + +- set(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}") ++ set(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}" ++ CACHE PATH "Set to system install for bindings only build") + add_definitions(-DOB_MODULE_PATH="\\"${OB_MODULE_PATH}\\"") + + # Add some visibility support when using GCC +@@ -380,7 +381,8 @@ if(UNIX AND BUILD_SHARED) + if(APPLE) + set(CMAKE_INSTALL_NAME_DIR ${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}) + else() +- set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}") ++ set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}" ++ CACHE PATH "Set sane rpath") + set(CMAKE_SKIP_BUILD_RPATH FALSE) + set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) + set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) +@@ -477,6 +479,13 @@ endif() + # Should the language bindings be regenereted? + option(RUN_SWIG "Generate language bindings with SWIG" OFF) + ++# Build bindings only ++option(BINDINGS_ONLY "Build bindings only" OFF) ++ ++# Point to library if building bindings only ++set(BABEL_SYSTEM_LIBRARY ${BABEL_LIBRARY} ++ CACHE PATH "Point to openbabel library if building bindings only") ++ + # Should all bindings be built? + option(ALL_BINDINGS "Build all languages bindings" OFF) + +diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt +index 16e9000..ecd2295 100644 +--- a/scripts/CMakeLists.txt ++++ b/scripts/CMakeLists.txt +@@ -92,16 +92,30 @@ if (DO_PYTHON_BINDINGS) + endif(RUN_SWIG) + + add_library(bindings_python MODULE ${openbabel_SOURCE_DIR}/scripts/python/openbabel-python.cpp) +- target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_LIBRARY}) ++ if(BINDINGS_ONLY) ++ target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_SYSTEM_LIBRARY}) ++ else() ++ target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_LIBRARY}) ++ endif() ++ + if(NOT WIN32) + set_target_properties(bindings_python PROPERTIES + OUTPUT_NAME _openbabel + PREFIX "" + SUFFIX .so ) +- add_dependencies(bindings_python openbabel) +- install(TARGETS bindings_python LIBRARY DESTINATION ${LIB_INSTALL_DIR}) +- install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py DESTINATION ${LIB_INSTALL_DIR}) +- install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py DESTINATION ${LIB_INSTALL_DIR}) ++ if(NOT BINDINGS_ONLY) ++ add_dependencies(bindings_python openbabel) ++ endif() ++ ++ install(TARGETS bindings_python ++ LIBRARY DESTINATION ${LIB_INSTALL_DIR} ++ COMPONENT bindings_python) ++ install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py ++ DESTINATION ${LIB_INSTALL_DIR} ++ COMPONENT bindings_python) ++ install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py ++ DESTINATION ${LIB_INSTALL_DIR} ++ COMPONENT bindings_python) + else(NOT WIN32) + set_target_properties(bindings_python PROPERTIES + OUTPUT_NAME _openbabel +diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt +index 7841782..6f3495f 100644 +--- a/test/CMakeLists.txt ++++ b/test/CMakeLists.txt +@@ -2,7 +2,12 @@ + add_definitions(-DTESTDATADIR="\\"${CMAKE_SOURCE_DIR}/test/files/\\"") + + # define FORMATDIR for location of format plugin binaries +-add_definitions(-DFORMATDIR="\\"${openbabel_BINARY_DIR}/lib/\\"") ++if(BINDINGS_ONLY) ++ set(FORMATDIR "${OB_MODULE_PATH}/") ++else() ++ set(FORMATDIR "${openbabel_BINARY_DIR}/lib${LIB_SUFFIX}/") ++endif() ++add_definitions(-DFORMATDIR="\\"${FORMATDIR}/\\"") + + ########################################################### + # new tests using obtest.h +@@ -89,7 +94,7 @@ foreach(test ${tests}) + add_test(${test}_Test ${TEST_PATH}/test_${test}) + set_tests_properties(${test}_Test PROPERTIES + FAIL_REGULAR_EXPRESSION "ERROR;FAIL;Test failed" +- ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib") ++ ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}") + endforeach(test ${tests}) + + ############################################################ +@@ -152,7 +157,7 @@ if(WITH_INCHI) + ${TEST_PATH}/test_inchiwrite ${inchidata}/${test} ${inchidata}/${test}.txt) + set_tests_properties(inchi${test}_Test PROPERTIES + FAIL_REGULAR_EXPRESSION "Not ok" +- ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib" ++ ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" + ) + endforeach(test ${inchitests}) + endif(WITH_INCHI) +@@ -166,7 +171,7 @@ foreach(test ${old_tests}) + add_test(${test}_Test ${TEST_PATH}/test_${test}) + set_tests_properties(${test}_Test PROPERTIES + FAIL_REGULAR_EXPRESSION "not ok" +- ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib" ++ ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" + ) + endforeach(test ${old_tests}) + +@@ -181,8 +186,8 @@ if(NOT BUILD_SHARED AND NOT BUILD_MIXED) + endif() + install(TARGETS roundtrip + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} + ) + + ########################### +@@ -199,10 +204,10 @@ if(NOT MINGW AND NOT CYGWIN) + babel sym smartssym fastsearch unique kekule) + foreach(pytest ${pytests}) + SET_SOURCE_FILES_PROPERTIES(test${pytest}.py PROPERTIES +- PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib" +- BABEL_LIBDIR "${CMAKE_BINARY_DIR}/lib" ++ PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" ++ BABEL_LIBDIR "${FORMATDIR}" + BABEL_DATADIR "${CMAKE_SOURCE_DIR}/data" +- LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib" ++ LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" + ) + ADD_PYTHON_TEST(pytest_${pytest} test${pytest}.py) + set_tests_properties(pytest_${pytest} PROPERTIES +@@ -221,10 +226,10 @@ if (PYTHON_BINDINGS) + bindings _pybel example) + foreach(pybindtest ${pybindtests}) + SET_SOURCE_FILES_PROPERTIES(test${pybindtest}.py PROPERTIES +- PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib" +- BABEL_LIBDIR "${CMAKE_BINARY_DIR}/lib" ++ PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" ++ BABEL_LIBDIR "${FORMATDIR}" + BABEL_DATADIR "${CMAKE_SOURCE_DIR}/data" +- LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib" ++ LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" + ) + if(MSVC) + SET_SOURCE_FILES_PROPERTIES(test${pybindtest}.py PROPERTIES +diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt +index 1f547bf..fb98441 100644 +--- a/tools/CMakeLists.txt ++++ b/tools/CMakeLists.txt +@@ -38,8 +38,8 @@ if(BUILD_SHARED) + target_link_libraries(${tool} ${BABEL_LIBRARY}) + install(TARGETS ${tool} + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} + ) + endforeach(tool) + +@@ -53,8 +53,8 @@ if(BUILD_SHARED) + target_link_libraries(obspectrophore ${BABEL_LIBRARY}) + install(TARGETS obspectrophore + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} + ) + + # obgrep -- requires getopt +@@ -66,8 +66,8 @@ if(BUILD_SHARED) + target_link_libraries(obgrep ${BABEL_LIBRARY}) + install(TARGETS obgrep + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} + ) + endif(NOT MINIMAL_BUILD) + +@@ -146,7 +146,7 @@ else(BUILD_SHARED) + + install(TARGETS babel + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib) ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX}) + + endif(BUILD_SHARED) diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-gcc-6_and_7-backport.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-gcc-6_and_7-backport.patch new file mode 100644 index 000000000000..e23dc6020ee5 --- /dev/null +++ b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-gcc-6_and_7-backport.patch @@ -0,0 +1,13 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 0ee545cf..7f4b944e 100755 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -239,7 +239,7 @@ check_type_size(clock_t CLOCK_T) + # Get the GCC version - from KDE4 cmake files + if(CMAKE_COMPILER_IS_GNUCXX) + exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info) +- string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}") ++ string(REGEX MATCH "[34567]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}") + # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the + # patch level, handle this here: + if (NOT _gcc_version) diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-swig-3.0.3.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-swig-3.0.3.patch new file mode 100644 index 000000000000..d30efd55bd92 --- /dev/null +++ b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-swig-3.0.3.patch @@ -0,0 +1,97 @@ + scripts/openbabel-python.i | 34 +++++++++++++++++----------------- + 1 file changed, 17 insertions(+), 17 deletions(-) + +diff --git a/scripts/openbabel-python.i b/scripts/openbabel-python.i +index 7cb8f24..d893129 100644 +--- a/scripts/openbabel-python.i ++++ b/scripts/openbabel-python.i +@@ -227,7 +227,7 @@ CAST_GENERICDATA_TO(SquarePlanarStereo) + %include <openbabel/math/transform3d.h> + %include <openbabel/math/spacegroup.h> + +-# CloneData should be used instead of the following method ++// CloneData should be used instead of the following method + %ignore OpenBabel::OBBase::SetData; + %include <openbabel/base.h> + +@@ -289,7 +289,7 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue + %ignore OpenBabel::OBDescriptor::LessThan; + %include <openbabel/descriptor.h> + +-# Ignore shadowed methods ++// Ignore shadowed methods + %ignore OpenBabel::OBForceField::VectorSubtract(const double *const, const double *const, double *); + %ignore OpenBabel::OBForceField::VectorMultiply(const double *const, const double, double *); + %include <openbabel/forcefield.h> +@@ -310,7 +310,7 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue + + %warnfilter(503) OpenBabel::OBBitVec; // Not wrapping any of the overloaded operators + %include <openbabel/bitvec.h> +-# Ignore shadowed method ++// Ignore shadowed method + %ignore OpenBabel::OBRotor::GetRotAtoms() const; + %include <openbabel/rotor.h> + %ignore OpenBabel::Swab; +@@ -321,13 +321,13 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue + %include <openbabel/math/align.h> + #endif + +-# The following %ignores avoid warning messages due to shadowed classes. +-# This does not imply a loss of functionality as (in this case) +-# the shadowed class is identical (from the point of view of SWIG) to +-# the shadowing class. +-# This is because C++ references (&) are transformed by SWIG back into +-# pointers, so that OBAtomIter(OBMol &) would be treated the same as +-# OBAtomIter(OBMol *). ++// The following %ignores avoid warning messages due to shadowed classes. ++// This does not imply a loss of functionality as (in this case) ++// the shadowed class is identical (from the point of view of SWIG) to ++// the shadowing class. ++// This is because C++ references (&) are transformed by SWIG back into ++// pointers, so that OBAtomIter(OBMol &) would be treated the same as ++// OBAtomIter(OBMol *). + + %ignore OBAtomAtomIter(OBAtom &); + %ignore OBAtomBondIter(OBAtom &); +@@ -346,9 +346,9 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue + %ignore OBResidueIter(OBMol &); + %ignore OBResidueAtomIter(OBResidue &); + +-# These classes are renamed so that they can be replaced by Python +-# classes of the same name which provide Pythonic iterators +-# (see %pythoncode section below) ++// These classes are renamed so that they can be replaced by Python ++// classes of the same name which provide Pythonic iterators ++// (see %pythoncode section below) + + %rename(_OBAtomAtomIter) OpenBabel::OBAtomAtomIter; + %rename(_OBAtomBondIter) OpenBabel::OBAtomBondIter; +@@ -367,8 +367,8 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue + + %include <openbabel/obiter.h> + +-# The following class, OBiter, is subclassed to provide Python iterators +-# equivalent to the C++ iterators in obiter.h and the plugin iterators ++// The following class, OBiter, is subclassed to provide Python iterators ++// equivalent to the C++ iterators in obiter.h and the plugin iterators + + %pythoncode %{ + class OBIter(object): +@@ -459,7 +459,7 @@ def double_array(mylist): + return c + %} + +-# Copy some of the global variables in cvar into the openbabel namespace ++// Copy some of the global variables in cvar into the openbabel namespace + + %pythoncode %{ + obErrorLog = cvar.obErrorLog +@@ -470,7 +470,7 @@ atomtyper = cvar.atomtyper + aromtyper = cvar.aromtyper + %} + +-# Functions to set the log file to std::cout and std::cerr ++// Functions to set the log file to std::cout and std::cerr + + %ignore OBForceField::SetLogFile(std::ostream *pos); + %extend OpenBabel::OBForceField { diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-testpybel.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-testpybel.patch new file mode 100644 index 000000000000..7a0114975fff --- /dev/null +++ b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-testpybel.patch @@ -0,0 +1,28 @@ +From b34edb6de512e5735d87cb0893804a4abd14f9b7 Mon Sep 17 00:00:00 2001 +From: baoilleach <baoilleach@71e0b675-c112-0410-beda-96664073b5c2> +Date: Mon, 1 Oct 2012 20:40:36 +0000 +Subject: [PATCH] scripts/python/testpybel.py: Minor fix to enable failing + test to pass. Failures due to the new MOL Chiral Flag data + that I stored a while ago. + +git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk@5022 71e0b675-c112-0410-beda-96664073b5c2 +--- + scripts/python/examples/testpybel.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/scripts/python/examples/testpybel.py b/scripts/python/examples/testpybel.py +index aa5fcd4..7951851 100644 +--- a/scripts/python/examples/testpybel.py ++++ b/scripts/python/examples/testpybel.py +@@ -336,7 +336,7 @@ class TestPybel(TestToolkit): + tpsaname = "TPSA" + Nbits = 3 + Nfpbits = 32 +- datakeys = ['NSC', 'Comment', 'OpenBabel Symmetry Classes'] ++ datakeys = ['NSC', 'Comment', 'OpenBabel Symmetry Classes', 'MOL Chiral Flag'] + + def testFP_FP3(self): + "Checking the results from FP3" +-- +1.7.12.3 + diff --git a/sci-chemistry/openbabel-python/metadata.xml b/sci-chemistry/openbabel-python/metadata.xml new file mode 100644 index 000000000000..06fa4d2398d3 --- /dev/null +++ b/sci-chemistry/openbabel-python/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +OpenBabel is a chemical toolbox designed to speak the many languages of +chemical data. It's an open, collaborative project allowing anyone to +search, convert, analyze, or store data from molecular modeling, chemistry, +solid-state materials, biochemistry, or related areas. This package enables +to access OpenBabel library from Python programs. +</longdescription> + <upstream> + <remote-id type="sourceforge">openbabel</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild b/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild new file mode 100644 index 000000000000..999a73bc7948 --- /dev/null +++ b/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild @@ -0,0 +1,93 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_4 ) + +inherit cmake-utils eutils multilib python-r1 + +DESCRIPTION="Python bindings for OpenBabel (including Pybel)" +HOMEPAGE="http://openbabel.sourceforge.net/" +SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz" + +KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux" +SLOT="0" +LICENSE="GPL-2" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + ~sci-chemistry/openbabel-${PV} + sys-libs/zlib" +DEPEND="${RDEPEND} + >=dev-lang/swig-2" + +S="${WORKDIR}"/openbabel-${PV} + +PATCHES=( + "${FILESDIR}"/${P}-testpybel.patch + "${FILESDIR}"/${P}-bindings_only.patch + "${FILESDIR}"/${P}-swig-3.0.3.patch + "${FILESDIR}"/${P}-gcc-6_and_7-backport.patch + ) + +src_prepare() { + cmake-utils_src_prepare + sed \ + -e "s:\"\.\.\":\"${EPREFIX}/usr\":g" \ + -i test/testbabel.py || die + swig -python -c++ -small -O -templatereduce -naturalvar \ + -I"${EPREFIX}/usr/include/openbabel-2.0" \ + -o scripts/python/openbabel-python.cpp \ + -DHAVE_EIGEN \ + -outdir scripts/python \ + scripts/openbabel-python.i \ + || die "Regeneration of openbabel-python.cpp failed" + sed \ + -e '/__GNUC__/s:== 4:>= 4:g' \ + -i include/openbabel/shared_ptr.h || die +} + +src_configure() { + my_impl_src_configure() { + local mycmakeargs=( + -DCMAKE_INSTALL_RPATH= + -DBINDINGS_ONLY=ON + -DBABEL_SYSTEM_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libopenbabel.so" + -DOB_MODULE_PATH="${EPREFIX}/usr/$(get_libdir)/openbabel/${PV}" + -DLIB_INSTALL_DIR="${D}$(python_get_sitedir)" + -DPYTHON_BINDINGS=ON + -DPYTHON_EXECUTABLE=${PYTHON} + -DPYTHON_INCLUDE_DIR="$(python_get_includedir)" + -DPYTHON_INCLUDE_PATH="$(python_get_includedir)" + -DPYTHON_LIBRARY="$(python_get_library_path)" + -DENABLE_TESTS=ON + ) + + cmake-utils_src_configure + } + + python_foreach_impl my_impl_src_configure +} + +src_compile() { + python_foreach_impl cmake-utils_src_make bindings_python +} + +src_test() { + python_foreach_impl cmake-utils_src_test -R py +} + +src_install() { + my_impl_src_install() { + cd "${BUILD_DIR}" || die + + cmake -DCOMPONENT=bindings_python -P cmake_install.cmake + + python_optimize + } + + python_foreach_impl my_impl_src_install +} diff --git a/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild b/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild new file mode 100644 index 000000000000..84f9aa89e74b --- /dev/null +++ b/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r1.ebuild @@ -0,0 +1,91 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) + +inherit cmake-utils python-r1 + +DESCRIPTION="Python bindings for OpenBabel (including Pybel)" +HOMEPAGE="http://openbabel.sourceforge.net/" +SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz" + +KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux" +SLOT="0/5" +LICENSE="GPL-2" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + ~sci-chemistry/openbabel-${PV} + sys-libs/zlib" +DEPEND="${RDEPEND} + >=dev-lang/swig-2" + +S="${WORKDIR}"/openbabel-${PV} + +PATCHES=( + "${FILESDIR}"/${PN}-2.3.2-gcc-6_and_7-backport.patch + ) + +src_prepare() { + cmake-utils_src_prepare + sed \ + -e "s:\"\.\.\":\"${EPREFIX}/usr\":g" \ + -i test/testbabel.py || die + swig -python -c++ -small -O -templatereduce -naturalvar \ + -I"${EPREFIX}/usr/include/openbabel-2.0" \ + -o scripts/python/openbabel-python.cpp \ + -DHAVE_EIGEN \ + -outdir scripts/python \ + scripts/openbabel-python.i \ + || die "Regeneration of openbabel-python.cpp failed" + sed \ + -e '/__GNUC__/s:== 4:>= 4:g' \ + -i include/openbabel/shared_ptr.h || die +} + +src_configure() { + my_impl_src_configure() { + local mycmakeargs=( + -DCMAKE_INSTALL_RPATH= + -DBINDINGS_ONLY=ON + -DBABEL_SYSTEM_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libopenbabel.so" + -DOB_MODULE_PATH="${EPREFIX}/usr/$(get_libdir)/openbabel/${PV}" + -DLIB_INSTALL_DIR="${D}$(python_get_sitedir)" + -DPYTHON_BINDINGS=ON + -DPYTHON_EXECUTABLE=${PYTHON} + -DPYTHON_INCLUDE_DIR="$(python_get_includedir)" + -DPYTHON_INCLUDE_PATH="$(python_get_includedir)" + -DPYTHON_LIBRARY="$(python_get_library_path)" + -DENABLE_TESTS=ON + -DCMAKE_INSTALL_PREFIX="${ED%/}/usr" + ) + + cmake-utils_src_configure + } + + python_foreach_impl my_impl_src_configure +} + +src_compile() { + python_foreach_impl cmake-utils_src_make bindings_python +} + +src_test() { + python_foreach_impl cmake-utils_src_test -R py +} + +src_install() { + my_impl_src_install() { + cd "${BUILD_DIR}" || die + + cmake -DCOMPONENT=bindings_python -P cmake_install.cmake + + python_optimize + } + + python_foreach_impl my_impl_src_install +} diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest new file mode 100644 index 000000000000..86ca7538cb5d --- /dev/null +++ b/sci-chemistry/openbabel/Manifest @@ -0,0 +1,9 @@ +AUX openbabel-2.3.2-gcc-6_and_7-backport.patch 635 SHA256 49f9fc47d1c864d501a266c4d1d7251d5921ce64f1de33a7679d369938bd8490 SHA512 e1b4402f34d01ced5b4caaa184b4e5544cf47893cfe7958054052b05a57dc34b4d44239a212c7d909f29b9366b83b6df74993f844a20f23748c01272ec093081 WHIRLPOOL 8789037e71722ee28d8769eadc574edf2d7d80e8e01f6a8475b18fd4ed0314757bd02854eacf375f7c23ca20b9ec8cc9a40797b51ad3fe64921440549a49cd3d +AUX openbabel-2.3.2-test_lib_path.patch 837 SHA256 2aa621bc05aeef47caef9a3a95922dcc6c6b819de9523ea4f0d0b4a72cbf1afb SHA512 d065eef0bb8d751d3292206feb25557394dc203e810b5f0eb7c52a28cb9e2bfaaf60f195d295ef6e58619ab9fa87d84e6b55ad822cfdefc22e02e8b5a8b49efb WHIRLPOOL 074c859d664ae00391119698f84aed2f883f06aab8182490f85faa69bb9b9d181c076d7db05e6004936493da367fb0c1fc8101e43d4c51453a66319994bde155 +DIST openbabel-2.3.2.tar.gz 20509105 SHA256 4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188 SHA512 d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919 WHIRLPOOL 74eff18b73d24c8f702e5573a58ba6afba8402e9ce8782de95dc0568575a7d2d632dbc8e8a98b3cd25efdfa7379494f7dcd449342c81ddf73f42a387bce77aaa +DIST openbabel-2.4.1.tar.gz 11618304 SHA256 204136582cdfe51d792000b20202de8950218d617fd9c6e18cee36706a376dfc SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6 WHIRLPOOL 88e333b47118449e1edba2b164af77ac7fac9c60e2965b5d6657ba8cf981845f49f6bac9427515ebbdf62668fddf38ae2422c4e107b98df46922c5bba860b216 +EBUILD openbabel-2.3.2-r1.ebuild 2061 SHA256 9de98b2a552db479eafc5c7ef1fcfb233494ad634dcbf0cada7ef23f83f31fc0 SHA512 acc8b99854f852375a19a5b6316cc439016aa258e369892bc524949e709c48412f7925e57f2b684de6a327960b09324d0327aee066560d8dd2194b279de53e0f WHIRLPOOL 0c0dd2b2aab21bff6299fca3f29914b4371dabc1c745f06300d98354c2be16842fb4d3f34a1911603d211beb7bf75998ced6f4a8fe9906b4f44cbea5719addc5 +EBUILD openbabel-2.4.1.ebuild 1981 SHA256 42ae40c260dc830d65dbee7c544f7f402890e65901f503f3965393d64daf94fd SHA512 bc0e729ed48e27b85be2c5f28f134b99247ad39493bf1fddae231161b049b765cecd183f77acc278c09a9a8fd3220fb00be84e72018df64968e6af69c8958fbe WHIRLPOOL f3db01964da09fc9c8f715be114452592c668aec14d5612bc2c2ba239ee9c50de53834dc4533f7eb3fc64ce774d824b2549b57b622ff30cd68ea2d33fd0f96b5 +MISC ChangeLog 4080 SHA256 a6e17816c99ddcbe4d1a5007227e27378860df564c2727f61973e1868c34b729 SHA512 f3b5872b3e4859359d9376fd105ee242fc72b81e558ea109b958e404823de7b430a3339b6f3a4f58a70f6c8e29888edbd3407efa6e1f0355fd6ed0dd380db484 WHIRLPOOL 7d67a816faf4561465832ccac62e5d84b8d97478ef4493060bb5c2303740394da9c2b9ab0414b0ca8d9194dfeb98f02e9712d1770ad65fdcb662bf3369e527e2 +MISC ChangeLog-2015 10475 SHA256 e40373f70624685bc366cdad53c33422e8cd239cb08dc636c10c3ec890dd4a8d SHA512 ddef7e88ca295fe84f241cfdf3bb3e69c3ec41c1030cc6a586bcbdc4eef698788b90ba9ca30c163fef66ff46727ff5cab4248be10d0d13d52c1bd15554627cc1 WHIRLPOOL 8851dc3203e35267b4ea77c34941254f8b3c913bf169352b9602847d46da4fc334fb357f55a63d0880ec377727b244c67e019a175dff9f398969d3d985567e84 +MISC metadata.xml 676 SHA256 6ea2058c7335057b66482dca5c460d664a79383350e1a2c6880218cb85f92e70 SHA512 bccb2d0f21b5186ca3b3f34a3e500afcee492326bb79f9a6143aa3fb61a3fae81581ae8d7c90f9d17cf92a0cdc5e8aab0dd8daf837509a6f3d956c3ef3434cf0 WHIRLPOOL 700f20f1d05231d8ce191551afad9ea2029412a2ac6c34650cc925c5c15865b8ee71a6045acd2350fdb9035312d221eb8db62135f3266e137c2bf21c3800bce0 diff --git a/sci-chemistry/openbabel/files/openbabel-2.3.2-gcc-6_and_7-backport.patch b/sci-chemistry/openbabel/files/openbabel-2.3.2-gcc-6_and_7-backport.patch new file mode 100644 index 000000000000..e23dc6020ee5 --- /dev/null +++ b/sci-chemistry/openbabel/files/openbabel-2.3.2-gcc-6_and_7-backport.patch @@ -0,0 +1,13 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 0ee545cf..7f4b944e 100755 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -239,7 +239,7 @@ check_type_size(clock_t CLOCK_T) + # Get the GCC version - from KDE4 cmake files + if(CMAKE_COMPILER_IS_GNUCXX) + exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info) +- string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}") ++ string(REGEX MATCH "[34567]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}") + # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the + # patch level, handle this here: + if (NOT _gcc_version) diff --git a/sci-chemistry/openbabel/files/openbabel-2.3.2-test_lib_path.patch b/sci-chemistry/openbabel/files/openbabel-2.3.2-test_lib_path.patch new file mode 100644 index 000000000000..66a796d17b7f --- /dev/null +++ b/sci-chemistry/openbabel/files/openbabel-2.3.2-test_lib_path.patch @@ -0,0 +1,27 @@ +diff -ru old/openbabel-2.3.0/test/CMakeLists.txt new/openbabel-2.3.0/test/CMakeLists.txt +--- a/test/CMakeLists.txt 2010-10-26 17:39:01.000000000 +0300 ++++ b/test/CMakeLists.txt 2010-11-14 18:13:32.000000000 +0200 +@@ -2,7 +2,7 @@ + add_definitions(-DTESTDATADIR="\\"${CMAKE_SOURCE_DIR}/test/files/\\"") + + # define FORMATDIR for location of format plugin binaries +-add_definitions(-DFORMATDIR="\\"${openbabel_BINARY_DIR}/lib/\\"") ++add_definitions(-DFORMATDIR="\\"${openbabel_BINARY_DIR}/lib${LIB_SUFFIX}/\\"") + + ########################################################### + # new tests using obtest.h +@@ -32,12 +35,12 @@ set(tests + uniqueid + ) + +-if (EIGEN2_FOUND) ++if(EIGEN2_FOUND OR EIGEN3_FOUND) + set(tests + align + ${tests} + ) +-endif (EIGEN2_FOUND) ++endif() + + set(TEST_PATH ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}) + diff --git a/sci-chemistry/openbabel/metadata.xml b/sci-chemistry/openbabel/metadata.xml new file mode 100644 index 000000000000..96ded5f8a242 --- /dev/null +++ b/sci-chemistry/openbabel/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> + Open Babel is a chemical toolbox designed to speak the many languages of + chemical data. It's an open, collaborative project allowing anyone to + search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas. + </longdescription> + <upstream> + <remote-id type="sourceforge">openbabel</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild b/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild new file mode 100644 index 000000000000..9665a2ffebcb --- /dev/null +++ b/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild @@ -0,0 +1,92 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +WX_GTK_VER="3.0" + +inherit cmake-utils eutils wxwidgets + +DESCRIPTION="Interconverts file formats used in molecular modeling" +HOMEPAGE="http://openbabel.sourceforge.net/" +SRC_URI="mirror://sourceforge/openbabel/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc openmp test wxwidgets" + +RDEPEND=" + dev-cpp/eigen:3 + dev-libs/libxml2:2 + sci-libs/inchi + sys-libs/zlib + wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )" +DEPEND="${RDEPEND} + >=dev-util/cmake-2.4.8 + doc? ( app-doc/doxygen )" + +DOCS="AUTHORS ChangeLog NEWS README THANKS doc/*.inc doc/README* doc/*.mol2" + +PATCHES=( + "${FILESDIR}"/${P}-test_lib_path.patch + "${FILESDIR}"/${P}-gcc-6_and_7-backport.patch + ) + +pkg_setup() { + if use openmp; then + if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi + FORTRAN_NEED_OPENMP=1 + fi +} + +src_prepare() { + sed \ + -e '/__GNUC__/s:== 4:>= 4:g' \ + -i include/openbabel/shared_ptr.h || die + cmake-utils_src_prepare +} + +src_configure() { + use wxwidgets && need-wxwidgets unicode + local mycmakeargs=() + mycmakeargs+=( + -DOPENBABEL_USE_SYSTEM_INCHI=ON + $(cmake-utils_use_enable openmp OPENMP) + $(cmake-utils_use wxwidgets BUILD_GUI) + ) + + cmake-utils_src_configure +} + +src_install() { + dohtml doc/{*.html,*.png} + if use doc ; then + insinto /usr/share/doc/${PF}/API/html + doins doc/API/html/* + fi + + cmake-utils_src_install +} + +src_test() { + local mycmakeargs="" + mycmakeargs="${mycmakeargs} + -DOPENBABEL_USE_SYSTEM_INCHI=ON + -DPYTHON_EXECUTABLE=false + $(cmake-utils_use_enable openmp OPENMP) + $(cmake-utils_use wxwidgets BUILD_GUI) + $(cmake-utils_use_enable test TESTS)" + + cmake-utils_src_configure + cmake-utils_src_compile + cmake-utils_src_test -E py +} + +pkg_postinst() { + optfeature "perl support" sci-chemistry/openbabel-perl + optfeature "python support" sci-chemistry/openbabel-python +} diff --git a/sci-chemistry/openbabel/openbabel-2.4.1.ebuild b/sci-chemistry/openbabel/openbabel-2.4.1.ebuild new file mode 100644 index 000000000000..3719af8c81d7 --- /dev/null +++ b/sci-chemistry/openbabel/openbabel-2.4.1.ebuild @@ -0,0 +1,92 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +WX_GTK_VER="3.0" + +inherit cmake-utils eutils wxwidgets + +DESCRIPTION="Interconverts file formats used in molecular modeling" +HOMEPAGE="http://openbabel.sourceforge.net/" +SRC_URI="mirror://sourceforge/openbabel/${P}.tar.gz" + +# See src/CMakeLists.txt for LIBRARY_VERSION +SLOT="0/5.0.0" +LICENSE="GPL-2" +KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc openmp test wxwidgets" + +RDEPEND=" + dev-cpp/eigen:3 + dev-libs/libxml2:2 + sci-libs/inchi + sys-libs/zlib + wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )" +DEPEND="${RDEPEND} + >=dev-util/cmake-2.4.8 + doc? ( app-doc/doxygen )" + +DOCS=( AUTHORS NEWS.md README.md THANKS doc/dioxin.{inc,mol2} doc/README.{dioxin.pov,povray} ) + +PATCHES=( + "${FILESDIR}"/${PN}-2.3.2-gcc-6_and_7-backport.patch + ) + +pkg_setup() { + if use openmp; then + if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi + FORTRAN_NEED_OPENMP=1 + fi +} + +src_prepare() { + sed \ + -e '/__GNUC__/s:== 4:>= 4:g' \ + -i include/openbabel/shared_ptr.h || die + cmake-utils_src_prepare +} + +src_configure() { + use wxwidgets && need-wxwidgets unicode + local mycmakeargs=( + -DOPENBABEL_USE_SYSTEM_INCHI=ON + -DOPENMP=$(usex openmp) + -DBUILD_GUI=$(usex wxwidgets) + ) + + cmake-utils_src_configure +} + +src_install() { + docinto html + dodoc doc/{*.html,*.png} + if use doc ; then + docinto html/API + dodoc -r doc/API/html/* + fi + + cmake-utils_src_install +} + +src_test() { + local mycmakeargs=( + -DOPENBABEL_USE_SYSTEM_INCHI=ON + -DPYTHON_EXECUTABLE=false + -DOPENMP=$(usex openmp) + -DBUILD_GUI=$(usex wxwidgets) + -DTESTS=$(usex test) + ) + + cmake-utils_src_configure + cmake-utils_src_compile + cmake-utils_src_test -E py +} + +pkg_postinst() { + optfeature "perl support" sci-chemistry/openbabel-perl + optfeature "python support" sci-chemistry/openbabel-python +} diff --git a/sci-chemistry/ortep3/Manifest b/sci-chemistry/ortep3/Manifest new file mode 100644 index 000000000000..4b78c7f7860a --- /dev/null +++ b/sci-chemistry/ortep3/Manifest @@ -0,0 +1,5 @@ +DIST ortep.f 177237 SHA256 622cdd2801d3959c08f71514de865cc18511fd8522b0b229467d0387047fc374 SHA512 83e78fde2a798d7ee6b902133790f04787f54ceb62a1296ce8262cb8085bebf26e1c3b8f9c9c51ee0823f827bae40a75cede758c6cbe2c1b98a48bc49be6dd0b WHIRLPOOL 09a6e23a90cff1a27d50d014ea29526a1586d7e2e51ea97c0db4a63561989fd0089329d1793f97672e2d52cf289952e4910039f083d8f017688f32f954a9f8f7 +EBUILD ortep3-1.0.3-r1.ebuild 716 SHA256 5b4f37dca52ceb13b4f6741bc4385cb4c191f5b901e5d33a3370a6c63743433a SHA512 a7bc01b102c140b1cfaf12135f3527af86def2ac9f3894b1f8efd8ddbbf5ddac35097c1ae06e5a59b826746311834fc383670e6c20bead46d820db451821605c WHIRLPOOL 9c239277831addc5e01e11480d629d41ebcd1639f8e0f262d2f49ccd914ca2dcc166b7447f3afc76350d0a45b73a3446e9041899a71c47b5825dc39fcc9cf3c1 +MISC ChangeLog 2435 SHA256 c9001913c4212c1904fd66581ba630a5d58d35bd15debc255116e51f6d4ef345 SHA512 17058a95ae14a50d8c620c74e00623bcb2b951610082b16344d07be9b6659191b266469131ac8fe1286f93ccdd8bc3ae895a9a02cc8c3c060d25810da8635109 WHIRLPOOL c02464652f643b93a5dfd24cf03e97153688457c06ed4699b7717d991f0b6f9317cb8f8a1d3f52888ba821e2a5ece2c4b5d7160ba856eac2024f52cf33dc413f +MISC ChangeLog-2015 1691 SHA256 8c7d9f2ab4a52500ce9757efab84f3d470b0af67f5cab56a0975a2774b2164c4 SHA512 54ab3a7a9fbdfed138c015b6335e45652512e408e463223ea817d2de766312e6089f4ffdde62030c37d7f95deb1c880e44f081bb3107d3ac6a3b54253be5494a WHIRLPOOL 8a9fba077f04b9b6c26dca23ce236e71bab8e149b2937f0b58cec23c869733905024986395b605b46d932b604b726b2a71675c121e1b4befcfa8f29f3180e47b +MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d diff --git a/sci-chemistry/ortep3/metadata.xml b/sci-chemistry/ortep3/metadata.xml new file mode 100644 index 000000000000..da36ecbfcd6a --- /dev/null +++ b/sci-chemistry/ortep3/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/ortep3/ortep3-1.0.3-r1.ebuild b/sci-chemistry/ortep3/ortep3-1.0.3-r1.ebuild new file mode 100644 index 000000000000..6998ade89559 --- /dev/null +++ b/sci-chemistry/ortep3/ortep3-1.0.3-r1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit fortran-2 toolchain-funcs + +DESCRIPTION="Thermal ellipsoid plot program for crystal structure illustrations" +HOMEPAGE="http://www.ornl.gov/sci/ortep/" +SRC_URI="ftp://ftp.ornl.gov/pub/ortep/src/ortep.f" + +SLOT="0" +LICENSE="public-domain" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + sci-libs/pgplot + x11-libs/libX11" +DEPEND="${RDEPEND}" + +S="${WORKDIR}" + +src_unpack() { + cp "${DISTDIR}"/${A} "${S}" || die +} + +src_compile() { + COMMAND="$(tc-getFC) ${FFLAGS:- -O2} ${LDFLAGS} -o ${PN} ortep.f -lpgplot -lX11" + echo ${COMMAND} + ${COMMAND} || die "Compilation failed" +} + +src_install() { + dobin ${PN} +} diff --git a/sci-chemistry/p3d/Manifest b/sci-chemistry/p3d/Manifest new file mode 100644 index 000000000000..d69b58c7d75f --- /dev/null +++ b/sci-chemistry/p3d/Manifest @@ -0,0 +1,6 @@ +DIST p3d-0.4.3.tar.gz 7213577 SHA256 b968eb37c0d27ad1f4f46f8a942fb2b62fbcdb50b31a1e66875e2cdc036a9932 SHA512 b4cf472b849ece96fe0b2b7f633c496fe3d12bf8cb82a2af10180ce5c27c5465dd0c16cb912d22c56c933b68c06e7de28c0c640da29eaa6bc6f95009bf10277f WHIRLPOOL 8b9a384e59a98fa643d1573fbde4707148ebd6d5e16ab7daf6ce264e7d9494096a3c3f6e01a46a73a3860c8ca463a47fdd8b56b0fd8986d71371404c02dcb8bb +EBUILD p3d-0.4.3-r1.ebuild 649 SHA256 fa82eefe46de5049aabbce1f447afeecacf1cff2ee490fa69287e99ecf67becb SHA512 e979d59ce970454ef0f8de72bb616b658b489c657bcc3077c2002b6389d00ff4515128da8f549eee5c2ed345d3e229f36de8ff5002e3a21ee5c744d63042295a WHIRLPOOL 821468ce3a7152d15874b7ee5b645e31e05196b56f4d9afe5fa753a842bc3a3c01c9437df7f2248e1195f3122a8936b8dcb3fd0f7a393fe24961b694f8e6461a +EBUILD p3d-9999.ebuild 528 SHA256 bae20f2dd236b02ad565f64bfca3edfef5d8f6150e6f415f8569b86b61c175cf SHA512 e8cdafe07f73c5b2b1f5573270214abf574d349f922f4514b3f00e00e09ecca731d35d1fe10ec7ee05ea95cc8154e26b876b031b68dcff2470acb810ae46ce07 WHIRLPOOL 32110a5b4ef744d44ba8bbc00c05102890f0b7e89c2b6d5938f5f3dcf79e18c9c5b1ecc1e8314c2677b4446a5ca09cdcdaea1d54a80d72432319d321ee40375e +MISC ChangeLog 2602 SHA256 d2b2c98a7092718f4048f91f4733a70a0e9799397f465361037cfc6c58da9fa2 SHA512 0a6bf9639bd61b209ce540c9ac57ec05ef9ec9d9109879973b709bb19c1e124b4f8846c8cb3956affee90ce105532cf338e57b09f56fc784db2182c5ad2dea8a WHIRLPOOL 8e12880d9d84954e3cfb0c129caf8953cdf7dfc44a957c206105515bf8e75bedd6d562ef5fbc13e8120ef9c4e14c0e4fe482776bee0a9985e5674e0d3be5c098 +MISC ChangeLog-2015 803 SHA256 d3d08ac9c5527228882711794857e7765fa4d843f9e9eb02092992bc54c4ad6f SHA512 6a01ae3790db2952c825a27a371106ee32c4c98acab5d95308eb7199f5846094236c9f2f2b22c0070c4621624dae1fce54c638228b8605e19a593e8cca4b0f9f WHIRLPOOL 6ad8c7a703c0070fd98e58e9f898db2e2902a258362d343036102bd9bef58956b5618c0c059eff0c24060a2671b241a039bd70510fbc80920289ab60977ea5d1 +MISC metadata.xml 1151 SHA256 f976eca80bca7e92808620ae324782b2eee07b12ee2db725d8b962b81e6d19c1 SHA512 322b35766a1e71129165a8559fe3caac109dfa85be2b0fa630fa249b28cf603e86f152c47835020ff1f5f0d12b7cbbff8758c08248522a7d2b1188812ec99722 WHIRLPOOL 34e8d0ed72614c2c89768c66bc51d53984901d4f62aaf134e9429a7f951d6f31aacbc837a069e4eb2161d7ac20e68797b8abdfec85ac46623b434ee0c337f460 diff --git a/sci-chemistry/p3d/metadata.xml b/sci-chemistry/p3d/metadata.xml new file mode 100644 index 000000000000..bd505aa96a4e --- /dev/null +++ b/sci-chemistry/p3d/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +p3d was developed in order to offer a Python module that is powerful and fast, +yet intuitive to use. The simplicity of p3d is due to the usage of object +oriented programming (i.e. atoms are treated as vectors), the implementation +of a query parser that translates queries readable by humans into a combination +of algebra set operations the fact that no additional Python packages are +necessary. The speed is due to the usage of a binary space partitioning (BSP) +tree which allows very fast queries in 3D (Henry et al. 1980). The additional +synergy is obtained by the flexible combination of both speed and complexity in +the queries to the structural data. The combination of these factors makes p3d +the optimal module to rapidly develop new and powerful bioinformatic tools that +follow the Python philosophy of making the source code readable. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/p3d/p3d-0.4.3-r1.ebuild b/sci-chemistry/p3d/p3d-0.4.3-r1.ebuild new file mode 100644 index 000000000000..04d5f49cf7b2 --- /dev/null +++ b/sci-chemistry/p3d/p3d-0.4.3-r1.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 vcs-snapshot versionator + +MY_P="${PN}-$(replace_version_separator 3 -)" +GITHUB_ID="gb8b9a75" + +DESCRIPTION="Python module for structural bioinformatics" +HOMEPAGE="http://p3d.fufezan.net/" +SRC_URI="https://nodeload.github.com/fu/${PN}/tarball/${PV} -> ${P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-3" +IUSE="examples" + +src_install() { + distutils-r1_src_install + + if use examples; then + insinto /usr/share/${PN} + doins -r pdbs exampleScripts + fi +} diff --git a/sci-chemistry/p3d/p3d-9999.ebuild b/sci-chemistry/p3d/p3d-9999.ebuild new file mode 100644 index 000000000000..f5eb1e8c1b42 --- /dev/null +++ b/sci-chemistry/p3d/p3d-9999.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 git-r3 versionator + +DESCRIPTION="Python module for structural bioinformatics" +HOMEPAGE="http://p3d.fufezan.net/" +SRC_URI="" +EGIT_REPO_URI="https://github.com/fu/p3d.git" + +SLOT="0" +KEYWORDS="" +LICENSE="GPL-3" +IUSE="examples" + +src_install() { + distutils-r1_src_install + + if use examples; then + insinto /usr/share/${PN} + doins -r pdbs exampleScripts || die + fi +} diff --git a/sci-chemistry/parassign/Manifest b/sci-chemistry/parassign/Manifest new file mode 100644 index 000000000000..94dee25bb160 --- /dev/null +++ b/sci-chemistry/parassign/Manifest @@ -0,0 +1,5 @@ +DIST PARAssign_Linux_x64_86.tgz 76693208 SHA256 56a322a8825c13cd3e7d90998471c47fb6062e79e2d20108b4fb6ed24664c89d SHA512 63018b0f1e3ce7821cebb90cd59ef5fdfa44b7ce6776956184b55a6247009f5e9df435332772dfa0db7294308c4d930ff0104daf45a46df709fb132dac10bd79 WHIRLPOOL 87ae85974f2a84c3814d261390e011f7ef2a012881df15f0f8ba4a7b5e88992e7932f12566847eaa38958394f7a243a4f0d536375e4640377d6f183e793bccc5 +EBUILD parassign-20130522.ebuild 1375 SHA256 8ba3200b371f0f2141a2e1788b5fe978b6f3f27d95c15b77dec75d330f6ad5c1 SHA512 7634d41463024be7606e63cd6fda1a9645c5fea48922232e1b404fe486416e89a454ea63220772ba75a327cf4c03140beef332f857c3a283063cd4687abadd46 WHIRLPOOL 552338a64f5cd36be567776b526e47a1a7fcbdd5311d6f16093c6a4df677046fc8c24bf5727e2ae0fe495b0e5b94ef488ca86461dfc2314c9460d2807a3eda47 +MISC ChangeLog 2932 SHA256 d0e349b0bda85091938cb845231989794f49603a5e7e857593cd6d010066df22 SHA512 065c8ce78bc6213d5a75803ddc9fbf1b511d4bcf06ef02ca055d93e3f34fdaafdfea55b418be6a35c6d83d081e6898f849960f4eb21bdcc61a43eff824b61ad4 WHIRLPOOL 1c4e9a6f969e55612331750dc0badddae00e0c95df8f5f0af48134b5563a51db253b3fbdfb3268ee90d30cedd15c981c36256ae2ea66bfbf9bc80085af84ea9d +MISC ChangeLog-2015 710 SHA256 6120da15577d59fc164364e020f944e51c230c3f09d900ba49cfc6c4518de06a SHA512 3c8bfb6d578c3e2c12662e5f5a21432712016a2acbba7ad1c30dbf05d15d3d17f4416bf573d81a60b8106bafe2230beb37db0c9c52a294a4614403bb552fe038 WHIRLPOOL dd4794621e710997f9ee6617fd84b6a79f0afabcc76934ce9181882cbf94e3ad3d3961f16372886c01e79a80b6a1dee05b2c08cf49d64436e6a09360455d6dba +MISC metadata.xml 1646 SHA256 4164a2b198ae08c9bd405ee3a0e09283a0462dcbd8cb8c464924a3a5a2175013 SHA512 73b07789bffc4fb45c5c3ca5c6b3e7fc75e358fc8a73b2cc2d76e8faf5bc1f2765fb1dcbdb2dcc34a21123d3f99bd8fc61ec3ca4a10e6887f26863b93fc1db1f WHIRLPOOL 32ece752cc3205c5b79045fff756ab926bbbe26a06c05722d2c60554e1d1856f9c2f4cc894292905bd276c17f9bf4e5a5c8af271ce2e88b79c9ec2c9597dc28d diff --git a/sci-chemistry/parassign/metadata.xml b/sci-chemistry/parassign/metadata.xml new file mode 100644 index 000000000000..f230593f73e9 --- /dev/null +++ b/sci-chemistry/parassign/metadata.xml @@ -0,0 +1,27 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +The use of paramagnetic NMR data for the refinement of structures of proteins +and protein complexes is widespread. However, the power of paramagnetism for +protein assignment has not yet been fully exploited. PARAssign is software that +uses pseudocontact shift data derived from several paramagnetic centers attached +to the protein to obtain amide and methyl assignments. The ability of PARAssign +to perform assignment when the positions of the paramagnetic centers are known +and unknown is demonstrated. PARAssign has been tested using synthetic data for +methyl assignment of a 47 kDa protein, and using both synthetic and experimental +data for amide assignment of a 14 kDa protein. The complex fitting space +involved in such an assignment procedure necessitates that good starting +conditions are found, both regarding placement and strength of paramagnetic +centers. These starting conditions are obtained through automated tensor +placement and user-defined tensor parameters. The results presented herein +demonstrate that PARAssign is able to successfully perform resonance assignment +in large systems with a high degree of reliability. This software provides a +method for obtaining the assignments of large systems, which may previously have +been unassignable, by using 2D NMR spectral data and a known protein structure. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/parassign/parassign-20130522.ebuild b/sci-chemistry/parassign/parassign-20130522.ebuild new file mode 100644 index 000000000000..c49d09b2ab0a --- /dev/null +++ b/sci-chemistry/parassign/parassign-20130522.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 python-r1 + +DESCRIPTION="Assign protein nuclei solely on the basis of pseudocontact shifts (PCS)" +HOMEPAGE="http://protchem.lic.leidenuniv.nl/software/parassign/registration" +SRC_URI="PARAssign_Linux_x64_86.tgz" +RESTRICT="fetch" + +SLOT="0" +LICENSE="Apache-2.0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS}" +DEPEND="${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/scientificpython[${PYTHON_USEDEP}] + sci-biology/biopython[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}]" + +S="${WORKDIR}"/PARAssign_Linux_x64_86/ + +src_prepare() { + sed \ + -e '1i#!/usr/bin/python2' \ + -i code/*py || die + + if use x86; then + sed \ + -e "s:munkres64:munkres:g" \ + -i modules/setup.py || die + elif use amd64; then + sed \ + -e "s:munkres:munkres64:g" \ + -i code/*py || die + fi + cd modules || die + rm *o *c || die + distutils-r1_src_prepare +} + +src_compile() { + cd modules || die + distutils-r1_src_compile +} + +src_install() { + python_foreach_impl python_doscript code/* || die + + dodoc PARAssign_Tutorial.pdf README + + cd modules || die + distutils-r1_src_install +} diff --git a/sci-chemistry/pdb-tools/Manifest b/sci-chemistry/pdb-tools/Manifest new file mode 100644 index 000000000000..5aeed090a90e --- /dev/null +++ b/sci-chemistry/pdb-tools/Manifest @@ -0,0 +1,6 @@ +DIST pdbTools_0.2.1.tar.gz 103835 SHA256 317a5246e806a2b3d0425d080d679646fc77388e3e855412527603f945fa37ae SHA512 9c43c10e8739f8a34dbb1a3bba710cc727f7d8392ff979681371bd4460c67203253fb01852438eb93b214c4a009789608d200ca551f30399652fb76d702cf724 WHIRLPOOL 36d8cf71ba9f9b28e3ad59828539f4e94bbb8bc4514f050ddcbec63857b154ecdc7c32c2945c0d15f4d718c4fe5ab3adcb2e62a4368bfd819b80e9641a9dfd88 +EBUILD pdb-tools-0.2.1-r1.ebuild 1675 SHA256 435fb08c68c9c04fd62d0c0cdd926fc2d7ced72df71cdf85d53abdb167c63202 SHA512 f356c319d545920d550bdee48fd84ceebc7ad022d3dc58c28c79060da2aeb953c87328b3faeb08b6b8c4973ee9dd2b97a42a857ef51b1b4949b91a5333f9d147 WHIRLPOOL 46939042237121eba404f029f92cce7dcf28776e79b7cfce7636846bb95e6be8873710b28a83284c003a9ea2230b45604efaf901925206a48d5c3398b71bdb74 +EBUILD pdb-tools-0.2.1-r2.ebuild 1740 SHA256 106af905d17dbb6449279519913ea60667e46f70e4f67363ee6febcab8f494ce SHA512 06ce18d1f7aaa9b2e4e1f8c29fa7e187737af741ee53570a65b41b28c9bdb3ba23e8cda4b37d70fb169eed84829ebf425c22193bef587dbc87dbbdfec2a8f30b WHIRLPOOL c2306ed61a9c8ffabe0360c00533c2a66a28ac6ec7bce7a2f8ae6600a82d2a0b1a02fbf0669ed110acdf506b432ae21fb164094349073ce0376b73c5fc7ebded +MISC ChangeLog 3379 SHA256 43a935f6490ec1e126bb9ec2e611971bd7752059c512b563a0491cda1f24687f SHA512 7b03f3807c361f84aca9a0788cbd59057991a7598b525e72522f3e3a0fd9efaab5bec335211a9733f302e93d1392fbe9f6088dbd3276063431871b2d0a092da7 WHIRLPOOL fc3ee4b9d62c2e21d7b8fc02b0148d424e0e1b55fd4813b2e1cabe3aef9e96f73b105789a5880ed3e418fd3d7fb5b7ccc296944aa41b208587efeed940e84805 +MISC ChangeLog-2015 3211 SHA256 286ecae6758c4a581103511115c76269aa93dc0cf75581e3c3cd68a880286ace SHA512 3152a37dd8ed05293941c2a01bb40f02988222706871b0459f2aea3de8c45607350553137839f3c2559ec5ad62a5aa0510deb79498751b515ec9614a9d2ba6cc WHIRLPOOL 8f98eaecbdc391768e2f98ea8e3c626cbae8fb6eb2fe3ec12f800c4297ff0e0ab738b522762bab0bf3bce8b504d90ed8bedb14f17878b2441f7fe291bf0bc08d +MISC metadata.xml 413 SHA256 bc95368bb1cf8894d12449e7b03caa3ac05f7a8fd661343a643a96c2229a8b37 SHA512 74abf290517514aa17fadf8271d2af124fef766b473199502959a662d3bf7a8fed59746b43b3084b83bc14f8d5b9048b419f59d901dec100cbdd81975864cce2 WHIRLPOOL 1983ce37297a5d9bb911c0f1c598a03d03e770746a276e0095de84134cd76434f04dd74f8bf9dfa9038671f92ed5bae7724122a772d77ea59d27fa34f9a77891 diff --git a/sci-chemistry/pdb-tools/metadata.xml b/sci-chemistry/pdb-tools/metadata.xml new file mode 100644 index 000000000000..25095bc4b42e --- /dev/null +++ b/sci-chemistry/pdb-tools/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="google-code">pdb-tools</remote-id> + <remote-id type="github">harmslab/pdbtools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild new file mode 100644 index 000000000000..88c1f246e8a2 --- /dev/null +++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild @@ -0,0 +1,79 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 pypy ) + +inherit fortran-2 python-single-r1 toolchain-funcs + +MY_PN="pdbTools" + +DESCRIPTION="Tools for manipulating and doing calculations on wwPDB macromolecule structure files" +HOMEPAGE="https://github.com/harmslab/pdbtools" +SRC_URI="https://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS}" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${MY_PN}_${PV} + +pkg_setup() { + python-single-r1_pkg_setup + fortran-2_pkg_setup +} + +src_prepare() { + sed \ + -e "s:script_dir,\"pdb_data\":\"${EPREFIX}/usr/share/${PN}\",\"pdb_data\":g" \ + -i pdb_sasa.py || die + sed \ + -e "/satk_path =/s:^.*$:satk_path = \"${EPREFIX}/usr/bin\":g" \ + -i pdb_satk.py || die + sed \ + -e 's:> %:>%:g' \ + -i pdb_seq.py || die +} + +src_compile() { + mkdir bin + cd satk + for i in *.f; do + einfo "$(tc-getFC) ${FFLAGS} ${LDFLAGS} ${i} -o ${i/.f}" + $(tc-getFC) ${FFLAGS} -c ${i} -o ${i/.f/.o} || die + $(tc-getFC) ${LDFLAGS} -o ../bin/${i/.f} ${i/.f/.o} || die + sed \ + -e "s:${i/.f}.out:${i/.f}:g" \ + -i ../pdb_satk.py || die + done +} + +src_install() { + local script + insinto /usr/share/${PN} + doins -r pdb_data/peptides + rm -rf pdb_data/peptides || die + + python_domodule helper pdb_data + + python_moduleinto ${PN/-/_} + python_domodule *.py + + for i in pdb_*.py; do + cat > ${i/.py} <<- EOF + #!${EPREFIX}/bin/bash + ${PYTHON} -O "$(python_get_sitedir)/${PN/-/_}/${i}" \$@ + EOF + dobin ${i/.py} + done + + dobin bin/* + dodoc README +} diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild new file mode 100644 index 000000000000..35910807746f --- /dev/null +++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit fortran-2 python-single-r1 toolchain-funcs + +MY_PN="pdbTools" + +DESCRIPTION="Tools for manipulating and doing calculations on wwPDB macromolecule structure files" +HOMEPAGE="https://github.com/harmslab/pdbtools" +SRC_URI="https://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS}" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${MY_PN}_${PV} + +pkg_setup() { + python-single-r1_pkg_setup + fortran-2_pkg_setup +} + +src_prepare() { + sed \ + -e "s:script_dir,\"pdb_data\":\"${EPREFIX}/usr/share/${PN}\",\"pdb_data\":g" \ + -i pdb_sasa.py || die + sed \ + -e "/satk_path =/s:^.*$:satk_path = \"${EPREFIX}/usr/bin\":g" \ + -i pdb_satk.py || die + sed \ + -e 's:> %:>%:g' \ + -i pdb_seq.py || die + + sed \ + -e "/import/s:helper:${PN/-/_}.helper:g" \ + -i *.py || die +} + +src_compile() { + mkdir bin + cd satk + for i in *.f; do + einfo "$(tc-getFC) ${FFLAGS} ${LDFLAGS} ${i} -o ${i/.f}" + $(tc-getFC) ${FFLAGS} -c ${i} -o ${i/.f/.o} || die + $(tc-getFC) ${LDFLAGS} -o ../bin/${i/.f} ${i/.f/.o} || die + sed \ + -e "s:${i/.f}.out:${i/.f}:g" \ + -i ../pdb_satk.py || die + done +} + +src_install() { + local script + insinto /usr/share/${PN} + doins -r pdb_data/peptides + rm -rf pdb_data/peptides || die + + python_domodule pdb_data + + python_moduleinto ${PN/-/_} + python_domodule helper *.py + + for i in pdb_*.py; do + cat > ${i/.py} <<- EOF + #!${EPREFIX}/bin/bash + ${PYTHON} -O "$(python_get_sitedir)/${PN/-/_}/${i}" \$@ + EOF + dobin ${i/.py} + done + + dobin bin/* + dodoc README +} diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest new file mode 100644 index 000000000000..afca6d9fee2d --- /dev/null +++ b/sci-chemistry/pdb2pqr/Manifest @@ -0,0 +1,9 @@ +AUX pdb2pka 270 SHA256 ae1112d6b793b10399a4ae14dc5cfd0518c463121d98e00ab08b2827db061303 SHA512 c6e66fa73a3119ea84a9bf304c9c8701a6eaf32870ba8c1755bfd8f2055e20af2f2ebc01fd2bf6a663e5873f3d6da7387a439efac3dcb7d4a415c176cb2f761b WHIRLPOOL ef5d1fac1bacd6403219e36955701b2a2d33a2aa9936b2334ed7ea48346b1cae74481bb634ba67f9250e7bac73723ce2e4da6c759b87c57111fad166624f0b82 +AUX pdb2pqr 263 SHA256 f07b197ec4903125e9566b394ed6a620f56511413bf14ba5fdd3484302d166e2 SHA512 5f8c963fc5addf782579b9312f601ec4547573c7ab88df5a6e38c71c9e31e7b7eea3cde99bdac8f8270f3646d933a0b510a94046e3a30736f75953af5d160b8d WHIRLPOOL 8e4889677ec874a88f3d485b133d3e92a3618d0ed90f4199d05add55f1819df94be762d3950ef9bd21db1112fa75adf26f909d04fdc57c4686cccb3244687fd2 +AUX pdb2pqr-1.9.0-flags.patch 1392 SHA256 478b86cf3871e39b9d231a10474abbcade07eceb32db2a83c0e68bbd2c1f5f32 SHA512 deed0aef88dc43515745204f2b4209bd6b42702d9004d48797d642b8f497229424bd0bb92017982cec54c448ea35de563bd42017cd5dc042840acae8495d135b WHIRLPOOL 7280c677dbfeb309c6c66d495c857a581fbac80801f9241c20ff17a2c6f4e051929f675807ec30f8dce1fd5337937c76e857b955570f2c1f134855a2b7c0ec2c +AUX pdb2pqr-1.9.0-install-py.patch 578 SHA256 c82c11eb421a839710d40bfb3de4d99852ef69dc9b35b1ac31f7b51b36ff512d SHA512 902ad717e32790e9c691851dc4b92412f07ac79caf74b2b5794a10fa75cca7fa19e8814df4d8ba71bd2ecc98a3d777d0b79e6e43009171a32e8c99756d81d4d2 WHIRLPOOL 94348fe88a1910e916ca0d428a78636e5fe8371582a80dbbbda07d433d1fb8a35157a73d525eac88bd9dac6dc1c3a913288fdb7bd06f7584553b0b5c17aa17da +DIST pdb2pqr-src-1.9.0.tar.gz 9051969 SHA256 d9d91bf27a023732be33d1d780ef283ae28d3b0e256c53e86c37ac001dd7ef53 SHA512 7f3f191cca9879a0e166e82700c706f8c99bb66558a218e54845f10c3324b6c45d413da80b0782d96a8d56df1463262609db075aba3768db3942cb928ee7b98f WHIRLPOOL 4a4b883200dad3e7467392e508c2372ad6876e78005da14e5747f3b7b12d0e3d5695e3cc590812b835ae67703819b201620809dff05af0a7c363c23d22046bae +EBUILD pdb2pqr-1.9.0-r1.ebuild 2911 SHA256 cf72fe67cd6beb7ca8ed88eaf06b5aceac4d325436b91e14f80be762273c4e0a SHA512 88d06dee9fcb6423a2cae4fbb8e1e175ef6b8b45bb371b556b2fd15314d2d11c5ec9ffec294f8fb814f03f2f1dfb37d92574361b9a8aa89c9c42c483a5dd79d8 WHIRLPOOL dd2c3bfc02521198a1c2bebfbd9c412b710fb2e7dde1f47f9870588ad540adf949b79fa51ce3e8c9da6688c639f9f87313fff9b04581797086b0ab7202b0dad5 +MISC ChangeLog 2547 SHA256 4328c0ec1b00310f457a27f7a68745f3b238bfdb2efee23abf23263c4a6e7149 SHA512 cbf16398e70334c83b038ce306d4c34ec3759fcf5bb676a788aa8a0c4635da9eec0967614a2157e97789553d0a2baa0914f74856548e6e7ac0a1a95b09530c07 WHIRLPOOL 79f6f4e5ae532b7a027fd3f2cbc80116b5880f33b06f8e8d9fde6efb12ee797fcdeb27f14b5bc72adb42b6490fbe0a2e9001f4a37fe35448d323df675d509aa6 +MISC ChangeLog-2015 8157 SHA256 c05694b5d9f6956e9beb4ef67234f8f8807c0f707696deafcd58dffbb48ec23c SHA512 515f7a96bd3a1b80b11f46d20d3865c5aab7975ff0c8c77266dbf26b5e54dc0718fc006a6d733bbd4f1946e6975df9dfd98232e6393bf38b7891392f57ffc4aa WHIRLPOOL 660a27a3c807e7a445e54ebba830cb0c84b1ab6d5ae9c20d7a9dafcea45af8f343cd608a4103f560a061cd7081b9b76a50cd0a4cfdd9c4be1b22333c341aaa09 +MISC metadata.xml 511 SHA256 c9214899d35b2713d0c9c36519ec66e3ac944aec2e7c0f464a90eb1aeba65829 SHA512 11a010eea3bbbaaf4150a23dadcd10c45737745d51a3341cd7e69cc8537215f313d1ab57059eff265e73e34aeaef435585bb652f5497508dd12b99f67b8580c0 WHIRLPOOL cbf77bc71337cce17e27394685b4e0b7e46156771da61ff48976d4e8e524a57362184c781b82cf6795a15874030869e8a590f9ce2196083232c277a4cfab7ced diff --git a/sci-chemistry/pdb2pqr/files/pdb2pka b/sci-chemistry/pdb2pqr/files/pdb2pka new file mode 100644 index 000000000000..2406b0c4773f --- /dev/null +++ b/sci-chemistry/pdb2pqr/files/pdb2pka @@ -0,0 +1,13 @@ +#!/usr/bin/env python + +import subprocess +import site +import sys +import os + +sitepackages = site.getsitepackages()[0] + +_cmd=[os.path.join(sitepackages, "pdb2pqr", "pdb2pka", "pka.py")] +_cmd.extend(sys.argv[1:]) + +subprocess.call(_cmd, stdout=sys.stdout, stderr=sys.stderr) diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr b/sci-chemistry/pdb2pqr/files/pdb2pqr new file mode 100644 index 000000000000..8c0635aea94e --- /dev/null +++ b/sci-chemistry/pdb2pqr/files/pdb2pqr @@ -0,0 +1,13 @@ +#!/usr/bin/env python + +import subprocess +import site +import sys +import os + +sitepackages = site.getsitepackages()[0] + +_cmd=[os.path.join(sitepackages, "pdb2pqr", "pdb2pqr.py")] +_cmd.extend(sys.argv[1:]) + +subprocess.call(_cmd, stdout=sys.stdout, stderr=sys.stderr) diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch new file mode 100644 index 000000000000..fac32b233e6b --- /dev/null +++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch @@ -0,0 +1,45 @@ + pdb2pka/SConscript | 9 ++++++++- + pdb2pka/substruct/SConscript | 6 ++++++ + 2 files changed, 14 insertions(+), 1 deletion(-) + +diff --git a/pdb2pka/SConscript b/pdb2pka/SConscript +index 583cdc5..6c30011 100644 +--- a/pdb2pka/SConscript ++++ b/pdb2pka/SConscript +@@ -1,4 +1,11 @@ + Import('env')
++import os
++
++env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())
++env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())
++env['CXX'] = os.environ['CXX']
++env['LINK'] = os.environ['CXX']
++
+
+ if env['REBUILD_SWIG']:
+ pyc = env.LoadableModule('_pMC_mult', ['pMC_mult.cpp', 'pMC_mult.i'])
+@@ -9,4 +16,4 @@ Default(pyc) +
+ algorithms_module = SConscript('substruct/SConscript')
+
+-Return('pyc algorithms_module') +\ No newline at end of file ++Return('pyc algorithms_module')
+diff --git a/pdb2pka/substruct/SConscript b/pdb2pka/substruct/SConscript +index 7dbcdb0..56fb577 100644 +--- a/pdb2pka/substruct/SConscript ++++ b/pdb2pka/substruct/SConscript +@@ -1,7 +1,13 @@ + import distutils
+ import numpy
++import os
+ Import('env')
+
++env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())
++env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())
++env['CXX'] = os.environ['CXX']
++env['LINK'] = os.environ['CXX']
++
+ env.Append(CPPPATH=[distutils.sysconfig.get_python_inc(), numpy.get_include()])
+
+ algorithms_pyc = env.LoadableModule('Algorithms', ['Algorithms.cpp'])
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch new file mode 100644 index 000000000000..2695b013c66a --- /dev/null +++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch @@ -0,0 +1,15 @@ + SConscript-install.py | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/SConscript-install.py b/SConscript-install.py +index e2f9f09..1fdf1a8 100644 +--- a/SConscript-install.py ++++ b/SConscript-install.py +@@ -41,6 +41,7 @@ def installFile(file_name, build_target='install'): + if GetOption("clean"):
+ env.Default(result)
+ Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), result))
++ Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), target))
+ else:
+ Alias(build_target, env.Install(env['PREFIX']+dirname(file_name), target))
+
diff --git a/sci-chemistry/pdb2pqr/metadata.xml b/sci-chemistry/pdb2pqr/metadata.xml new file mode 100644 index 000000000000..36fd8c04ac52 --- /dev/null +++ b/sci-chemistry/pdb2pqr/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="opal">Add web interface via opal</flag> + <flag name="pdb2pka">Install experimental pdb2pka interface</flag> + </use> + <upstream> + <remote-id type="github">Electrostatics/apbs-pdb2pqr</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild new file mode 100644 index 000000000000..8b58ae48c5c7 --- /dev/null +++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r1.ebuild @@ -0,0 +1,129 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit scons-utils fortran-2 flag-o-matic python-r1 toolchain-funcs + +DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations" +HOMEPAGE="http://www.poissonboltzmann.org/" +SRC_URI="https://github.com/Electrostatics/apbs-${PN}/releases/download/${P}/${PN}-src-${PV}.tar.gz" + +SLOT="0" +LICENSE="BSD" +IUSE="doc examples opal +pdb2pka" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + dev-python/numpy[${PYTHON_USEDEP}] + sci-chemistry/openbabel-python[${PYTHON_USEDEP}] + opal? ( dev-python/zsi[${PYTHON_USEDEP}] ) + pdb2pka? ( sci-chemistry/apbs[${PYTHON_USEDEP},-mpi] )" +DEPEND="${RDEPEND} + dev-lang/swig:0" + +PATCHES=( + "${FILESDIR}"/${P}-flags.patch + "${FILESDIR}"/${P}-install-py.patch +) + +pkg_setup() { + if [[ -z ${MAXATOMS} ]]; then + einfo "If you like to have support for more then 10000 atoms," + einfo "export MAXATOMS=\"your value\"" + export MAXATOMS=10000 + else + einfo "Allow usage of ${MAXATOMS} during calculations" + fi + fortran-2_pkg_setup +} + +src_prepare() { + find -type f \( -name "*\.pyc" -o -name "*\.pyo" \) -delete || die + + export CXXFLAGS="${CXXFLAGS}" + export LDFLAGS="${LDFLAGS}" + + epatch "${PATCHES[@]}" + tc-export CXX + rm -rf scons || die + + python_copy_sources +} + +src_configure() { + python_configure() { + cd "${BUILD_DIR}" || die + + cat > build_config.py <<- EOF + PREFIX="${D}/$(python_get_sitedir)/${PN}" + #URL="http://<COMPUTER NAME>/pdb2pqr/" + APBS="${EPREFIX}/usr/bin/apbs" + #OPAL="http://nbcr-222.ucsd.edu/opal2/services/pdb2pqr_1.8" + #APBS_OPAL="http://nbcr-222.ucsd.edu/opal2/services/apbs_1.3" + MAX_ATOMS=${MAXATOMS} + BUILD_PDB2PKA=$(usex pdb2pka True False) + REBUILD_SWIG=True + EOF + } + + python_foreach_impl python_configure +} + +src_compile() { + python_compile() { + cd "${BUILD_DIR}" || die + escons + } + python_foreach_impl python_compile +} + +src_test() { + python_test() { + local myesconsargs=( -j1 ) + cd "${BUILD_DIR}" || die + escons test + escons advtest + escons complete-test + } + python_foreach_impl python_test +} + +src_install() { + dodir /usr/share/doc/${PF}/html + python_install() { + local lib + + cd "${BUILD_DIR}" || die + + escons install + + find "${D}$(python_get_sitedir)"/${PN}/{jmol,examples,doc,contrib} -delete || die + + python_doscript "${FILESDIR}"/{${PN},pdb2pka} + + for lib in apbslib.py{,c,o}; do + dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib} + done + dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so + python_optimize + } + python_foreach_impl python_install + + if use doc; then + pushd doc > /dev/null + docinto html + dodoc -r *.html images pydoc + popd > /dev/null + fi + + use examples && \ + insinto /usr/share/${PN}/ && \ + doins -r examples + + dodoc *md NEWS +} diff --git a/sci-chemistry/pdbcat/Manifest b/sci-chemistry/pdbcat/Manifest new file mode 100644 index 000000000000..a6b8d7f1e3bf --- /dev/null +++ b/sci-chemistry/pdbcat/Manifest @@ -0,0 +1,7 @@ +AUX CMakeLists.txt 172 SHA256 f91b445bce562b3de8e82d593ad54960ed58e1c99bb3f9d908c159dcc4615894 SHA512 c8aa60098be10a25dcebf4c764e30f886f39a7d95da228d9d7fdcdedf3124ace32307197bbb2901b89ee3a8ce78411e61a4147eb395add65df6583683d3d5277 WHIRLPOOL 0345309440453b6827740e32f0e7f63b343caadfa8cf8b72214cc8a7d1d2584800d225e0b1eab34321a0062a890da8cdfae1d0e543db5f7e05ed2d9ff2e061e6 +AUX pdbcat-1.3-gcc.patch 423 SHA256 c42a7d4eaaa13c8bf253a786dc2ea5a1fb186c22c3684ab48ca36f8cf5e65347 SHA512 0a4b85ad2a4ec8014829e0c1449aecc90d65b57c4d0062ecd537991219c58c75dce138d901718a790c014d240afa9a063d46db5625d1e1c50727f1b1e468b032 WHIRLPOOL 1a33d959108dae3be74a1e6f518db55c723d504d7c64b0986e657db11f6f3882f3d97f0ab67f95115073fcb11c956890612eb83246f6ee91bcb1e1f6817c799d +DIST pdbcat-1.3.tar.gz 12750 SHA256 a9c554c00b34e5131ca1be61aad9332ab26eca5a905b716c47f657521368babc SHA512 369ac0c4c1d8396eaa0450feb9852d2d75ebd9862a2e403ccd42a2801e924f99c28c5d71c0b66feb4588076a8948b503823d2c75420128dd04d020253f821f4c WHIRLPOOL ba6599d06814929bf23c83bb6df7084592fcc23603a8e3116e2661df3c9d97b335c627d09249be6c862466b2d83a0100d94b366df171e1c45ec6221a22b2ca78 +EBUILD pdbcat-1.3.ebuild 590 SHA256 afb4c1dc066e0ad2fd557791a5b2a8a7ee8e639e997d9eefc141e7ba194c6802 SHA512 d9a9734e6df0dd3773fab52b617a1dd6dff2aeaf3110903ba3af5d11644db1b14013371ba020bdae412c311648f72f955c358bd995c2ef2df659984ab6090077 WHIRLPOOL 43c3c260224f7e1af6385998bd113778c1ab19086c8e6a8575f404c7f38a16860736c760998452b0fa6778a3b3c65afb47b0ca01561c2d77ba91014ff2e00c6d +MISC ChangeLog 2617 SHA256 bbbb971674500ca74e1f1626cff6f995d2dd6634ad776ee2a75dd44f06b143d4 SHA512 2cba87f9a17a513d8b6f32666213c4072f1f010bad9cefe2dcad62327c5b4becd848c2636b1c7fc47095fbf9425999b096f0ae4327edaef735b1bf5796700487 WHIRLPOOL 7395c37ff369c633b045733a813cc190fb174fa604517af3e8131e3d63353a8a53733e41cf650528222d8298f960ac7e392e1a5408d21f7e265aac117babad6c +MISC ChangeLog-2015 651 SHA256 bccc631d4b77cd3c16f37c16f8389e7e283a5dc6847ed15142e0cc1e0faba922 SHA512 4e16b089ec80c7a6ae10865b412bafa7fda7b1b9468207c0086d06cd5e033d7bfda2329222ee29866591610f28b0f1a78d91b0c1dde40bd08d93c59608c3e44b WHIRLPOOL 00b1a861274324a9614d21298eca6cef5dacaf3af35bd12beb07ba03973685377d1ce2393613b6877ae794ae7053bbde072baa4d655c6d618c3ea36bfe30a0ae +MISC metadata.xml 1145 SHA256 e0b0ff0a906bf4609dcfa891c5c6a1ec169d4100b0e19db7ee96b1d23877d6dc SHA512 4f4711173cdae81767ed2519c158fba751764b62f936d91a53ec0f275b6a52a9fc72c4dc4f6fa942376d81e741952c2e5c777465d520f2158b0bb125ba1b7ff0 WHIRLPOOL d0fb929e83d86689a47ee3410d23374296bc89118c557da37b8f4b633fd1c46fb4f20c9aa68964ed4d1ec783582d946c7702835e9ffbdc9b799827d8e937ae28 diff --git a/sci-chemistry/pdbcat/files/CMakeLists.txt b/sci-chemistry/pdbcat/files/CMakeLists.txt new file mode 100644 index 000000000000..7a6f348f5929 --- /dev/null +++ b/sci-chemistry/pdbcat/files/CMakeLists.txt @@ -0,0 +1,11 @@ +cmake_minimum_required (VERSION 2.6) +project (pdbcat) +add_executable(pdbcat + Common.C + Common.h + pdbcat.C + PDBData.C + PDBData.h) + +install (TARGETS pdbcat DESTINATION bin) + diff --git a/sci-chemistry/pdbcat/files/pdbcat-1.3-gcc.patch b/sci-chemistry/pdbcat/files/pdbcat-1.3-gcc.patch new file mode 100644 index 000000000000..b45c36bd8a8d --- /dev/null +++ b/sci-chemistry/pdbcat/files/pdbcat-1.3-gcc.patch @@ -0,0 +1,17 @@ + pdbcat.C | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +diff --git a/pdbcat.C b/pdbcat.C +index 0786d9b..387edf9 100644 +--- a/pdbcat.C ++++ b/pdbcat.C +@@ -17,7 +17,8 @@ + #include <stdlib.h> // for exit + #include <stdio.h> // for feof() and other file manip stuff + #include <string.h> // for strcasecmp +-#include <iostream.h> ++#include <iostream> ++using namespace std; + #include "Common.h" + #include "PDBData.h" + diff --git a/sci-chemistry/pdbcat/metadata.xml b/sci-chemistry/pdbcat/metadata.xml new file mode 100644 index 000000000000..29177ef0643c --- /dev/null +++ b/sci-chemistry/pdbcat/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +The Brookhaven Protein Data Bank stores atomic coordinate information +for protein structures in a column based format. This is designed to +be read easily read by FORTRAN programs. Indeed, if you get the +format description (from anonymous ftp to ftp.pdb.bnl.gov, the file +/pub/format.desc.ps) they show the single input line needed to read +each record type. +However, I am a C/C++ programmer in the Unix environment. It is a +easier for me to deal with field based input than column based ones. +If the fields are white space delimited I can easily use awk and perl +to manipulate the coordinate information. So I needed some way to +convert the ATOM and HETATM records of PDB files from the standard +column based format to a field based one and back again. It needed +to denote missing fields if they exist. +That converter is `pdbcat'. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/pdbcat/pdbcat-1.3.ebuild b/sci-chemistry/pdbcat/pdbcat-1.3.ebuild new file mode 100644 index 000000000000..ccdbd9928160 --- /dev/null +++ b/sci-chemistry/pdbcat/pdbcat-1.3.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils + +DESCRIPTION="Manipulate and process PDB files using tools such as Perl, awk, etc" +HOMEPAGE="http://www.ks.uiuc.edu/Development/MDTools/pdbcat/" +SRC_URI="http://www.ks.uiuc.edu/Development/MDTools/${PN}/files/${P}.tar.gz" + +LICENSE="free-noncomm" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +PATCHES=( "${FILESDIR}"/${P}-gcc.patch ) +DOCS=( README ) + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + cmake-utils_src_prepare +} diff --git a/sci-chemistry/pdbcns/Manifest b/sci-chemistry/pdbcns/Manifest new file mode 100644 index 000000000000..037e72990c61 --- /dev/null +++ b/sci-chemistry/pdbcns/Manifest @@ -0,0 +1,5 @@ +DIST pdbcns.2.0.010504.perl.tgz 6806 SHA256 a2c66e44e036b6a1ff2eff90b59c4adf20edb70d3f704bd7bc7f356040d8f98a SHA512 5174cb51dbe3ead405fa1005d81a7ee063bf4be4268b0e728f1ca0aa3e6cbc005fb0bac3e21e06f872c6f4d42c23f50b6e6130391e3b825260c890070e6f766b WHIRLPOOL b3749fadfe274bcdfca5e18a4f9044ebb8804f2a26e3ebaa22d813c37433c6eefc614a5740744296b1c3b549e3cc39dd8c73772da1a84b010556f8a36a465c39 +EBUILD pdbcns-2.0.010504.ebuild 683 SHA256 179de68129b0be088eaabb581c5fd1382d510ee96d8ecaf799b7bbf9908a77cd SHA512 e0db8eaa8405403e4b41e1501706a8ccbea5a3b28f6a421ff8daa6e4dadbfc6fc8c86f4646b322a31e4865f1d49f31bd1d387a8c812de51d977fe9a1bf20ef7c WHIRLPOOL 4825352751cf333ce6b078b4ab50a705a8425a34d613d37a731608f26b485efb0e35424d3cb406c002337dfdb96ca88c5f460bfa41467c0163edb8ef004db563 +MISC ChangeLog 2607 SHA256 369d2ca770a91024519d0c57134e73264fac22fe4aa240cd5d68c7070048d743 SHA512 8fc3e1f591475329c6d132254bb5de1effa9365d240e79932d0fd45c15211a9af47501e819491c42bcbda426ca59ec078a3a8316b96e3559b7b62eed295d1f00 WHIRLPOOL 00acdde88f48ef9b7db90c960150ab262f7b81cbc463b58f558d849c14ce9a881eeca06c897b4ad51e0810c7d972b6cb2ee28dd83b87d8390aec2818eb811445 +MISC ChangeLog-2015 352 SHA256 60bf0257fe6de06175a913e6abad3441eceff609aeb27f8f68fc6c11169ae9d8 SHA512 4ca61546cbdbc9dd4d15f582be1ae418e65dfe9bb821d3cf349adf61d7c295d43cf47c7225e33441e11f31499c72b7f3c993b4ce59d02228802fedd16fd148ba WHIRLPOOL d49430acf601f7d6404a185559ee344bb4dd8804007f4e9a3c2c7ac45987c82c6e4dfdc7885e5e873809b3852743268f8e6621e45cf1cd818e5bab896182ddfb +MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d diff --git a/sci-chemistry/pdbcns/metadata.xml b/sci-chemistry/pdbcns/metadata.xml new file mode 100644 index 000000000000..da36ecbfcd6a --- /dev/null +++ b/sci-chemistry/pdbcns/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild b/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild new file mode 100644 index 000000000000..90903a11b2de --- /dev/null +++ b/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +DESCRIPTION="Convert atom names for common amino acids and nucleic acid bases from PDB format to CNS or back" +HOMEPAGE="http://www.mybiosoftware.com/3d-molecular-model/314/" +#SRC_URI="http://kinemage.biochem.duke.edu/php/downlode.php?filename=/downloads/software/scripts/${PN}.${PV}.perl.tgz" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${PN}.${PV}.perl.tgz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="BSD" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + dev-lang/perl" + +S="${WORKDIR}"/${PN} + +src_install() { + newbin ${PN}*.pl ${PN} + dohtml *html +} diff --git a/sci-chemistry/pdbmat/Manifest b/sci-chemistry/pdbmat/Manifest new file mode 100644 index 000000000000..c204ee8a4130 --- /dev/null +++ b/sci-chemistry/pdbmat/Manifest @@ -0,0 +1,6 @@ +AUX CMakeLists.txt 414 SHA256 3892dbed23bf2283ce369dc5a2d89c0eded875d615704532fb038ccbe2c90436 SHA512 d539a6cc947cf6f16d634ccc5e2c0f1783f000564cc78c2103c1bcbc8619cb7f0d97a461ffa91ab3fb7d4dbe11102614983456c9bd8597a2f4d9f9a6538185ff WHIRLPOOL b8b64d1e3e1b1972513f2fdfc7fee647c7622ef34589c3cbdd53ab6a00e551315f188b1d9f2f5e4ac35a1ee9ea0b307bb84cfc9dd6af13a4ba0d595113bf46aa +DIST pdbmat-3.89.tar.gz 124727 SHA256 98f75acd3da3f172213de0688825abad8b3a59c516b5b4ac411a494f6d355f72 SHA512 2c7f8f32344fe1abc662878c2556c10bd6671e683787231827399866f485389c3a63253b00d5a5bdbe8d0b8b779891e846962c9372d927b94c45f0fac59a4fb6 WHIRLPOOL 62f0b8cb2a99797d49c427a085ad24b41e045ba96433cb8c1769c614402cf729737b2335fcb356ad42de1e24079eadccd2c3db6eaa8ff062eb1249a13723b7f0 +EBUILD pdbmat-3.89.ebuild 649 SHA256 ee2383f446330b652796d60983775cdab35c80b50ce4b13d719bcc0ed247c112 SHA512 22e5765e35daab42e8c013ee1a2ddc8b08318d215c1eea6def16ff0559be4f5d521ed85f73fc82fbac3d0a0ae06fc07935bb666fdccf47f1268316a668b1f3e7 WHIRLPOOL 0e57acdfd15e14fc9992db67e248bbb2cd7caf98c0033ea257f001cfe77cce9c1d247954830f301b44a0212c122306a77d3ef4c3a14cb50371504351274cd5d4 +MISC ChangeLog 2590 SHA256 50db9413836098e902c20b1aee592f339aa666e9f5f251303374b0373bcee9d3 SHA512 2d0f080506e33382fc88d7fd6780e08abb7ecf1c5ab6643632020b9c8a4049cba9cb1631c357deeaa887e05de8652ca3065910d5f362a7cf85e302763f2cccc9 WHIRLPOOL b08416978b2e8f8991c8a718d0a24d2f0ba97d24a2204767920399a37237e6f52c6031ba69117cde3e04dba8fa596d5d0786a4f60591544fb1276fb178355172 +MISC ChangeLog-2015 829 SHA256 30fb3dea3b7f1ad5269cde35e3dd5728a328bb5d7a0c8f65623619f87e94be38 SHA512 ca6b9615ea017ae19fe1716fa80655ca0c91416f3951b1e1fa5655f0a95f64a925392396e51ef40cc7d3b389789cf4bc00951360f754407a93d76bbba2356e1b WHIRLPOOL b61c47824d21c03323663b660a9de1ff5a2003fa9947bd3ff22ccb60e6a9d8605a4c946cea446ee67fb094528efb4d93d0f5a4114c00169408b0d483f4e85aa3 +MISC metadata.xml 1091 SHA256 13df1e320c0cb4ed41f204b582cbcdc6c97bbbca8f3192845b4c88aa72266e5b SHA512 1316419ffe8d75ae6596e456563f2a8eec3b734cc4e54c0b6708adf71ac355dae4ee1934ff1f7e44071e70f3c1b3796cb51b144d84fdd8367cac2ca8d3f70542 WHIRLPOOL 8031fbe75de764c3380b2c8d875b277d8a02590bf00077ab49983a85a6db01c9dbbd5ac47c2ef6e36f38a8a7dc8cd995b5a5a7b62a69afa7913e1f488d045c6f diff --git a/sci-chemistry/pdbmat/files/CMakeLists.txt b/sci-chemistry/pdbmat/files/CMakeLists.txt new file mode 100644 index 000000000000..2f1937d84b3f --- /dev/null +++ b/sci-chemistry/pdbmat/files/CMakeLists.txt @@ -0,0 +1,14 @@ +cmake_minimum_required (VERSION 2.6) +project (PDBMAT Fortran) + +option (EXAMPLES "Instal additional example files" OFF) + +add_executable(diagstd diagstd.f) +add_executable(pdbmat pdbmat.f) + +install (TARGETS diagstd pdbmat DESTINATION bin) +install (FILES diagstd.README pdbmat.README DESTINATION share/doc/pdbmat) + +if ( EXAMPLES ) + install (DIRECTORY ../Try_ENM2011 DESTINATION share/pdbmat/examples) +endif (EXAMPLES) diff --git a/sci-chemistry/pdbmat/metadata.xml b/sci-chemistry/pdbmat/metadata.xml new file mode 100644 index 000000000000..5116112c89eb --- /dev/null +++ b/sci-chemistry/pdbmat/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +A fortran program in which Tirion's model (also called the Elastic Network +Model) is implemented. Within the frame of this model, atoms (particles) +less than cutoff (angstroms) away from each others are linked by springs of +same strength. Alternatively, a list of interacting atoms can be given to the +program. +Requirements: a file with the coordinates of the system, in PDB (Protein Data +Bank) or "x y z mass" format. + +Output: the hessian (the mass-weighted second derivatives of energy matrix), +in the "i j non-zero-ij-matrix-element" format. + +Diagstd, a fortran program with a standard diagonalization routine, can next +be used in order to obtain the corresponding normal modes of the system. If +the system is large, the RTB approximation can prove usefull (see below). +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/pdbmat/pdbmat-3.89.ebuild b/sci-chemistry/pdbmat/pdbmat-3.89.ebuild new file mode 100644 index 000000000000..6c14461b5019 --- /dev/null +++ b/sci-chemistry/pdbmat/pdbmat-3.89.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils fortran-2 + +DESCRIPTION="Calculate Tirion's model from pdb structures" +HOMEPAGE="http://ecole.modelisation.free.fr/modes.html" +SRC_URI="http://ecole.modelisation.free.fr/enm2011.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="CeCILL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +S="${WORKDIR}"/Source_ENM2011 + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DEXAMPLES=$(usex examples) + ) + + cmake-utils_src_configure +} diff --git a/sci-chemistry/platon/Manifest b/sci-chemistry/platon/Manifest new file mode 100644 index 000000000000..de4eee31b1c3 --- /dev/null +++ b/sci-chemistry/platon/Manifest @@ -0,0 +1,5 @@ +DIST platon-20151001.tar.gz 12076455 SHA256 0f693de9b8ef601bc502d56a203c851ee350185e0816ede4b1b4d154917fa5b2 SHA512 fc93e4c425c25ddc9ae634c82b63e95c5ce99bcbada43976478a58783e3b369f082e08e2ee24ff7d9ebe2d9d2d730cd42f6361276a53bed9edd0c0476cfb5148 WHIRLPOOL 458e6a263958473bf39d460524fb98963e701d96050db5c622a6cb934796271bb45313526614b3bd28ce372e7bd6a60d76cb6aaa8e80d1e18d7fdc436a03b702 +EBUILD platon-20151001.ebuild 1746 SHA256 d442002449d7f3bcad14f40edb2cedbe19081017971eaa3b822f8cc239d499e0 SHA512 7f9eba83b8287737f0a0552948917ab0469bca08b99425aebbb6475e547cdbaf682269c867001cc9b081af7c4d4a0eab2b6a77ef4ff60cbbcd63b82958e58c4c WHIRLPOOL 656547e0be0d7a2aea7036c3b881e26c461780c7810492c7de7ed9a29df5ea6e62731329e281ff7b1ae2bd728935fad43835a79561dee4c063a733b8370d7307 +MISC ChangeLog 3085 SHA256 231eaa03a8dde3445a639edc8c06a68dcbd2855ef25de4b5a9944259b103a9f9 SHA512 79e9ac3451ba321195df912119e4261b4a974fb56f987a5d651ed5ae6ceeeee7f63f4368f2149ba92bcea1576af3740e3fe3757895ba63a0af202ec2de631aaf WHIRLPOOL 27e5334c4661e9c3150ef1760b057b162a04950375b5f04b7ad2179223e6408789ba30dce2e98b2cd7c8f4a9cf6fe715e426017e24033547f0e97bf5f1375d58 +MISC ChangeLog-2015 4965 SHA256 d7e865d1e5ecba50d1a722d0233afb44012ad66f1db7899f18814718d7b0c412 SHA512 5dd3ddcbb9517b52fd6513266ab88332f6e8282d2c106029b221791df831c4fe15f97959d2ceef16faf0b0a8d929ec578cfffcf89f7a81d989a432bb15cd608e WHIRLPOOL bfaf5a6a223abea78fa40c4684d9593ffd512455dc502f5711f6e0f23b9f43522e5433640db21bd469a07c52960725d590faf5f33ade4889723547b5b4e998fb +MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d diff --git a/sci-chemistry/platon/metadata.xml b/sci-chemistry/platon/metadata.xml new file mode 100644 index 000000000000..da36ecbfcd6a --- /dev/null +++ b/sci-chemistry/platon/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/platon/platon-20151001.ebuild b/sci-chemistry/platon/platon-20151001.ebuild new file mode 100644 index 000000000000..7fcfb6bfc853 --- /dev/null +++ b/sci-chemistry/platon/platon-20151001.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils fortran-2 flag-o-matic multilib toolchain-funcs + +DESCRIPTION="Versatile, SHELX-97 compatible, multipurpose crystallographic tool" +HOMEPAGE="http://www.cryst.chem.uu.nl/platon/" +SRC_URI="http://www.cryst.chem.uu.nl/xraysoft/unix/${PN}.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="free-noncomm" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +# Can't do libf2c dependent on whether <gcc-4 is selected for the build, +# so we must always require it +RDEPEND="x11-libs/libX11" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}/${PN}" + +pkg_nofetch() { + elog "If there is a digest mismatch, please file a bug" + elog "at https://bugs.gentoo.org/ -- a version bump" + elog "is probably required." +} + +src_unpack() { + default + cd "${S}" || die + gunzip platon.f.gz xdrvr.c.gz || die +} + +src_compile() { + # easy to ICE, at least on gcc 4.3 + strip-flags + + COMMAND="$(tc-getCC) -c ${CFLAGS} xdrvr.c" + echo ${COMMAND} + ${COMMAND} || die "Compilation of xdrvr.c failed" + COMMAND="$(tc-getFC) -c ${FFLAGS:- -O2} -fno-second-underscore platon.f" + echo ${COMMAND} + ${COMMAND} || die "Compilation of platon.f failed" + COMMAND="$(tc-getFC) -o platon ${LDFLAGS} platon.o xdrvr.o -lX11 ${F2C}" + echo ${COMMAND} + ${COMMAND} || die "Linking failed" +} + +src_install() { + dobin platon + + for bin in pluton s cifchk helena stidy; do + dosym platon /usr/bin/${bin} + done + + insinto /usr/$(get_libdir)/platon + doins check.def + + echo "CHECKDEF=\"${EPREFIX}/usr/$(get_libdir)/platon/check.def\"" > "${T}"/env.d + newenvd "${T}"/env.d 50platon + + dodoc README.* + + if use examples; then + insinto /usr/share/${PN} + doins -r TEST + fi +} diff --git a/sci-chemistry/povscript+/Manifest b/sci-chemistry/povscript+/Manifest new file mode 100644 index 000000000000..ac86554c6587 --- /dev/null +++ b/sci-chemistry/povscript+/Manifest @@ -0,0 +1,8 @@ +AUX povscript+-2.1.2.2.19-libpng15.patch 542 SHA256 13cebc2b3d96e9fc650e38a95d7ff21b5fd25db7ae00110aa26e91e7601f4214 SHA512 5f795238f95adfa0712c92afda669d461cc292b358aa51907ceea1c2d5e5e470d1817d75f461a46efb962ffefafa2606400d32c1f681192f8e161d6e23ee5224 WHIRLPOOL 5dd04bf068d1cc5db88b3345a10fcbc7f67ec33e3adb47268c8958e17c6209c054e7b23731483858f56ae724afa42c2b1c2c2098e38241fd14da517c9c8c784b +DIST molscript-2.1.2pov2.19.tar.gz 845101 SHA256 4d35ed30898508df85c1db6e18385b56f8aed1f79db65195be6fdb23d3c49b68 SHA512 11796552a889ae309ebac31047440732921cd300d89ad284beb3655e2797fe1a68adf9a5a7e54e6668ea240c5b0897c22f65d839870ee43591854976000ab05f WHIRLPOOL cf19cf28304f49a1de6a1d787de18c939b4dcd5ae2d813ac48e8d5f2a572de4cee6bafdd8613e47ca7a5b5b3891108308c808687162deb23d39dcd07a69dcd35 +DIST molscript-2.1.2pov2.20.tar.gz 822930 SHA256 a3a9ae8792fbfba1df6e279c913db3ee4a89612c94b6088be874ed69372ab7a6 SHA512 f7cae4d9b583a05962742ee36ec717f0ecac6bb88086bcfa484b51b0d2e16a15920bc7c09d9d777453d7ef7b81be444924d15a889e4725bfca7bf517d4e52db2 WHIRLPOOL 8c12ea5ebc234f2277e04e502a314cb0065cb717e1cff067d9ad8d306395972f2b6d7589f3a7e58dfa019dc3eb0cf11582ee9b92f1bb3b17c8f9cfc5c4b57a2a +EBUILD povscript+-2.1.2.2.19.ebuild 1244 SHA256 d4e792ce4b098b42e7ba53bc97813e25fa6645cc5b7135165cf3dff26e02b86f SHA512 b3e58b153ee8a5e1145f87c24742de76518a6e0792185256b2d8463782a93e37357801bda4a586054576cde9040d39ac140a68af796c1661cbe1f06e4d448694 WHIRLPOOL 2edf4aa0bdd11ea9fd0f9fe0f340d04d37f170b6341cb1f2297871b485d2fd408a1387756d1b86d37089122adea4003fc19b5e8b5564a840469a61207430e85a +EBUILD povscript+-2.1.2.2.20.ebuild 1263 SHA256 e06432173e1a1a472c9d4565f7fe002b1be880d705ed5048d9ba0d332315518f SHA512 54cebb95ef03430d1071a894b2a47f118ae0e952bcacc0f80f3d727aa18912d4701a116c97469bf2a37b28e01fa5fe51cf7aa02fe2fb69134bf98465210d4770 WHIRLPOOL 0a20654908b41423d21c95c6a99bd75b6ca16100e7e2d9fd5fcc7cad84093553766a7006c9f93b7d9d4b9975af275d8171e373567e251db4a42dc37a9ea52c86 +MISC ChangeLog 2703 SHA256 df66a92d3766e859a9e7428fb62bcabba14554e9d58a501d3347b73ec93bfc5d SHA512 ce071eeb61e8a750202f1bbe962ed9fe3d02200a824b6a48a89d8e2f45becfb6172e9a8419fcb3c3d4086095597ed07edb000a59391f39ac23a3ade7a8f297c5 WHIRLPOOL 0fabcf99d85671e503f1327bc4bec32434078c71c3ce025389e89ae399b3c592457ba512989b202a5919da0501c223adfd9ac455476b7ebf5ff97d068f417b1a +MISC ChangeLog-2015 1421 SHA256 2045b996379a2f09521d0df41763e06544574af12e3614b9730d7a9c45a63fb0 SHA512 cff1a7d5d107172f24dde688c76bb540d794c6ce2c0b95cd9d533a2b4d0b2dd639e493e71da460e950d579e60c9ce9479da12e9b9e40e57f4730060d4ed4d939 WHIRLPOOL 3e9c26b38429314a4a64da683e60acc0406217db4186383c7ab517e6ff43b96f8ec82c79610624a16128ae295f4336613d366807df4ed2d948fdce22d8f8cbec +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/povscript+/files/povscript+-2.1.2.2.19-libpng15.patch b/sci-chemistry/povscript+/files/povscript+-2.1.2.2.19-libpng15.patch new file mode 100644 index 000000000000..054967d6555c --- /dev/null +++ b/sci-chemistry/povscript+/files/povscript+-2.1.2.2.19-libpng15.patch @@ -0,0 +1,19 @@ +--- src/png_img.c ++++ src/png_img.c +@@ -18,6 +18,7 @@ + + #include MS_GL_H + ++#include <zlib.h> + #include <png.h> + + #include "clib/str_utils.h" +@@ -69,7 +70,7 @@ + info_ptr = png_create_info_struct (png_ptr); + if (info_ptr == NULL) + yyerror ("png_img: could not create PNG info structure"); +- if (setjmp (png_ptr->jmpbuf)) yyerror ("png_img: could not setjmp"); ++ if (setjmp (png_jmpbuf(png_ptr))) yyerror ("png_img: could not setjmp"); + + png_init_io (png_ptr, outfile); + png_set_compression_level (png_ptr, compression_level); diff --git a/sci-chemistry/povscript+/metadata.xml b/sci-chemistry/povscript+/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/povscript+/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/povscript+/povscript+-2.1.2.2.19.ebuild b/sci-chemistry/povscript+/povscript+-2.1.2.2.19.ebuild new file mode 100644 index 000000000000..ed9dc48f4d5c --- /dev/null +++ b/sci-chemistry/povscript+/povscript+-2.1.2.2.19.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils versionator + +V1=$(get_version_component_range 1 ${PV}) +V2=$(get_version_component_range 2 ${PV}) +V3=$(get_version_component_range 3 ${PV}) +V4=$(get_version_component_range 4 ${PV}) +V5=$(get_version_component_range 5 ${PV}) + +MY_P=molscript-${V1}.${V2}.${V3}pov${V4}.${V5} + +DESCRIPTION="Modified molscript that uses POV-Ray, does thermal ellipsoids, and more" +HOMEPAGE="https://sites.google.com/site/timfenn/povscript" +SRC_URI="https://sites.google.com/site/timfenn/povscript/${MY_P}.tar.gz" + +LICENSE="glut molscript" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="" + +RDEPEND=" + dev-libs/glib:2 + media-libs/freeglut + media-libs/giflib + >=media-libs/libpng-1.4 + sci-libs/gts + sys-libs/zlib + virtual/glu + virtual/jpeg + virtual/opengl + x11-libs/libX11" +DEPEND="${RDEPEND}" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + epatch "${FILESDIR}"/${P}-libpng15.patch +} + +src_install() { + emake DESTDIR="${D}" install + cd "${D}"/usr/bin + mv molscript povscript+ + mv molauto povauto+ +} + +pkg_postinst() { + elog "You must install media-gfx/povray to use the POV backend," + elog "which is one of the main features of this over molscript." +} diff --git a/sci-chemistry/povscript+/povscript+-2.1.2.2.20.ebuild b/sci-chemistry/povscript+/povscript+-2.1.2.2.20.ebuild new file mode 100644 index 000000000000..905006c1d66c --- /dev/null +++ b/sci-chemistry/povscript+/povscript+-2.1.2.2.20.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils versionator + +V1=$(get_version_component_range 1 ${PV}) +V2=$(get_version_component_range 2 ${PV}) +V3=$(get_version_component_range 3 ${PV}) +V4=$(get_version_component_range 4 ${PV}) +V5=$(get_version_component_range 5 ${PV}) + +MY_P=molscript-${V1}.${V2}.${V3}pov${V4}.${V5} + +DESCRIPTION="Modified molscript that uses POV-Ray, does thermal ellipsoids, and more" +HOMEPAGE="https://sites.google.com/site/timfenn/povscript" +SRC_URI="https://sites.google.com/site/timfenn/povscript/${MY_P}.tar.gz" + +SLOT="0" +LICENSE="glut molscript" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="" + +RDEPEND=" + dev-libs/glib:2 + media-libs/freeglut + media-libs/giflib + >=media-libs/libpng-1.4:0= + sci-libs/gts + sys-libs/zlib + virtual/glu + virtual/jpeg:0 + virtual/opengl + x11-libs/libX11" +DEPEND="${RDEPEND}" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + epatch "${FILESDIR}"/${PN}-2.1.2.2.19-libpng15.patch +} + +src_install() { + default + + cd "${ED}"/usr/bin || die + mv molscript povscript+ || die + mv molauto povauto+ || die +} + +pkg_postinst() { + elog "You must install media-gfx/povray to use the POV backend," + elog "which is one of the main features of this over molscript." +} diff --git a/sci-chemistry/prekin/Manifest b/sci-chemistry/prekin/Manifest new file mode 100644 index 000000000000..93e42d87a87f --- /dev/null +++ b/sci-chemistry/prekin/Manifest @@ -0,0 +1,7 @@ +AUX 6.51.081122-Makefile.patch 1456 SHA256 7f1b2d39007683b4ecb391ec5bd711ca32115f361dcfc0aa05b25fe52817bb4c SHA512 96b8cda8fc71b2e72c0e8e0a70560a7928456fe81aaa40810a8bcbe77835a7242e8e0d39fac3258e5848a4e4ac14bf9d7dfd4dff8385eb983f359a9f85af9838 WHIRLPOOL ab82e73a70d83b625e8e2e130327ab34a5eaabdce3ccf07a6bb5b62be9e6bb9067b653bfcb9fc1f90607b5d990053c1b4c92732a4dfc21e37dd2142168829f5b +AUX 6.51.081122-overflow.patch 1156 SHA256 987a530c35f34b25783ce1b4ce0094614f06e97ae8ed652324b8b8ea7f897259 SHA512 fe0ff6e3432177653d29ef51ef3a767dc3872fc0a5350c786b3623b6b4d63866fbfbaf4369676feb545766cac5620b209bd87e92c0ecf2280bb39470e7dd5f7b WHIRLPOOL c868dd1fb4af3c855cd7c2f3e57719b857aab535e26de3c4a1bbc827fd52397e66d23c95670e69796537c34d39a6a964f241fff627f2b8b1186028dbfd04977c +DIST prekin.6.51.081122.src.tgz 350756 SHA256 74a771cd8be000df13ac908f23a2e945e8bd3590884c6bc6ccff75804cc0fb7a SHA512 9a41f30a9de955c78ee5685807482b2b073705643cceb53bf57eaf7c0c4753dc88fa8dc19f09d4c8a07124c3c3c73716f29126860ae37ff4dd6fb6178b829d1f WHIRLPOOL 29e5b3a0f060bd46c8e00322a31365526be8e3eec0c4c95b630d3e5d6a22bd3e2538c649774a88c7a3c10841ae34f1b23163ab4b625237b46aabaadec35b0c79 +EBUILD prekin-6.51.081122-r1.ebuild 1082 SHA256 c5ea3cced7edb90b35d1c531602c44c5034b104d45e231280c78209d3c55b5ab SHA512 582752645be5f5b5c672b1f69cf3e42415dc0c7bfeefc8f5f7304457b59530cc3ca2eb936416113db203dbf12ec0651db8d96af1acaabd8125d3fa959461f41b WHIRLPOOL 662af50263e0bba42d9d405e0f439337b4a58962d4013402571fa1abcc58c6d99ff57ddec099304a4a253c0b690ece375da7e45d19fce80662d6a102ec3c0120 +MISC ChangeLog 2519 SHA256 0e38123839a278664cb938da296125d2605cee7b96ebec7121559d788e15b1f6 SHA512 9dc8e5b49371a5c48deeb8bcab04f45964942154fb837e148cc639ce757f1ca35f885fb6f0c339869316043e162d2647cfa1bb28d2a0a8a3f0cb9164e99068b8 WHIRLPOOL 8a438acbe16bbdb75578517577c0397cf68a02dbfe2350798cb1f8edbfbc3f16104ee26b9a14315731cbf0e34e94c5903349a2a95ddc74c8c773eaf9c78a4472 +MISC ChangeLog-2015 1159 SHA256 97f9e130cd473c501b2183c603d8c5b6a23f5eb4fa95093a8235b56afca2620a SHA512 b510a37b2fd93968dc832d2cf40ee9a9ea94b26ed4300c96c61726b82416dbf93e2097009e0b45bccd092f5e1573bbaad18e2e88c929f489dfc9786f818ae504 WHIRLPOOL 7e442bba4ab73b96c62c879de1f29000dd71b93f2d12eb9c86c33dfb6eb4ea30981fdc7945ebced76d9ba48ad6e0874006d20551a36e2045f2a35057915c7bb9 +MISC metadata.xml 261 SHA256 f53f2259ad8695c56f1457bcbd63ad8f51108ec471d728cd2fe6f523b36b09d8 SHA512 72682d17ec2b918131b551bd1ff41004965d3cf0c00d24222b34741d2eabf601cf36d4266be70ba7fb7bd0ab55d9dcb5b8e4ca41125bc31f176516797459c8c7 WHIRLPOOL 8ae9531cec25662e7d2a9df3c46039a66da22cb0becfc5cb2eacbb0ea5cfedf0491bd7110465ae37c4e8263b5a962f4973eed3dc569db0d524506943014444a2 diff --git a/sci-chemistry/prekin/files/6.51.081122-Makefile.patch b/sci-chemistry/prekin/files/6.51.081122-Makefile.patch new file mode 100644 index 000000000000..5fd9d00d9b06 --- /dev/null +++ b/sci-chemistry/prekin/files/6.51.081122-Makefile.patch @@ -0,0 +1,41 @@ +diff --git a/Makefile.linux b/Makefile.linux +index 65a021a..3daacd8 100755 +--- a/Makefile.linux ++++ b/Makefile.linux +@@ -1,15 +1,15 @@ + # +-CFLAGS = -I/usr/X11R6/include ++CFLAGS += -I/usr/X11R6/include + + ifeq ($(MAKECMDGOALS),debug) + CFLAGS = -g -I/usr/X11R6/include + endif + +-LIBS = -L/usr/lib -L/usr/X11R6/lib -lXmu -lXm -lXt -lSM -lICE -lXext -lX11 ++LIBS = -L/usr/GENTOOLIBDIR -L/usr/X11R6/lib -lXmu -lXm -lXt -lSM -lICE -lXext -lX11 + + ifeq ($(MAKECMDGOALS),nogui) +-CFLAGS = -D NOGUI -I/usr/X11R6/include +-LIBS = -L/usr/lib -L/usr/X11R6/lib -lXmu -lXt -lSM -lICE -lXext -lX11 ++CFLAGS += -D NOGUI -I/usr/X11R6/include ++LIBS = -L/usr/GENTOOLIBDIR -L/usr/X11R6/lib -lXmu -lXt -lSM -lICE -lXext -lX11 + endif + + FIN = -lm -pthread #for RH9.0, ok for RH7.3 & RH8.0 +@@ -26,13 +26,13 @@ OBJS = PKINANGL.o PKINCRTL.o PKINCSBS.o PKINCSUB.o PKINCOUT.o PKINMENU.o PKINROT + # Commands specific to clients created by this Makefile + + prekin: $(OBJS) +- cc -o prekin $(CFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) ++ cc -o prekin $(CFLAGS) $(LDFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) + + debug: $(OBJS) +- cc -o prekin $(CFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) ++ cc -o prekin $(CFLAGS) $(LDFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) + + nogui: $(OBJS) +- cc -o prekin $(CFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) ++ cc -o prekin $(CFLAGS) $(LDFLAGS) $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) + + clean: + rm *.o diff --git a/sci-chemistry/prekin/files/6.51.081122-overflow.patch b/sci-chemistry/prekin/files/6.51.081122-overflow.patch new file mode 100644 index 000000000000..27bc01d61a52 --- /dev/null +++ b/sci-chemistry/prekin/files/6.51.081122-overflow.patch @@ -0,0 +1,28 @@ +diff --git a/PKIN.h b/PKIN.h +index 6cb6670..c9c6b89 100755 +--- a/PKIN.h ++++ b/PKIN.h +@@ -533,8 +533,8 @@ EXTERN float xnext,ynext,znext,onext,Bnext,Uvalnext; + EXTERN char aspectstrnext[MAXaspects+3]; /*in parens: (XXXX)*/ + + /* possible overlap with earlier PREKIN variables */ +-EXTERN char word[256],texts[256],temps[256]; +-EXTERN char alertstr[256],alertstr2[256],alertstr3[256]; ++EXTERN char word[256],texts[256],temps[512]; ++EXTERN char alertstr[1024],alertstr2[256],alertstr3[256]; + EXTERN char oldstr[256],olderstr[256],newstr[256],InfoStr[256],MolNameStr[16]; + EXTERN char NameStr[256],OutfileStr[256],ScriptinStr[256],ShortNameStr[256]; + EXTERN char DirStr[256],PDBfileStr[256],helpoutStr[256]; /*040425 helpout*/ +diff --git a/PKINCOUT.c b/PKINCOUT.c +index af8eb24..a9f3a5f 100755 +--- a/PKINCOUT.c ++++ b/PKINCOUT.c +@@ -17,7 +17,7 @@ static float VRMLx=0,VRMLy=0,VRMLz=0; + void writeoutput() + { + char cntl[5]; /* 4 actual characters */ +- char kol[20],extra[256],aname[13]; ++ char kol[20],extra[256],aname[32]; + char chain[32],atoms[32],cpks[32],hygen[32],hbond[32]; + char subname[32],allstr[32]; + char mastername[32]; /*051128*/ diff --git a/sci-chemistry/prekin/metadata.xml b/sci-chemistry/prekin/metadata.xml new file mode 100644 index 000000000000..4ac68c154bb0 --- /dev/null +++ b/sci-chemistry/prekin/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> +</maintainer> +</pkgmetadata> diff --git a/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild b/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild new file mode 100644 index 000000000000..7f90ace13b9b --- /dev/null +++ b/sci-chemistry/prekin/prekin-6.51.081122-r1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="2" + +inherit toolchain-funcs eutils multilib + +MY_P=${PN}.${PV} + +DESCRIPTION="Prepares molecular kinemages (input files for Mage & KiNG) from PDB-format coordinate files" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/prekin.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${MY_P}.src.tgz" + +LICENSE="richardson" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="X" + +RDEPEND="x11-libs/libXext + x11-libs/libXmu + x11-libs/libX11 + x11-libs/libXt + X? ( >=x11-libs/motif-2.3:0 )" +DEPEND="${RDEPEND}" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-Makefile.patch \ + "${FILESDIR}"/${PV}-overflow.patch + sed \ + -e 's:cc:$(CC):g' \ + -e "s:GENTOOLIBDIR:$(get_libdir):g" \ + "${S}"/Makefile.linux > Makefile || die +} + +src_compile() { + local mytarget + + if use X; then + mytarget="${PN}" + else + mytarget="nogui" + fi + + emake CC="$(tc-getCC)" ${mytarget} || die +} + +src_install() { + dobin "${S}"/prekin || die +} diff --git a/sci-chemistry/probe/Manifest b/sci-chemistry/probe/Manifest new file mode 100644 index 000000000000..bbbe5ae5a1ed --- /dev/null +++ b/sci-chemistry/probe/Manifest @@ -0,0 +1,7 @@ +AUX as-needed.patch 594 SHA256 1f46ff455ac4167fe56051fa2fb8859ee5c504429b70abb787ccf8a480fb7065 SHA512 6478862bc967614e8fc57abaa03b92f62943508ae77710b179bb71ae96d21c289b4f2836d76236297ba66ed97954997f4e6c8874f369af03200bf13e5226f8c9 WHIRLPOOL 74f203b062ac5ee744f0f0798644b5b82d72c2e7427c418b6889d3d9f1ed06b1b03030883d0a60df81d218dd4f26e7f993ce4572aeee562c9feb30721abdb326 +AUX probe-2.13.110909-as-needed.patch 634 SHA256 d40ce6144d7e5bd075ae2aace729fce2f44d3412d063300cb50e8428f00faf7f SHA512 24b291cffbc00588626ac9da3e38e9bbb9a9ba121a3ae74fa5e91c94cd30489d61a559351d5a4b89ebb4c1564be30144d1eec295032ed612fa6e80d47d9ba8a6 WHIRLPOOL 2b13f34271064911755e3d13276856d3fe016d6a53c8dd5aac516c7b1afc44abcd0062ee89e086ae4734f201b6c86c43e0b893e599b6aafa0d674a2a6b34dba1 +DIST probe.2.13.110909.src.zip 131063 SHA256 df14b76d27a7c43b2b57c315d0ad71cdf6acc7943c43195a797162be7816fa71 SHA512 5efa066873d0e139da66bf8edb541fe42df94e99cab171ad8d06a8a6f5caada982ef5b18481e748b224dbed86f63c99237d04ecd107c82855b44de91fb6d2b16 WHIRLPOOL 12f6fefe1b03b71268f39fa3aa7ad796230c76c2e029b8dc86955abd43c8e3f09f7591f84cd79c7ba11037d5b323c922ddf36abf6911d556981f5cc21378912f +EBUILD probe-2.13.110909.ebuild 705 SHA256 bb5b52f7ebf6801681e87c2257b1e69a5c8eb25538126cada8ae67e97b198596 SHA512 525ecf8ed9db9b5c99f618c3186bd54f1b99d3c97f6c05c48d51a8a8e672b41d548c62d9468f05c95794bb71fbd9f49f24e9c21686dc48414211600b1f5256ce WHIRLPOOL 23839f2b8217096f389802b97122d7e805f0d5358db10e91b3823190b0345c1be2c95a3b94fea9d0258f291940f85510a64f12f156ddcfd59a74273c1059cf27 +MISC ChangeLog 3256 SHA256 5be84b575f19f3369e083148359921347046f9f921254a573dde57321d49ccc4 SHA512 1962c22bbe3a4e18e3169ea0463c7c922ff58041fedc6dc89ad94d164ab05cb94fdf72f5ffbec4e4f26af5f94b948d76901593014c34e4ea3c0258b901e84e69 WHIRLPOOL 65f58ebf51e0cee8db8382e227497aed4482e59f55d3340c2062f6524c713f1cd3b890a0def43bdd5a504d7adc15699717389be0220f971aca21410777d8d8c7 +MISC ChangeLog-2015 2976 SHA256 d27e5a84397bd92cafd131c60e40019019bdac705c081caaf7c6ce7676ab485d SHA512 7e75fe8f16d170f6c4587a4b4bedc42b88c752c7f88db02bdecddc7c27842af3987dac88e0bffeab59a8edc0d533178de207910f74d476a84dedba8cfa04c24f WHIRLPOOL 7bb1b0ec9f90b79c923f65b3c4befdd61f82124b689bf965e3e219378c17a431e299ed7b2ccd65717a55032bc47ca908cdde8a1a63c1b0f5a5603a20ca3cb3f7 +MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d diff --git a/sci-chemistry/probe/files/as-needed.patch b/sci-chemistry/probe/files/as-needed.patch new file mode 100644 index 000000000000..9ddecf5f569e --- /dev/null +++ b/sci-chemistry/probe/files/as-needed.patch @@ -0,0 +1,21 @@ +diff --git a/Makefile b/Makefile +index 68d7469..bcb821c 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,6 +1,6 @@ + MACHINEFLAGS = + CFLAGS = $(MACHINEFLAGS) +-LFLAGS = -lm $(MACHINEFLAGS) ++LFLAGS = -lm + OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \ + parse.o atomprops.o stdconntable.o autobondrot.o hybrid_36_c.o + +@@ -8,7 +8,7 @@ OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \ + cc -c $*.c $(CFLAGS) + + probe: probe.o $(OBJLIST) +- cc -o $@ probe.o $(OBJLIST) $(LFLAGS) ++ cc $(MACHINEFLAGS) -o $@ probe.o $(OBJLIST) $(LFLAGS) + + clean: + @rm -f *.o *.ckp diff --git a/sci-chemistry/probe/files/probe-2.13.110909-as-needed.patch b/sci-chemistry/probe/files/probe-2.13.110909-as-needed.patch new file mode 100644 index 000000000000..df7040c3ba1d --- /dev/null +++ b/sci-chemistry/probe/files/probe-2.13.110909-as-needed.patch @@ -0,0 +1,25 @@ + Makefile | 8 +++----- + 1 files changed, 3 insertions(+), 5 deletions(-) + +diff --git a/Makefile b/Makefile +index 9031bd0..8f74d6a 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,14 +1,12 @@ +-MACHINEFLAGS = +-CFLAGS = $(MACHINEFLAGS) +-LFLAGS = -static -lm $(MACHINEFLAGS) ++LIBS = -lm + OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \ + parse.o atomprops.o stdconntable.o autobondrot.o hybrid_36_c.o + + .c.o: +- cc -c $*.c $(CFLAGS) ++ $(CC) $(CFLAGS) -c $*.c + + probe: probe.o $(OBJLIST) +- cc -o $@ probe.o $(OBJLIST) $(LFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ probe.o $(OBJLIST) $(LIBS) + + clean: + @rm -f *.o *.ckp diff --git a/sci-chemistry/probe/metadata.xml b/sci-chemistry/probe/metadata.xml new file mode 100644 index 000000000000..da36ecbfcd6a --- /dev/null +++ b/sci-chemistry/probe/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/probe/probe-2.13.110909.ebuild b/sci-chemistry/probe/probe-2.13.110909.ebuild new file mode 100644 index 000000000000..66b1ac8c56da --- /dev/null +++ b/sci-chemistry/probe/probe-2.13.110909.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +MY_P="${PN}.${PV}" + +DESCRIPTION="Evaluates atomic packing within or between molecules" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/probe.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/probe/${MY_P}.src.zip" + +SLOT="0" +LICENSE="richardson" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND} + app-arch/unzip" + +S="${WORKDIR}"/${MY_P}.src + +src_prepare() { + epatch "${FILESDIR}"/${P}-as-needed.patch + tc-export CC +} + +src_install() { + dobin "${S}"/probe + dodoc "${S}"/README* +} diff --git a/sci-chemistry/procheck/Manifest b/sci-chemistry/procheck/Manifest new file mode 100644 index 000000000000..ac9339e2d620 --- /dev/null +++ b/sci-chemistry/procheck/Manifest @@ -0,0 +1,9 @@ +AUX procheck-3.5.4-close.patch 1073 SHA256 8819ed952ac6361f19141dc589e2ce81310729c4308ec010dae187cc8308f340 SHA512 3d18df23858acc46a12f884d4904ca3f60e05e663746e768f5f08d0370b2e335cfde09c08566c4869adfa0f9c0d75ae527fe0ed2666f603818b11f91a3349307 WHIRLPOOL dc76f7d4cc062e8aa7a8bcee738c06a11b28670ee989aaf0290e5e57442f3627c9287361c073d9fb077ca8280c8c76217217142e53cc6f0a7fc345c355e067f3 +AUX procheck-3.5.4-ldflags.patch 1649 SHA256 d46c5f8fbb6d7f6f1fedc522f311ae4c5baa12b9ff47e6d3970312e1b2b34e57 SHA512 f7f2e06a77058f7e743a1c1367d40c2683a2aefbf2910a807d1b0a77d19024446f978ec34a8e5187338a7e98b6651592a37c024e8a2ea955d9bd736d47bfeb4f WHIRLPOOL 1b4c6b1563251d2b37edfcdaeb49c8c963559c1823a3cf724e78c6f8a2ba4e53fd79b0da4a40339a55a608f470c3db38c5869cc4c058cf5bc9cc21cf8ee77b52 +DIST procheck-3.5.4-README 6585 SHA256 202d5b4d9ffaebdad19c368e6e6fd8ab54744c511609b1c609ef46c21fa0ffa0 SHA512 c6eff94cef9b67fd61884e88fa77ec381553d4dba53f477023738e1e44a6191c4241b14543ee7ecb93b049f16f262db2a09cf5d1a63248057633aab290f1f82a WHIRLPOOL 53a618978a9285e8a8f09c7ebd3e34951a8c1056c0894c1f4e4c11f73ad3127829322c9c7597fc6dea98f1fa4c40552e6caf383eed15aaeef0594cf93887d196 +DIST procheck-3.5.4-manual.tar.gz 517840 SHA256 3c2faa505be05102ccbe23473abdddc1cd4dc87c6b5e74222b7ea5c27b18db5a SHA512 0fa9c7d50b7ca43c626d5261c524166938d3a92be1d02221721bc7ce7e91ac4919e7200b946ce563f9bb696d7dab9588c1d1b31a4d551cafa2f2bce4931a212c WHIRLPOOL 591afad0a534762d654779722b229e3dcb9cc1ed0f9216c443d4872dd7379257638e5cf3ee5844adf15b2ec55d5c5b15ab585ae52ae993678311985642aa8eaf +DIST procheck-3.5.4.tar.gz 522013 SHA256 4923fe5a7b86d5369fd639d0c77cfb866e574f076ec8c52424d746e843a404f4 SHA512 1dd78b53070484fbcdca51001fd147ab13fd5e51b3d1da54fd529531917c31012393751ee514f0c79d579b17a1701dde04f81b1c9ac27b2b835a43fa96785ecc WHIRLPOOL 2732981bdbb5269567019a645b401009bd48d782ab20b4f68bd213a90f7248a9fa3f46ab3a026aa0515a677a99826040d4c3f5464816ed4390b5091a6a98b375 +EBUILD procheck-3.5.4-r3.ebuild 1687 SHA256 53450ba0e302dd1f7a4930235e114d3212851f8725969aabeaaa1323905aa688 SHA512 abc659dbe5947b16259e05128c5e0607fdbe3c251595b7c5589502c8d6465264bfec243820abec345980d66cfe0b3eaa8183a41aeb2e2a8a81a929b0128364e7 WHIRLPOOL 3ee37116675c8133ab0047a301364921bc78573f1bd0d4925ab49e19405e93f01677c0d0d632cf201f2505d658fbedc897c8fd1d9622d17a359fdae933ffe617 +MISC ChangeLog 2706 SHA256 59b2234decdf7f54d1f1eb4490cd94211d6a1ced3f7b535764178cfe7b6914f0 SHA512 f536b799232fd119c8531c4300b48761a41678cd85cb0270410d9a44aee0ac74c1955b40adb5bdbb8c259699fd327134c66bb13d27210e30aa2cf19ac62a72bd WHIRLPOOL 57331e6b198004b3c635f77983ae2c36f2fb2ba2fc83358b8f8571f643b41fb87465ebfc898b384fd543b8c69d594230b2a9f99cf735402ac80a754721dfc3a3 +MISC ChangeLog-2015 1737 SHA256 32c08c17c06bea867f3d413a81040737bd92aba7c5e0e0b738f739ce808d7ccc SHA512 b1a1c456069655bdebbc15db326ab7efcacef6d56a0cac67858676831529f41730fc2060e150623a571f9bcbde38d893231960a042f0e1aa4561a8e00048bae7 WHIRLPOOL 325a3d995cb55fefc26ff4dff076cd2f3bab9cfb0540521bd187c6c4e6af9cc35e03447fc6675da1dcd7f2478b0ab1e0e12f07b718d9fcae2b25ba3dc5b68bd1 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/procheck/files/procheck-3.5.4-close.patch b/sci-chemistry/procheck/files/procheck-3.5.4-close.patch new file mode 100644 index 000000000000..16a0658e654d --- /dev/null +++ b/sci-chemistry/procheck/files/procheck-3.5.4-close.patch @@ -0,0 +1,35 @@ +diff --git a/pplot.f b/pplot.f +index 7e06e68..c86b2b2 100644 +--- a/pplot.f ++++ b/pplot.f +@@ -4720,6 +4720,7 @@ C---- Initialise variables + SCORE(IDIST) = 0.0 + 50 CONTINUE + ++ REWIND(3) + C---- If the required residue is of a greater number than that required, + C read through the file until come to it + IF (IRESID.GT.INRES) THEN +diff --git a/ps.f b/ps.f +index b652a7d..858b8e5 100644 +--- a/ps.f ++++ b/ps.f +@@ -1705,12 +1705,14 @@ CVAX - CARRIAGECONTROL='LIST', + C---- If this is an existing file, then read through all its records until + C get to the end of file + IF (.NOT.NEWFIL) THEN ++ CLOSE(14) ++ OPEN(14, file=fname, status='old', position='append', err=900) + + C---- Loop through the file until reach the end +- 100 CONTINUE +- READ(14,110,END=500) IREC +- 110 FORMAT(A) +- GO TO 100 ++C 100 CONTINUE ++C READ(14,110,END=500) IREC ++C 110 FORMAT(A) ++C GO TO 100 + + C---- If this is a new file, then write the header records to it + ELSE
\ No newline at end of file diff --git a/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch b/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch new file mode 100644 index 000000000000..453aebe3211f --- /dev/null +++ b/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch @@ -0,0 +1,49 @@ +diff --git a/Makefile b/Makefile +index c5bb58f..0394b0a 100644 +--- a/Makefile ++++ b/Makefile +@@ -35,31 +35,31 @@ distrib : + # Individual executables + # ---------------------- + anglen : anglen.o +- $(F77) $(FOPTS) -o $@ anglen.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ anglen.o + clean : clean.o +- $(F77) $(FOPTS) -o $@ clean.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ clean.o + rmsdev : rmsdev.o +- $(F77) $(FOPTS) -o $@ rmsdev.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ rmsdev.o + secstr : secstr.o +- $(F77) $(FOPTS) -o $@ secstr.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ secstr.o + gfac2pdb : gfac2pdb.o ps.o +- $(F77) $(FOPTS) -o $@ gfac2pdb.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ gfac2pdb.o ps.o + pplot : pplot.o ps.o +- $(F77) $(FOPTS) -o $@ pplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ pplot.o ps.o + bplot : bplot.o ps.o +- $(F77) $(FOPTS) -o $@ bplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ bplot.o ps.o + tplot : tplot.o ps.o +- $(F77) $(FOPTS) -o $@ tplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ tplot.o ps.o + mplot : mplot.o ps.o +- $(F77) $(FOPTS) -o $@ mplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ mplot.o ps.o + vplot : vplot.o ps.o +- $(F77) $(FOPTS) -o $@ vplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ vplot.o ps.o + viol2pdb : viol2pdb.o ps.o +- $(F77) $(FOPTS) -o $@ viol2pdb.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ viol2pdb.o ps.o + wirplot : wirplot.o ps.o +- $(F77) $(FOPTS) -o $@ wirplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ wirplot.o ps.o + nb : nb.c +- $(CC) $(COPTS) -o nb nb.c $(CLIBS) ++ $(CC) $(COPTS) $(LDFLAGS) -o nb nb.c $(CLIBS) + + # Individual rules for FORTRAN files with .inc files + # -------------------------------------------------- diff --git a/sci-chemistry/procheck/metadata.xml b/sci-chemistry/procheck/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/procheck/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild b/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild new file mode 100644 index 000000000000..4b188e5a9824 --- /dev/null +++ b/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild @@ -0,0 +1,86 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit fortran-2 multilib toolchain-funcs versionator + +DESCRIPTION="Checks the stereochemical quality of a protein structure" +HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html" +SRC_URI=" + ${P}.tar.gz ${P}-README + doc? ( ${P}-manual.tar.gz )" + +LICENSE="procheck" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="doc" + +RDEPEND="app-shells/tcsh" +DEPEND="${RDEPEND}" + +RESTRICT="fetch" + +S="${WORKDIR}/${PN}" + +pkg_nofetch() { + elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html" + elog "And follow the instruction for downloading." + elog "Files should be stored in following way" + elog "${PN}.tar.gz -> ${DISTDIR}/${P}.tar.gz" + elog "README -> ${DISTDIR}/${P}-README" + use doc && elog "manual.tar.gz -> ${DISTDIR}/${P}-manual.tar.gz" +} + +PATCHES=( + "${FILESDIR}"/${P}-ldflags.patch + "${FILESDIR}"/${P}-close.patch +) + +src_compile() { + emake \ + F77=$(tc-getFC) \ + CC=$(tc-getCC) \ + COPTS="${CFLAGS}" \ + FOPTS="${FFLAGS} -std=legacy" +} + +src_install() { + for i in *.scr; do + newbin ${i} ${i%.scr} + done + + exeinto /usr/libexec/${PN}/ + doexe \ + anglen \ + clean \ + rmsdev \ + secstr \ + gfac2pdb \ + pplot \ + bplot \ + tplot \ + mplot \ + vplot \ + viol2pdb \ + wirplot \ + nb + dodoc "${DISTDIR}"/${P}-README + + insinto /usr/libexec/${PN}/ + doins *.dat *.prm + newins resdefs.dat resdefs.data + + cat >> "${T}"/30${PN} <<- EOF + prodir="${EPREFIX}/usr/libexec/${PN}/" + EOF + + doenvd "${T}"/30${PN} + + if use doc; then + pushd "${WORKDIR}" > /dev/null + docinto html + dodoc -r manual + popd > /dev/null + fi +} diff --git a/sci-chemistry/prodecomp/Manifest b/sci-chemistry/prodecomp/Manifest new file mode 100644 index 000000000000..f9d0e84abf08 --- /dev/null +++ b/sci-chemistry/prodecomp/Manifest @@ -0,0 +1,5 @@ +DIST prodecomp-3.0.tar.bz2 18377446 SHA256 097b97aa6503ff1aecd4147a6e3ef9997807773a7ef58aab8b10baf73b65e457 SHA512 8d23f174e125d4c7776432a37b063d2f39af8497050bd7f7ff358c67d509b1eef2c2865596efae632855fd583fb52c233b67d0e667c6c2a03ba6f5a2f2ac9b0d WHIRLPOOL c06f4bf32e3d5ff4f2b5f1b1c4fd03d7a5b734651707e6fc101ce0ea5ba17c9377edb60166c4e9313b616b37bd580febea01bf62a71e15389174b301c4d70738 +EBUILD prodecomp-3.0-r1.ebuild 1096 SHA256 c0b19eff8f2a631e8631d552bef915abea176e1addc8a9b13940e41943931462 SHA512 163404741f8cdfcc6e8c550850f79470d9a7c0accf73386351c5ce9ad2068fe0aed5316b346144b888cd5726f2b80312d1d5bcf3476c13b6009279e0c71b3362 WHIRLPOOL 4a9eab9f2b28c40dae5b82a04e5862b268ffc346bb1945242d1933a334af0e4708b42e0121a2ce586482bf99436825b7ebfa35ed84107a296e3a3c9203b99531 +MISC ChangeLog 2825 SHA256 ce5113fb958658dc20dd1b94a6dc83f97bec44dcdba7da84973e62af91385823 SHA512 9dc2bfa7780eef7f8ae393615ba79365cc68fa4ff790cfe0c13e2094ef1eb177928b559ef93f9a2f11c040653426ea19ae5986ab4b76c554a1f9f8a8e820f621 WHIRLPOOL 7096dff8745648e64bb7bcbd02fbcc22984e3cb861da3b914899306d98243f11cacf6a9cce936534e040740a9ab96758c10dd615d051a73af672d862f58ebeec +MISC ChangeLog-2015 482 SHA256 025278e6acf7ed39c0994dce0e6f89ab6ea98d1d4ed5726ddd0818c2ffc388b5 SHA512 ec14e5d7c8675f0e51a6903a7342162fd6d680965612cb116062bf9f3ea854827965cb33ac7b6d6889e0026d108407950e43ab59c30bbfa3d78f2c89f5140cd7 WHIRLPOOL e4daaf63bcbb1ff72206530a41661626ccb30e0721edb791ed3f7d973fec51c7c27f06ab909fc960800c63bf90773d4caf71ff6230663655a230565326ac3e9f +MISC metadata.xml 829 SHA256 e7455bd5bd2caf55d0e4a8ee8913a3b73fa803bf4c4ea3c393d6a30dcd4c3007 SHA512 5eeeb29cddc506a6eee1fa4b84cf047746450393421d5f8270d0757ff92d20f6976176f7e957c8e751b76b75750312ce756b0d15f43b43ad5de0fb94e46988ef WHIRLPOOL 7080b4ffac780286fd7706383b3cdf7e5cf85ae561d9e0e3a5f64ea676b1717f47761b84afad60a8d8b89c7efcd14d9b7d9caaea3c67354a1b03b98128289831 diff --git a/sci-chemistry/prodecomp/metadata.xml b/sci-chemistry/prodecomp/metadata.xml new file mode 100644 index 000000000000..46831628e89a --- /dev/null +++ b/sci-chemistry/prodecomp/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> + PRODECOMP (PROjection DECOMPosition) is a software tool for + decomposition of 2D projections of high-dimensional NMR spectra to a set + of components (defined in turn by one-dimensional "shapes"). + Simultaneous analysis of projections from one or several + high-dimensional experiments provide unambigous chemical shifts for + large spin systems. The latter can be used for backbone and side-chain + assignments as well as structural studies of proteins + (Malmodin and Billeter 2005; 2006; Staykova et al. 2008a,b). +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/prodecomp/prodecomp-3.0-r1.ebuild b/sci-chemistry/prodecomp/prodecomp-3.0-r1.ebuild new file mode 100644 index 000000000000..ad5fb6271a2b --- /dev/null +++ b/sci-chemistry/prodecomp/prodecomp-3.0-r1.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="tk" + +inherit python-single-r1 + +DESCRIPTION="Decomposition-based analysis of NMR projections" +HOMEPAGE="http://www.lundberg.gu.se/nmr/software.php?program=PRODECOMP" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND="${PYTHON_DEPS}" +RDEPEND="${DEPEND} + sci-libs/scipy[${PYTHON_USEDEP}]" + +S="${WORKDIR}"/NMRProjAnalys + +src_install() { + python_export + if use examples; then + insinto /usr/share/${PN} + doins -r ExampleData Results + fi + + dodoc ProjTools/Manual.pdf + rm -rf ProjTools/Manual.pdf ProdecompOutput || die + + python_moduleinto ${PN} + python_domodule ProjTools/. + python_optimize + + cat >> "${T}"/${PN} <<- EOF + #!/bin/bash + ${PYTHON} -O $(python_get_sitedir)/${PN}/ProjAnalys.py \$@ + EOF + dobin "${T}"/${PN} + + dosym ../../../../share/doc/${PF}/Manual.pdf "${PYTHON_SITEDIR##${EPREFIX}}"/${PN}/Manual.pdf +} diff --git a/sci-chemistry/prody/Manifest b/sci-chemistry/prody/Manifest new file mode 100644 index 000000000000..c4ab436b4602 --- /dev/null +++ b/sci-chemistry/prody/Manifest @@ -0,0 +1,4 @@ +DIST prody-1.6.tar.gz 5333629 SHA256 db5f2223005640e64b5bfd5ef147744381b9b170ced61db7bc8f3a0fdb583c86 SHA512 d913ad45b034f1b0e7e36428a6f8f199b365b94bd85bee5ade8eb9eb2b04a18c93d894a2abd18b3a1342597725ffbf96f8ce8a49191fc27e5608f3d2c9a3c49a WHIRLPOOL a6435d88046970cca53290b258017d09b19457c4bbd5530743a3dc9cbc023ee78a28a4df81b190a5499df114d9909afff0697e571ef5bc4726311f4ea287c4be +EBUILD prody-1.6.ebuild 989 SHA256 cf6f8c50d9ae71194d66891d4a694feb913e03f6ffc30b89e30b3230c402e6dd SHA512 c7d56510fcdf606616fde3b0e7199237c3114e053d3ccb03851db34b56cfbac7077e6c714b5a758942be5a29f6e2e92a0fc2945e29382234f439e8225b559cc1 WHIRLPOOL d053e9bf44605192a582f1948a50f0964d62b12eb7b0a7e81c781b323dea7f14da9af254986ff29d8e76b416ceb7686b11fcf4b50fdb9e592a8ac0cecc7b9e6e +MISC ChangeLog 1413 SHA256 9c31f64932108ff256b7e84eb1026ce250e42f789f0e8016421b9ea7e3e0619b SHA512 5cec8c96399f4a966b040da71f18cb19e45391de3a8f822514883e362320e7ff6b5578a074f314346f0a1cbf322cbae73198b02bc65ea6eaae419c6c6aef40d0 WHIRLPOOL 2fc31e43b170a21457e446245dc088332700249848480d23e4481a29fc60c80a47350d9b645828c7a11c64cf2f1465c9ef9a1068aecc682a5bb5d111cac36d69 +MISC metadata.xml 351 SHA256 478c1e6dcab22d397cb9f6551a1d2c979e7e3d7daa344ba368a7d10bf386a02e SHA512 7e6be0c59b593d2de0f9e0237a039624a136b791c28afddad157c878a3d7efdf02637bb0e6b862957a057f3ab7aaf3db113eed6208e1491e4950795547ea4b2c WHIRLPOOL a05d743b0b1b5964093b1ef86ec3740382ea3027f8aa943631ed2b4386281bdd3e827e41e964f341afe355b1434f2c922049885dbe9e780ba17253df6d2262aa diff --git a/sci-chemistry/prody/metadata.xml b/sci-chemistry/prody/metadata.xml new file mode 100644 index 000000000000..d798ea1d6cdf --- /dev/null +++ b/sci-chemistry/prody/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="github">prody/ProDy</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/prody/prody-1.6.ebuild b/sci-chemistry/prody/prody-1.6.ebuild new file mode 100644 index 000000000000..abab32d7927e --- /dev/null +++ b/sci-chemistry/prody/prody-1.6.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="Protein Dynamics Analysis" +HOMEPAGE="http://prody.csb.pitt.edu/ https://github.com/prody/ProDy" +SRC_URI="https://github.com/prody/ProDy/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="MIT" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + dev-python/ipython[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + >=dev-python/numpy-1.7[${PYTHON_USEDEP}] + dev-python/pyparsing[${PYTHON_USEDEP}] + sci-biology/biopython[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND} + test? ( dev-python/nose[${PYTHON_USEDEP}] )" + +S="${WORKDIR}"/ProDy-${PV} + +DISTUTILS_IN_SOURCE_BUILD=true + +python_prepare_all() { + emake remove + distutils-r1_python_prepare_all +} + +python_test() { + cd "${BUILD_DIR}" || die + PATH="${S}"/scripts:${PATH} \ + nosetests --verbose || die +} diff --git a/sci-chemistry/propka/Manifest b/sci-chemistry/propka/Manifest new file mode 100644 index 000000000000..acfaf1d3b1f5 --- /dev/null +++ b/sci-chemistry/propka/Manifest @@ -0,0 +1,5 @@ +DIST propka-3.1_p140511.tar.xz 151284 SHA256 42b4f6b98bbbefa11fba5e603aa33f1747362746c1170c9958ad408dc34e39af SHA512 c2938af41ed386e267cd045b14e34779889b3c206016d747b68c400f2c8b37bd50cc3b74d055d931476065ac6817a2dd2cb87d68de9911adfff1c8e34a667fc3 WHIRLPOOL 0553ef5f519d41af508885f1900a68627fcf3fb2f901c5d1cef54fe6a5774ef08caf42bf5e80f08cba4c76c9e330be89502e648cf5604aca411c168d4ecda6fa +EBUILD propka-3.1_p140511.ebuild 818 SHA256 568917ebba9f4d9159aa144edf44b2348a5d4f561aaade1e63b5b1ebadb61182 SHA512 11067e38fe55d39e0379f739db6385d28e6bdb45545d61607c3e2f4d5780235eb0959c40d5c2f4ef0e2a7965c169c720cb27be9ef445f272953d308479a2f430 WHIRLPOOL ea3c5b02706c489e67da1e61ab09c3d8bb9086a5641ad964045ac69500c58c28c1185c49926af4dc3f1b42607203bc6d6bd48458ec9204a7f3c7953e7865d4e6 +MISC ChangeLog 2610 SHA256 c4511975ad37b4b6ed1779889eb129f2621575c5ccc7f8caefaa64ab2818449f SHA512 bd703eadda91df30582ec6c8a40a00297ed44a8cf0dbbb969bddad363148b0f76663a8bb03c4f0c5a9b31fd8327982a3749360d0d85784da621899bcf31c6627 WHIRLPOOL 31ce537bca57194da805ad7706b67ba81927ee9e1a0c40516236b5317734e33893275e5f6d310227d3e94c05434537fb12b4fec7da2631ee368176c7b39c1211 +MISC ChangeLog-2015 688 SHA256 b179256c54c4904ae62f71c291d2ebac533f046b69bc0c5d85bd86336b14fbe1 SHA512 303e4f21cc7dd8c15ad8fce70675a745dbf605ad99c6158f46eafbbc10f6507dc330ab2f2143b1ca0dcaa5bcdbff3415b1b2d54896bf9dc721db7bb668b18696 WHIRLPOOL 20382d843673c78962219392e1e60a1827259b61856e93118520d12a8d612804099879651fa239f0dfde46dda2503b5109a7be77b0fb2b3cd90d2aa629a46e38 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/propka/metadata.xml b/sci-chemistry/propka/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/propka/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/propka/propka-3.1_p140511.ebuild b/sci-chemistry/propka/propka-3.1_p140511.ebuild new file mode 100644 index 000000000000..2d34b8da5d5f --- /dev/null +++ b/sci-chemistry/propka/propka-3.1_p140511.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="Prediction of the pKa values of ionizable groups in proteins and protein-ligand complexes" +HOMEPAGE="http://propka.ki.ku.dk/" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="all-rights-reserved" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]" + +RESTRICT="mirror bindist" + +python_prepare_all() { + sed -e "/exclude/s:scripts:\', \'Tests:g" \ + -i setup.py || die + distutils-r1_python_prepare_all +} + +python_test() { + cd Tests || die + ${PYTHON} runtest.py || die +} + +python_install_all() { + dosym ${PN}31 /usr/bin/${PN} + distutils-r1_python_install_all +} diff --git a/sci-chemistry/psi/Manifest b/sci-chemistry/psi/Manifest new file mode 100644 index 000000000000..e894cfc0d529 --- /dev/null +++ b/sci-chemistry/psi/Manifest @@ -0,0 +1,15 @@ +AUX 3.4.0-destdir.patch 1320 SHA256 17909af7b5dff643ef8ea134bf4468cd361457ba9192a1f9155a5870470af7a6 SHA512 cacd44ce2b5d0a1d7ccc2c2bb0429973b3d5d7cf145bc99ea5cbbbe693bef3bb624641761f93ba7f275f1d41fce0b14f15134167071fff4bce0542429d4d1098 WHIRLPOOL 3589a0e751d2ce2321b9495191be831d78997044bc15a07a38aecc29df08b40c0cbe4038593ede60872de3f45c441d765887b6395f546e4d9a4bd25fb378fdc0 +AUX 3.4.0-dont-build-libint.patch 432 SHA256 2bceacc5e924b033b2ef774df789cb5cd11278452da7ea2aad5d51d3b7a8d43c SHA512 db4dd3607c5fad353d9a692f38250c75f12330d6b9a10b2ea2d1ce265526310f7407c57f6846c063185f890089bcd325b13b04bf1d16742b019c0a86c766b05d WHIRLPOOL 170ec68dd4479b272e92ec38b0fb29050c30487b46cdd4537562ee099f63ba91018de9901259ca6a2bb92872c0bc738958602db8552f2c6234dbbe61865f622c +AUX 3.4.0-fortify.patch 1889 SHA256 f901b42e64e6fdf1aed2d87bfc8efa503ab193d0464e9739be67c60daf249cd6 SHA512 b8433288aac07fe973bfcb24d17de94d2d40368c9bba4859b104c14bc2b38503307fa00145f88a00bb5185dfb1996df74786e990c132edd4f3cf4f228a03bdae WHIRLPOOL ad1eff61ef467c37a23ff986d1b3cc633c8213dc2242802c8ba49d682799c6a91bce4b64e1910fe935b68061b44ba9798488e6cab0b8fbb9707063fbd9eb3ba5 +AUX 3.4.0-gcc-4.3.patch 8000 SHA256 f0b354c3ce8c65956f4ace3ed19afd9ff9b6ab43b3cf21aa33a94c8af44989da SHA512 023a266d1b853e70b49f5e95f6ec78a4e13afc262dc95cef7b7dc580b0e11d68b36b78b0a1e8fa46b678bfd2f4a091800014393e1db812c6483d8c0e484d2ea5 WHIRLPOOL 42b92175b683a49b35e9b608a3b0feb9b31363fa73ee1116027f2972415d63f841eb0f7b72d5d69fe7844114c73e50a248d45b319370ccf7d6879d9c7d5eb9c0 +AUX 3.4.0-ldflags.patch 403 SHA256 edd2030d2d1f4f62d5297d7eab453fbe4d81d1b9ab8fe5f88b7ca8ca8ac70077 SHA512 208431df306d07562ba46a4f18327c8b8978452c250963c5a403e548817ea2709530675faf0b35929d0b2e6c214154a88e5e0e92066e2030c6988ec86681daf1 WHIRLPOOL f1ad2ef3984fef0d567ad443fbf53db718989c570cfc86201bb7f9563719be2f67b4a8419ce220ec8dbb04cd479d703ac80ba0ce242377d35bd943dedac4f65a +AUX 3.4.0-man_paths.patch 603 SHA256 a8307a45d0af403e88299ea474f8af9cf26eafc3207cd991e53af1796ff8357b SHA512 d3b351b76f94f37cf7de34194b8a3fc92226e22cad5a25f9310721dddfa074ff62e6ce8aff856b59b040f0547efa5405647e664fd2e08248438592b3ca06b64d WHIRLPOOL 64a8c6262e60f57f2cad59c6fb51fc299bf888ff630652c72abfa754f5becf0806a3f0a4575186576a61e7c173b8721c4aac1149424e864fb400d380fe426b2e +AUX 3.4.0-parallel_fix.patch 10682 SHA256 4853f395db93db2777fcda7427f4f75cc27ec03ac7ca5e238a56137c596f79c2 SHA512 44cbf4e159168ba9495f34031d409f2f22311f8c4899ca414fbcc789306aac2d8b0c165fdc0fb24907b1ddd69c79c4c2c980e2d9157a38aa94e7511914a7ff9d WHIRLPOOL 53f5ce9c1a775c284d0949ecda32897a0536ce73eb354a765cee58f8dc6d475a9240f7f6df8cd759f14f6f8597e894e1c7394d6384e4b3388f10df5dc9e4ab7c +AUX psi-3.4.0-format-security.patch 1021 SHA256 5e39927ce8237a12fee5345f75dd9d2aa223749c48bad4d06d401bf65d38532d SHA512 f828866ae90711f244104c6443c750a148e9c848eedfe38d9a74fc2e5b56543ced7ae0beadbafa3fe338eddd391969e197104838afb5820b50f227ecbfa472de WHIRLPOOL fad11c794f467ef5cb03bd90d9f9f4720faa7ac0fa6f7fe158a34faa5bc6986adebd5da95c68f9afae06ba58c5bada6fc87e13442509e4d80d7dd65e32599979 +AUX psi-3.4.0-parallel-make.patch 445 SHA256 5c3592741513bacf70e1a642e59356e1e76a98239b615fc3299cc472a09d5634 SHA512 bf574c6c9c1e1ffc8747fb51896b8f9d8b29c4796b0a06529a58a2ab1ed5ee0a4270fe071eb86ca745bad2c760701c4d9eb7f269cd390f6d9cadf4065962e52e WHIRLPOOL cf1c8fd9b46d5aa0d1237ab5612efd465f7525b9f99a09ff277792034a38d1969b69cefb162e91d6ca22573b584911d428d26d062d4a9907bcd28e8abb0cc70f +AUX use-external-libint.patch 1359 SHA256 41faa20ba804e98a81cb6809c789c643fd17458b6f6bc95dbe6311dd2fb16713 SHA512 8b4749b0c449dbc89067eec466d3d557da86e7f2d950cc0a94409e158a31a3fb8ceafefd090168acd97975ff3ccc7859e6f2df3c2cd57a3571b79f71aca6fff7 WHIRLPOOL ea034da3121075ae566b1e99de48c6c4f39aeff8bb4b9030e5cae4cc31e402da2861bbc194b4c9f1ce242b1e4c213971700c603699a29f405eb0c69ea9ff12b4 +DIST psi-3.4.0.tar.gz 7413072 SHA256 c87a7f63cb4e34bfd1a8b3731474eb417d9933338327143415a985bcedb619d4 SHA512 b13d2464502545cceec3a3b6048b505b918da26730c1614617b04ee6c1d637c9f799ef7fd92ad9554fa2db87617004aa810a6a81400a04df3c06787d51654ca6 WHIRLPOOL 9c0b9de2c9fbed298eaf958f0c135cadff16eac8754d4064dba0ac2275aabd36204bcad92f90236030bc62ef9917b967653ec608e40ad631e70a0ce1c16f2127 +EBUILD psi-3.4.0-r2.ebuild 1935 SHA256 c4b835d3f5fbf5b9e6326b3f7227e8a0eacc5457a190c78ccf5436eda9573086 SHA512 75c1615bb6510bfa0ef2a771a78a4d262dfac80ce5c597d69cba1c030e0a3db90902d3a9330ce9d2440918e2ee649fc44bca9c7453ff5099d592188d8142bfda WHIRLPOOL 3499d4fb4011475aa7e968217a01a5598094ffd75a96cc7b290af4b6f4f45c064d9b1d688892b5168d20d374571584563ce02a4b0f43bf1577c76f6c7f96c066 +MISC ChangeLog 3353 SHA256 4ab0e7198528e63ea6cab3697b2ad1ee1f4c4c9028160d913a9a6b7663772610 SHA512 1587184d1dbc4647df453e5b3f42a0b86c9bebfcb25e9b82407d9e831fecc3390a67664c23d625ecff9abeb9a3e63faad31310975ac384aa94dbc26b569cf72f WHIRLPOOL f31170f3ef210f55daf61215504224fdc5e7dd8c63f02616e745224f41fa4323ac3cae1ad160ebd6aeaf64a68b49c70fb7a85cebeda0ed2aaac3f6cd7fbc49b4 +MISC ChangeLog-2015 4266 SHA256 2edd997f887c0ee6ca527d01614844371deaef75c960c4b65ed73a502b691a77 SHA512 964d92590ca461950f2a2a3f47cd90068041420af03e8266b2f4238d763e9af33a02197dbd2df91a5bff7b88991d1391ffb377cada3bd7796be70efccec7ab35 WHIRLPOOL c78108a4048531b3ca22a73b189fb25470af719c9778c90c14bed1be28b5687a1ad0fc0faedc8e4433d427d44b7221830c6f306eb0e158b19f05c8178db4bb6d +MISC metadata.xml 352 SHA256 ffcde8b1ae3a6c638299b892e9db2784cdebd6ecaf6baf589b0c4a2f159ffb36 SHA512 0ef2b193bcadef21bcad1e3fd3745b37f75bd65fe44645c667c99634d9047b28c82504002ed6967cf1cc2d5c8c43f5757ad08264613088ca36c7e94ac683b7e2 WHIRLPOOL 0b8e8609c669de5244adc767862fb184912b94bfc5d212a33a339fd246f51845165a008c9544078989f88723975bba399f72138683b88b11911bad339d0b84ac diff --git a/sci-chemistry/psi/files/3.4.0-destdir.patch b/sci-chemistry/psi/files/3.4.0-destdir.patch new file mode 100644 index 000000000000..45db9529aa4d --- /dev/null +++ b/sci-chemistry/psi/files/3.4.0-destdir.patch @@ -0,0 +1,41 @@ +diff --git a/Makefile.in b/Makefile.in +index aca5a16..2e49f0a 100644 +--- a/Makefile.in ++++ b/Makefile.in +@@ -8,6 +8,7 @@ subdirs = lib include src + + top_srcdir = @top_srcdir@ + srcdir = @srcdir@ ++datarootdir = @datarootdir@ + VPATH = @srcdir@ + top_objdir = . + +diff --git a/lib/ruby/Makefile.in b/lib/ruby/Makefile.in +index b31ce7f..e099e1b 100644 +--- a/lib/ruby/Makefile.in ++++ b/lib/ruby/Makefile.in +@@ -29,10 +29,10 @@ ccenergy.rb cclambda.rb chkpt.rb color.rb deriv2.rb frequ + cceom.rb ccsort.rb cints.rb cphf.rb detci.rb input.rb optking.rb psi3.rb testcases.rb + + install: $(RUBYSRC) +- $(MKDIRS) $(rubydatadir) ++ $(MKDIRS) $(DESTDIR)/$(rubydatadir) + for rbfile in $(RUBYSRC); \ + do \ +- ($(INSTALL_DATA) $(srcdir)/$${rbfile} $(rubydatadir)) || exit 1; \ ++ ($(INSTALL_DATA) $(srcdir)/$${rbfile} $(DESTDIR)/$(rubydatadir)) || exit 1; \ + done + + install_man: +diff --git a/src/bin/Makefile.in b/src/bin/Makefile.in +index e1abb46..4eddf8d 100644 +--- a/src/bin/Makefile.in ++++ b/src/bin/Makefile.in +@@ -65,6 +65,7 @@ targetclean: + + top_srcdir = @top_srcdir@ + srcdir = @srcdir@ ++datarootdir = @datarootdir@ + top_objdir = ../.. + + $(top_srcdir)/configure: $(top_srcdir)/configure.ac $(top_srcdir)/aclocal.m4 diff --git a/sci-chemistry/psi/files/3.4.0-dont-build-libint.patch b/sci-chemistry/psi/files/3.4.0-dont-build-libint.patch new file mode 100644 index 000000000000..0d65cee8a1a9 --- /dev/null +++ b/sci-chemistry/psi/files/3.4.0-dont-build-libint.patch @@ -0,0 +1,13 @@ +diff --git a/src/lib/Makefile.in b/src/lib/Makefile.in +index 42e025d..b098a36 100644 +--- a/src/lib/Makefile.in ++++ b/src/lib/Makefile.in +@@ -2,7 +2,7 @@ + .PHONY: default all install depend clean dclean targetclean + + subdirs = libipv1 libciomr libchkpt libqt libpsio libiwl libdpd libutil \ +- liboptions libmoinfo libint libderiv libr12 libbasis libmints ++ liboptions libmoinfo libbasis libmints + + all: default + diff --git a/sci-chemistry/psi/files/3.4.0-fortify.patch b/sci-chemistry/psi/files/3.4.0-fortify.patch new file mode 100644 index 000000000000..5f098399ad3f --- /dev/null +++ b/sci-chemistry/psi/files/3.4.0-fortify.patch @@ -0,0 +1,58 @@ + src/bin/ccenergy/get_params.cc | 2 +- + src/bin/cclambda/get_params.cc | 2 +- + src/bin/ccresponse/get_params.cc | 2 +- + src/bin/ccsort/get_params.cc | 2 +- + 4 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/src/bin/ccenergy/get_params.cc b/src/bin/ccenergy/get_params.cc +index 53f4c83..a2fa932 100644 +--- a/src/bin/ccenergy/get_params.cc ++++ b/src/bin/ccenergy/get_params.cc +@@ -193,7 +193,7 @@ void get_params() + } + } + else if(params.local) { +- local.weakp = (char *) malloc(4 * sizeof(char)); ++ local.weakp = (char *) malloc(5 * sizeof(char)); + sprintf(local.weakp, "%s", "NONE"); + } + +diff --git a/src/bin/cclambda/get_params.cc b/src/bin/cclambda/get_params.cc +index 4a9d2c8..8a2ae17 100644 +--- a/src/bin/cclambda/get_params.cc ++++ b/src/bin/cclambda/get_params.cc +@@ -150,7 +150,7 @@ void get_params(void) + } + } + else if(params.local) { +- local.weakp = (char *) malloc(4 * sizeof(char)); ++ local.weakp = (char *) malloc(5 * sizeof(char)); + sprintf(local.weakp, "%s", "NONE"); + } + +diff --git a/src/bin/ccresponse/get_params.cc b/src/bin/ccresponse/get_params.cc +index a96db13..5c40aa0 100644 +--- a/src/bin/ccresponse/get_params.cc ++++ b/src/bin/ccresponse/get_params.cc +@@ -207,7 +207,7 @@ void get_params() + } + } + else if(params.local) { +- local.weakp = (char *) malloc(4 * sizeof(char)); ++ local.weakp = (char *) malloc(5 * sizeof(char)); + sprintf(local.weakp, "%s", "NONE"); + } + +diff --git a/src/bin/ccsort/get_params.cc b/src/bin/ccsort/get_params.cc +index ad7f0c3..6ee1993 100644 +--- a/src/bin/ccsort/get_params.cc ++++ b/src/bin/ccsort/get_params.cc +@@ -120,7 +120,7 @@ void get_params() + } + } + else if(params.local) { +- local.weakp = (char *) malloc(4 * sizeof(char)); ++ local.weakp = (char *) malloc(5 * sizeof(char)); + sprintf(local.weakp, "%s", "NONE"); + } + diff --git a/sci-chemistry/psi/files/3.4.0-gcc-4.3.patch b/sci-chemistry/psi/files/3.4.0-gcc-4.3.patch new file mode 100644 index 000000000000..8283e6d8d8ea --- /dev/null +++ b/sci-chemistry/psi/files/3.4.0-gcc-4.3.patch @@ -0,0 +1,293 @@ +diff --git a/src/bin/mcscf/block_matrix.cc b/src/bin/mcscf/block_matrix.cc +index fe1e131..3ad0bcd 100644 +--- a/src/bin/mcscf/block_matrix.cc ++++ b/src/bin/mcscf/block_matrix.cc +@@ -1,6 +1,7 @@ + #include "block_matrix.h" + #include "matrix_base.h" + #include "memory_manager.h" ++#include <cstdio> + + extern FILE* outfile; + +diff --git a/src/bin/mcscf/block_vector.cc b/src/bin/mcscf/block_vector.cc +index fb383c7..36f55d4 100644 +--- a/src/bin/mcscf/block_vector.cc ++++ b/src/bin/mcscf/block_vector.cc +@@ -1,6 +1,7 @@ + #include "block_vector.h" + #include "vector_base.h" + #include "memory_manager.h" ++#include <cstdio> + + extern FILE* outfile; + +diff --git a/src/bin/mcscf/sblock_matrix.cc b/src/bin/mcscf/sblock_matrix.cc +index 61aa7cc..4da4263 100644 +--- a/src/bin/mcscf/sblock_matrix.cc ++++ b/src/bin/mcscf/sblock_matrix.cc +@@ -1,4 +1,5 @@ + #include <cstdlib> ++#include <cstdio> + #include <psifiles.h> + #include "sblock_matrix.h" + +@@ -103,4 +104,4 @@ void SBlockMatrix::check(const char* cstr) + } + } + +-}} +\ No newline at end of file ++}} +diff --git a/src/bin/mcscf/sblock_vector.cc b/src/bin/mcscf/sblock_vector.cc +index 63c3926..f24fc5b 100644 +--- a/src/bin/mcscf/sblock_vector.cc ++++ b/src/bin/mcscf/sblock_vector.cc +@@ -1,4 +1,5 @@ + #include <cstdlib> ++#include <cstdio> + #include <psifiles.h> + + #include "sblock_vector.h" +@@ -58,4 +59,4 @@ void SBlockVector::check(const char* cstr) + } + } + +-}} +\ No newline at end of file ++}} +diff --git a/src/bin/mcscf/scf.cc b/src/bin/mcscf/scf.cc +index 77318fd..7d1e17f 100644 +--- a/src/bin/mcscf/scf.cc ++++ b/src/bin/mcscf/scf.cc +@@ -5,6 +5,7 @@ + + #include <iostream> + #include <cmath> ++#include <cstdio> + + extern FILE* outfile; + +diff --git a/src/bin/mcscf/scf_Feff.cc b/src/bin/mcscf/scf_Feff.cc +index 584aa83..8a99c3b 100644 +--- a/src/bin/mcscf/scf_Feff.cc ++++ b/src/bin/mcscf/scf_Feff.cc +@@ -1,4 +1,5 @@ + #include <liboptions/liboptions.h> ++#include <cstdio> + + #include "scf.h" + +diff --git a/src/bin/mcscf/scf_canonicalize_MO.cc b/src/bin/mcscf/scf_canonicalize_MO.cc +index a2b3915..96bb6cc 100644 +--- a/src/bin/mcscf/scf_canonicalize_MO.cc ++++ b/src/bin/mcscf/scf_canonicalize_MO.cc +@@ -1,6 +1,7 @@ + #include "scf.h" + + #include <liboptions/liboptions.h> ++#include <cstdio> + + namespace psi{ namespace mcscf{ + +diff --git a/src/bin/mcscf/scf_check_orthonormality.cc b/src/bin/mcscf/scf_check_orthonormality.cc +index 63fbbbb..a13436c 100644 +--- a/src/bin/mcscf/scf_check_orthonormality.cc ++++ b/src/bin/mcscf/scf_check_orthonormality.cc +@@ -1,5 +1,6 @@ + #include <iostream> + #include <cmath> ++#include <cstdio> + + #include "scf.h" + +diff --git a/src/bin/mcscf/scf_compute_energy.cc b/src/bin/mcscf/scf_compute_energy.cc +index fe7ee6d..20194eb 100644 +--- a/src/bin/mcscf/scf_compute_energy.cc ++++ b/src/bin/mcscf/scf_compute_energy.cc +@@ -1,4 +1,5 @@ + #include <iostream> ++#include <cstdio> + + #include "scf.h" + +diff --git a/src/bin/mcscf/scf_diis.cc b/src/bin/mcscf/scf_diis.cc +index 9bcde15..261492a 100644 +--- a/src/bin/mcscf/scf_diis.cc ++++ b/src/bin/mcscf/scf_diis.cc +@@ -1,4 +1,5 @@ + #include <iostream> ++#include <cstdio> + + #include <liboptions/liboptions.h> + +diff --git a/src/bin/mcscf/scf_iterate_scf_equations.cc b/src/bin/mcscf/scf_iterate_scf_equations.cc +index 9e96360..3a3acc3 100644 +--- a/src/bin/mcscf/scf_iterate_scf_equations.cc ++++ b/src/bin/mcscf/scf_iterate_scf_equations.cc +@@ -1,6 +1,7 @@ + #include <cstdlib> + #include <iostream> + #include <cmath> ++#include <cstdio> + + #include <liboptions/liboptions.h> + +diff --git a/src/bin/mcscf/scf_pairs.cc b/src/bin/mcscf/scf_pairs.cc +index b0a8c9d..af5fc35 100644 +--- a/src/bin/mcscf/scf_pairs.cc ++++ b/src/bin/mcscf/scf_pairs.cc +@@ -1,4 +1,5 @@ + #include <iostream> ++#include <cstdio> + + #include <libmoinfo/libmoinfo.h> + +diff --git a/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc b/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc +index 3aac92a..e28e9e3 100644 +--- a/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc ++++ b/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc +@@ -3,6 +3,7 @@ + #include <string> + #include <utility> + #include <algorithm> ++#include <cstdio> + + #include <libmoinfo/libmoinfo.h> + +diff --git a/src/bin/psimrcc/blas_algorithms.cc b/src/bin/psimrcc/blas_algorithms.cc +index bb36025..0a5a3e2 100644 +--- a/src/bin/psimrcc/blas_algorithms.cc ++++ b/src/bin/psimrcc/blas_algorithms.cc +@@ -1,5 +1,6 @@ + #include <libmoinfo/libmoinfo.h> + #include <libutil/libutil.h> ++#include <cstdio> + + #include "blas.h" + #include "memory_manager.h" +diff --git a/src/bin/psimrcc/blas_compatibile.cc b/src/bin/psimrcc/blas_compatibile.cc +index 8de6d73..7caf4f3 100644 +--- a/src/bin/psimrcc/blas_compatibile.cc ++++ b/src/bin/psimrcc/blas_compatibile.cc +@@ -1,6 +1,7 @@ + #include "blas.h" + #include <libutil/libutil.h> + #include <cstdlib> ++#include <cstdio> + + extern FILE *infile, *outfile; + +diff --git a/src/bin/psimrcc/blas_parser.cc b/src/bin/psimrcc/blas_parser.cc +index d211a24..78fe60a 100644 +--- a/src/bin/psimrcc/blas_parser.cc ++++ b/src/bin/psimrcc/blas_parser.cc +@@ -3,6 +3,7 @@ + #include "debugging.h" + #include <libutil/libutil.h> + #include <algorithm> ++#include <cstdio> + + namespace psi{ namespace psimrcc{ + +diff --git a/src/bin/psimrcc/blas_solve.cc b/src/bin/psimrcc/blas_solve.cc +index b138a5b..f5dcdfc 100644 +--- a/src/bin/psimrcc/blas_solve.cc ++++ b/src/bin/psimrcc/blas_solve.cc +@@ -1,6 +1,7 @@ + #include "blas.h" + #include "debugging.h" + #include <libmoinfo/libmoinfo.h> ++#include <cstdio> + + namespace psi{ namespace psimrcc{ + +diff --git a/src/bin/psimrcc/index.cc b/src/bin/psimrcc/index.cc +index 3465d88..68c2b77 100644 +--- a/src/bin/psimrcc/index.cc ++++ b/src/bin/psimrcc/index.cc +@@ -5,6 +5,7 @@ + ***************************************************************************/ + #include <iostream> + #include <algorithm> ++#include <cstdio> + + #include <libmoinfo/libmoinfo.h> + +diff --git a/src/bin/psimrcc/operation.cc b/src/bin/psimrcc/operation.cc +index edbaed5..f4e881f 100644 +--- a/src/bin/psimrcc/operation.cc ++++ b/src/bin/psimrcc/operation.cc +@@ -7,6 +7,7 @@ + #include "debugging.h" + #include "blas.h" + #include <libutil/libutil.h> ++#include <cstdio> + + namespace psi{ namespace psimrcc{ + +diff --git a/src/bin/psimrcc/operation_compute.cc b/src/bin/psimrcc/operation_compute.cc +index 7d2553c..72a1b39 100644 +--- a/src/bin/psimrcc/operation_compute.cc ++++ b/src/bin/psimrcc/operation_compute.cc +@@ -11,6 +11,7 @@ + #include "algebra_interface.h" + #include <libmoinfo/libmoinfo.h> + #include <cstdlib> ++#include <cstdio> + + extern FILE *infile, *outfile; + +diff --git a/src/bin/psimrcc/sort_out_of_core.cc b/src/bin/psimrcc/sort_out_of_core.cc +index 3f255c9..8fa31a3 100644 +--- a/src/bin/psimrcc/sort_out_of_core.cc ++++ b/src/bin/psimrcc/sort_out_of_core.cc +@@ -8,6 +8,7 @@ + #include "sort.h" + #include "matrix.h" + #include <libmoinfo/libmoinfo.h> ++#include <cstdio> + + extern FILE* outfile; + +diff --git a/src/lib/libmoinfo/moinfo_model_space.cc b/src/lib/libmoinfo/moinfo_model_space.cc +index 3bf2030..0a63cde 100644 +--- a/src/lib/libmoinfo/moinfo_model_space.cc ++++ b/src/lib/libmoinfo/moinfo_model_space.cc +@@ -1,6 +1,7 @@ + #include <iostream> + #include <cmath> + #include <cstdlib> ++#include <cstdio> + + #include <psifiles.h> + #include <liboptions/liboptions.h> +@@ -322,4 +323,4 @@ vector<string> MOInfo::get_matrix_names(std::string str) + return(names); + } + +-} +\ No newline at end of file ++} +diff --git a/src/lib/libmoinfo/moinfo_slaterdeterminant.cc b/src/lib/libmoinfo/moinfo_slaterdeterminant.cc +index 8831cd5..a046679 100644 +--- a/src/lib/libmoinfo/moinfo_slaterdeterminant.cc ++++ b/src/lib/libmoinfo/moinfo_slaterdeterminant.cc +@@ -1,4 +1,5 @@ + #include <iostream> ++#include <cstdio> + #include "moinfo.h" + + extern FILE *infile, *outfile; +diff --git a/src/lib/libutil/stl_string.cc b/src/lib/libutil/stl_string.cc +index 0ec247d..f719dcd 100644 +--- a/src/lib/libutil/stl_string.cc ++++ b/src/lib/libutil/stl_string.cc +@@ -2,6 +2,7 @@ + #include <cmath> + #include <iomanip> + #include <algorithm> ++#include <cstdio> + + #include "libutil.h" + diff --git a/sci-chemistry/psi/files/3.4.0-ldflags.patch b/sci-chemistry/psi/files/3.4.0-ldflags.patch new file mode 100644 index 000000000000..9d7f2767e8ec --- /dev/null +++ b/sci-chemistry/psi/files/3.4.0-ldflags.patch @@ -0,0 +1,21 @@ +Respect LDFLAGS + +--- configure.ac ++++ configure.ac +@@ -288,15 +288,13 @@ + ) + AC_SUBST(LDLIBS) + +-LDFLAGS= + LIBDIRS= + AC_ARG_WITH(libdirs, + [ --with-libdirs Specifies library directories (-Ldir1 -Ldir2).], + LIBDIRS=$withval +-LDFLAGS=$withval + AC_MSG_RESULT([Using extra library directories: $withval]) + ) +-AC_SUBST(LDFLAGS) ++AC_SUBST(LIBDIRS) + + AC_CHECK_PROGS(PERL,perl,perl) AC_SUBST(PERL) + diff --git a/sci-chemistry/psi/files/3.4.0-man_paths.patch b/sci-chemistry/psi/files/3.4.0-man_paths.patch new file mode 100644 index 000000000000..02cced160847 --- /dev/null +++ b/sci-chemistry/psi/files/3.4.0-man_paths.patch @@ -0,0 +1,25 @@ +Fix man paths + +http://bugs.gentoo.org/show_bug.cgi?id=326185 + +--- src/bin/nonbonded/Makefile.in ++++ src/bin/nonbonded/Makefile.in +@@ -19,5 +19,5 @@ + endif + + install_man:: nonbonded.1 +- $(MKDIRS) $(mandir)/man1 +- $(INSTALL_INCLUDE) $^ $(mandir)/man1 ++ $(MKDIRS) $(DESTDIR)$(mandir)/man1 ++ $(INSTALL_INCLUDE) $^ $(DESTDIR)$(mandir)/man1 +--- src/bin/intder/Makefile.in ++++ src/bin/intder/Makefile.in +@@ -21,6 +21,6 @@ + endif + + install_man:: intder.1 +- $(MKDIRS) $(mandir)/man1 +- $(INSTALL_INCLUDE) $^ $(mandir)/man1 ++ $(MKDIRS) $(DESTDIR)$(mandir)/man1 ++ $(INSTALL_INCLUDE) $^ $(DESTDIR)$(mandir)/man1 + diff --git a/sci-chemistry/psi/files/3.4.0-parallel_fix.patch b/sci-chemistry/psi/files/3.4.0-parallel_fix.patch new file mode 100644 index 000000000000..65234fb40dcb --- /dev/null +++ b/sci-chemistry/psi/files/3.4.0-parallel_fix.patch @@ -0,0 +1,400 @@ +--- Makefile.in ++++ Makefile.in +@@ -17,62 +17,19 @@ + INSTALL = @INSTALL@ + INSTALL_PROGRAM = @INSTALL_PROGRAM@ + +-all: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making in $${dir} && $(MAKE) all) || exit 1; \ +- done +- +-install: install_host +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making install in $${dir} && $(MAKE) install) || exit 1; \ +- done +- +-install_inc: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_inc) || exit 1; \ +- done +- +-install_man: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_man) || exit 1; \ +- done +- +-depend: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making depend in $${dir} && $(MAKE) depend) || exit 1; \ +- done +- +-clean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making clean in $${dir} && $(MAKE) clean) || exit 1; \ +- done +- +-dclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making dclean in $${dir} && $(MAKE) dclean) || exit 1; \ +- done +- +-targetclean: +- for dir in $(subdirs) tests doc; \ +- do \ +- (cd $${dir} && echo Making clean in $${dir} && $(MAKE) targetclean) || exit 1; \ +- done ++all clean install install_inc install_man depend dclean targetclean: ++ for dir in $(subdirs); do \ ++ $(MAKE) -C $$dir $@; \ ++ done + + tests: +- (cd tests && echo Running test suite... && $(MAKE)) || exit 1; ++ $(MAKE) -C tests + + testsclean: +- (cd tests && echo Cleaning test suite... && $(MAKE) clean) || exit 1; ++ $(MAKE) -C tests clean + + doc: +- (cd doc && echo Building documentation... && $(MAKE)) || exit 1; ++ $(MAKE) -C doc + + $(top_srcdir)/configure: $(top_srcdir)/configure.ac $(top_srcdir)/aclocal.m4 + cd $(top_srcdir) && autoconf +--- lib/Makefile.in ++++ lib/Makefile.in +@@ -31,7 +31,7 @@ + $(INSTALL_DATA) $(srcdir)/psi.dat $(DESTDIR)$(pkgdatadir) + for dir in $(subdirs); \ + do \ +- (cd $${dir}; echo Making in $${dir}; $(MAKE) install) || exit 1; \ ++ $(MAKE) -C $$dir install; \ + done + + install_man: macro.psi +--- src/Makefile.in ++++ src/Makefile.in +@@ -6,53 +6,10 @@ + + default: all + +-all: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making in $${dir} && $(MAKE) all) || exit 1; \ +- done +- +-install: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making install in $${dir} && $(MAKE) install) || exit 1; \ +- done +- +-install_inc: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_inc) || exit 1; \ +- done +- +-install_man: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_man) || exit 1; \ +- done +- +-depend: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making depend in $${dir} && $(MAKE) depend) || exit 1; \ +- done +- +-clean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making clean in $${dir} && $(MAKE) clean) || exit 1; \ +- done +- +-dclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making dclean in $${dir} && $(MAKE) dclean) || exit 1; \ +- done +- +-targetclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo Making clean in $${dir} && $(MAKE) targetclean) || exit 1; \ +- done ++all clean install depend dclean targetclean: ++ for dir in $(subdirs); do \ ++ $(MAKE) -C $$dir $@; \ ++ done + + top_srcdir = @top_srcdir@ + srcdir = @srcdir@ +--- src/lib/Makefile.in ++++ src/lib/Makefile.in +@@ -4,56 +4,10 @@ + subdirs = libipv1 libciomr libchkpt libqt libpsio libiwl libdpd libutil \ + liboptions libmoinfo libbasis libmints + +-all: default +- +-default: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \ +- done +- +-install: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \ +- done +- +-install_inc: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \ +- done +- +-install_man: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \ +- done +- +-depend: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \ +- done +- +-clean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \ +- done +- +-dclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \ +- done +- +-targetclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \ +- done +- ++all clean install install_inc install_man depend dclean targetclean: ++ for dir in $(subdirs); do \ ++ $(MAKE) -C $$dir $@; \ ++ done + + # + # keep the configuration information and makefile up-to-date +--- src/bin/Makefile.in ++++ src/bin/Makefile.in +@@ -13,55 +13,10 @@ + subdirs += psirb + endif + +-all: default +- +-default: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \ +- done +- +-install: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \ +- done +- +-install_inc: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \ +- done +- +-install_man: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \ +- done +- +-depend: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \ +- done +- +-clean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \ +- done +- +-dclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \ +- done +- +-targetclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \ +- done ++all install depend clean dclean targetclean: ++ for dir in $(subdirs); do \ ++ $(MAKE) -C $$dir $@; \ ++ done + + top_srcdir = @top_srcdir@ + srcdir = @srcdir@ +--- src/samples/Makefile.in ++++ src/samples/Makefile.in +@@ -5,55 +5,10 @@ + + subdirs = mints + +-all: default +- +-default: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \ +- done +- +-install: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \ +- done +- +-install_inc: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \ +- done +- +-install_man: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \ +- done +- +-depend: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \ +- done +- +-clean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \ +- done +- +-dclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \ +- done +- +-targetclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \ +- done ++all install depend clean dclean targetclean: ++ for dir in $(subdirs); do \ ++ $(MAKE) -C $$dir $@; \ ++ done + + top_srcdir = @top_srcdir@ + srcdir = @srcdir@ +--- src/util/Makefile.in ++++ src/util/Makefile.in +@@ -3,55 +3,10 @@ + + subdirs = tocprint psi2molden + +-all: default +- +-default: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \ +- done +- +-install: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \ +- done +- +-install_inc: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \ +- done +- +-install_man: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \ +- done +- +-depend: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \ +- done +- +-clean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \ +- done +- +-dclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \ +- done +- +-targetclean: +- for dir in $(subdirs); \ +- do \ +- (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \ +- done ++all install depend clean dclean targetclean: ++ for dir in $(subdirs); do \ ++ $(MAKE) -C $$dir $@; \ ++ done + + top_srcdir = @top_srcdir@ + srcdir = @srcdir@ +--- src/lib/libipv1/Makefile.in ++++ src/lib/libipv1/Makefile.in +@@ -58,4 +58,4 @@ + # in case DODEPEND is no + # + +-ip_read.o: y.tab.h ++ip_read.o: y.tab.c y.tab.h diff --git a/sci-chemistry/psi/files/psi-3.4.0-format-security.patch b/sci-chemistry/psi/files/psi-3.4.0-format-security.patch new file mode 100644 index 000000000000..10efa813ba3d --- /dev/null +++ b/sci-chemistry/psi/files/psi-3.4.0-format-security.patch @@ -0,0 +1,33 @@ + src/lib/libmints/matrix.cc | 12 +++++------- + 1 file changed, 5 insertions(+), 7 deletions(-) + +diff --git a/src/lib/libmints/matrix.cc b/src/lib/libmints/matrix.cc +index 2ce5ede..2c7b5de 100644 +--- a/src/lib/libmints/matrix.cc ++++ b/src/lib/libmints/matrix.cc +@@ -549,10 +549,9 @@ void Matrix::save(const char *filename, bool append, bool saveLowerTriangle, boo + } else { + out = fopen(filename, "w"); + } +- +- fprintf(out, name_.c_str()); +- fprintf(out, "\n"); +- ++ ++ fprintf(out, "%s\n", name_.c_str()); ++ + if (saveSubBlocks == false) { + // Convert the matrix to a full matrix + double **fullblock = to_block_matrix(); +@@ -1083,9 +1082,8 @@ void SimpleMatrix::save(const char *filename, bool append, bool saveLowerTriangl + } else { + out = fopen(filename, "w"); + } +- +- fprintf(out, name_.c_str()); +- fprintf(out, "\n"); ++ ++ fprintf(out, "%s\n", name_.c_str()); + + if (saveLowerTriangle) { + // Count the number of non-zero element diff --git a/sci-chemistry/psi/files/psi-3.4.0-parallel-make.patch b/sci-chemistry/psi/files/psi-3.4.0-parallel-make.patch new file mode 100644 index 000000000000..2805cb195e24 --- /dev/null +++ b/sci-chemistry/psi/files/psi-3.4.0-parallel-make.patch @@ -0,0 +1,19 @@ +diff --git a/src/lib/libipv1/Makefile.in b/src/lib/libipv1/Makefile.in +index eafe8e2..141bf3b 100644 +--- a/src/lib/libipv1/Makefile.in ++++ b/src/lib/libipv1/Makefile.in +@@ -33,10 +33,12 @@ LIBOBJ = $(ALLCSRC:%.c=%.o) $(ALLCXXSRC:%.cc=%.o) + + include ../MakeRules + +-y.tab.c y.tab.h: parse.y ++y.tab.h: y.tab.c ++ ++y.tab.c: parse.y + $(YACC) -v -d $< + +-scan.c: scan.l ++scan.c: scan.l y.tab.h + $(LEX) -t $^ > scan.c + + install_inc:: $(ALLINCLUDE) diff --git a/sci-chemistry/psi/files/use-external-libint.patch b/sci-chemistry/psi/files/use-external-libint.patch new file mode 100644 index 000000000000..1d9ce91e3111 --- /dev/null +++ b/sci-chemistry/psi/files/use-external-libint.patch @@ -0,0 +1,37 @@ +--- psi3.orig/src/bin/cints/Makefile.in 2003-11-14 08:15:19.000000000 -0800 ++++ psi3/src/bin/cints/Makefile.in 2006-02-10 22:42:31.000000000 -0800 +@@ -51,25 +51,25 @@ + # and form the list of the libraries. Remember that libderiv and libr12 + # depend on libint, and hence need to come first for GNU ld to work. + # +-INTLIBS := -lPSI_int ++INTLIBS := -lint + ifeq ($(findstring MP2R12,$(SUBDIRS)),MP2R12) +- ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12) +- INTLIBS := -lPSI_r12 $(INTLIBS) ++ ifneq ($(findstring -lr12,$(INTLIBS)),-lr12) ++ INTLIBS := -lr12 $(INTLIBS) + endif + endif + ifeq ($(findstring R12_Ints,$(SUBDIRS)),R12_Ints) +- ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12) +- INTLIBS := -lPSI_r12 $(INTLIBS) ++ ifneq ($(findstring -lr12,$(INTLIBS)),-lr12) ++ INTLIBS := -lr12 $(INTLIBS) + endif + endif + ifeq ($(findstring Default_Deriv1,$(SUBDIRS)),Default_Deriv1) +- ifneq ($(findstring -lPSI_deriv,$(INTLIBS)),-lPSI_deriv) +- INTLIBS := -lPSI_deriv $(INTLIBS) ++ ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv) ++ INTLIBS := -lderiv $(INTLIBS) + endif + endif + ifeq ($(findstring Default_Deriv2,$(SUBDIRS)),Default_Deriv2) +- ifneq ($(findstring -lderiv,$(INTLIBS)),-lPSI_deriv) +- INTLIBS := -lPSI_deriv $(INTLIBS) ++ ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv) ++ INTLIBS := -lderiv $(INTLIBS) + endif + endif + diff --git a/sci-chemistry/psi/metadata.xml b/sci-chemistry/psi/metadata.xml new file mode 100644 index 000000000000..e18109f21fcd --- /dev/null +++ b/sci-chemistry/psi/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">psicode</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/psi/psi-3.4.0-r2.ebuild b/sci-chemistry/psi/psi-3.4.0-r2.ebuild new file mode 100644 index 000000000000..34dd75b6c1df --- /dev/null +++ b/sci-chemistry/psi/psi-3.4.0-r2.ebuild @@ -0,0 +1,85 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit autotools-utils fortran-2 multilib toolchain-funcs + +DESCRIPTION="Suite for ab initio quantum chemistry computing various molecular properties" +HOMEPAGE="http://www.psicode.org/" +SRC_URI="mirror://sourceforge/psicode/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="static-libs test" + +RDEPEND=" + !sci-visualization/extrema + virtual/blas + virtual/lapack + >=sci-libs/libint-1.1.4:1" +DEPEND="${RDEPEND} + virtual/pkgconfig + dev-util/byacc + test? ( dev-lang/perl )" + +S="${WORKDIR}/${PN}${PV:0:1}" + +PATCHES=( + "${FILESDIR}"/${PV}-dont-build-libint.patch + "${FILESDIR}"/use-external-libint.patch + "${FILESDIR}"/${PV}-gcc-4.3.patch + "${FILESDIR}"/${PV}-destdir.patch + "${FILESDIR}"/${P}-parallel-make.patch + "${FILESDIR}"/${PV}-man_paths.patch + "${FILESDIR}"/${PV}-ldflags.patch + "${FILESDIR}"/${PV}-parallel_fix.patch + "${FILESDIR}"/${PV}-fortify.patch + "${FILESDIR}"/${P}-format-security.patch + ) + +src_prepare() { + autotools-utils_src_prepare + # Broken test + sed \ + -e 's:scf-mvd-opt ::g' \ + -e 's:scf-mvd-opt-puream ::g' \ + -i tests/Makefile.in || die + + sed \ + -e "/LIBPATTERNS/d" \ + -i src/{bin,util,samples}/MakeVars.in || die + eautoreconf +} + +src_configure() { + # This variable gets set sometimes to /usr/lib/src and breaks stuff + unset CLIBS + + local myeconfargs=( + --with-opt="${CXXFLAGS}" + --datadir="${EPREFIX}"/usr/share/${PN} + --with-blas="$($(tc-getPKG_CONFIG) blas --libs)" + --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile \ + SCRATCH="${WORKDIR}/libint" \ + DODEPEND="no" \ + YACC=byacc +} + +src_test() { + emake EXECDIR="${S}"/bin TESTFLAGS="" -j1 tests +} + +src_install() { + autotools-utils_src_install DODEPEND="no" + if ! use static-libs; then + rm -f "${ED}"/usr/$(get_libdir)/*.a || die + fi +} diff --git a/sci-chemistry/pymol-plugins-bni-tools/Manifest b/sci-chemistry/pymol-plugins-bni-tools/Manifest new file mode 100644 index 000000000000..dfb798d76f48 --- /dev/null +++ b/sci-chemistry/pymol-plugins-bni-tools/Manifest @@ -0,0 +1,5 @@ +DIST bni-tools-027.zip 33753 SHA256 9ddb9785146b12c5c2ff03d34262fec8ff04bfaa9c56ec4665bac5e33879cd7c SHA512 9c0ef1ca5bbb3040192ab2668f354f947e93d42c91a0cfdde5d05be273e6ba9f29ec3c6ee86367f18d87316282b4e0141183b8d6259bd36d44010b7bbb7666e5 WHIRLPOOL 7e14a2ef86009237f53e28f6ac95b56687dd7275e8bd8a856c4d408a6c57cffb7131cb9a505d01da7b2f58bf20bae9b400e478d994bb04f9e799ecf09a60edd3 +EBUILD pymol-plugins-bni-tools-0.27.ebuild 912 SHA256 a0395a390016e3de6821357ac0c48cfe8848bfbc3fb763d1c3a081298da6dee6 SHA512 4e685c3c1c96849cf7f5144fa3ac6114c943e4feb2d66f2797f2b611150d06d1849a140ffc8a8ba50d20dd9ee032392c38c144ebc52576666229854ff21544dc WHIRLPOOL 81fdbe4f624a6992f4517803d858e0b3a0caa62b8fdb9f9b6cf3536e8691252869f3c3379cdbc2ca6fcbe076d4d5f675cadcdcc3102d7b8ff5f220c0297660c3 +MISC ChangeLog 3066 SHA256 deb9e8ebcd8866e508bfd3f44a110f7a8e62041e30a589ef174f2a6c2035cf7a SHA512 2507e6a2e57cde067f844e1153f9eee2ae8f8d5ff859175976e4b828569ba53512f0867cd8bb4d9fcba407cc8247507b9d27377b97ef9fae7596c1b9b1599801 WHIRLPOOL 5846319e6a66e39d07d6f4dc1d1ffa1baf4e2ea5e636b78a9b38180cafd2d46124aaccacd925de5aeebc52993402124d93a1c0c01bd79694da0f888516cab207 +MISC ChangeLog-2015 745 SHA256 aa56e68f8e3f788d6925006664023d51a35dab5916544c3c28f2ff454850f014 SHA512 d580832679bfd4ff10032ecb549db06150bd9b28db05cea03957b2b775282b921a47485516d3fc52c6cad06da4b4264c8ea6d8316276ec34361a1c900fa3a87b WHIRLPOOL 80a7712e994ba0d74ec8ec70517c78a2fafaeed62c6f37445c0b72a3d122119e7527b1cbe6a57e03d6eafad78e2c2f904a22b46332bca3b4d36cc92dbfc6690c +MISC metadata.xml 354 SHA256 3589352b3a0262edff58e2131c426fe772eb3bbefb24b7ac40b97135c51f3e13 SHA512 b5f667e6315a0841a28c45fcd7c218d0b5c5e0ad3cdd63870001f1fcd2e4adf598d2b1270a77aa71c1d5d2fe985ca1d98d4c3f88cd540740e67f3469709a94a8 WHIRLPOOL ecd12ea2220fdcb3985fdc253e4ee25e3e6822275a242a0fc754de46f7eb057026ab4e0f1088cb1768d857d9f1afdb06509e40c54710cf4fc439377d0aee6cf7 diff --git a/sci-chemistry/pymol-plugins-bni-tools/metadata.xml b/sci-chemistry/pymol-plugins-bni-tools/metadata.xml new file mode 100644 index 000000000000..0f732a212193 --- /dev/null +++ b/sci-chemistry/pymol-plugins-bni-tools/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">bni-tools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.27.ebuild b/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.27.ebuild new file mode 100644 index 000000000000..1de68c64d64f --- /dev/null +++ b/sci-chemistry/pymol-plugins-bni-tools/pymol-plugins-bni-tools-0.27.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-r1 versionator + +MY_PN="${PN#pymol-plugins-}" +MY_P="${MY_PN}-$(delete_version_separator 1)" +MY_P_DOT="${MY_PN}-${PV}" + +DESCRIPTION="Gives Pymol additional functionalities and presets to the PyMOL GUI" +HOMEPAGE="http://bni-tools.sourceforge.net/" +SRC_URI="mirror://sourceforge/${MY_PN}/${MY_PN}/${MY_P_DOT}/${MY_P}.zip" + +LICENSE="CNRI" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + sci-chemistry/pymol[${PYTHON_USEDEP}]" +DEPEND="${PYTHON_DEPS} + app-arch/unzip" + +S="${WORKDIR}" + +src_install() { + python_moduleinto pmg_tk/startup + python_foreach_impl python_domodule bni-tools.py + python_foreach_impl python_optimize + dodoc readme.txt + dohtml ShortCommandDescription.html +} diff --git a/sci-chemistry/pymol-plugins-caver/Manifest b/sci-chemistry/pymol-plugins-caver/Manifest new file mode 100644 index 000000000000..037377b0bf00 --- /dev/null +++ b/sci-chemistry/pymol-plugins-caver/Manifest @@ -0,0 +1,5 @@ +DIST Caver2_1_2_pymol_plugin.zip 5698331 SHA256 1dcc61ba13247c05710c4cd68491d0c867ce1d0c11c824be85a516250b2874e3 SHA512 9d28e059bb20f30cf6a0d25ed2eb080dcf9dbb753e9d4578d95e293b31c5cf5fe23d5177dccdb79c192ab3e65bb484b6eb22b26c267637b125404f871e01a52c WHIRLPOOL 33e6893d2114b5ce197fc098d09dfc67ce88f38741e30f1fa574873836c636b5e0c180301849fd98f1f93de5ce51554d2245d0bd615b938d39a802e91e68ebb9 +EBUILD pymol-plugins-caver-2.1.2.ebuild 1288 SHA256 9e012936884d8e1ebe5042f379e2e607581786ca19080d999cdb66d3697e6042 SHA512 7afa7038ef1fdbdc04120f15ac85a58152429d8f3cd03408c67355ffc6c825e4accc6f503b2522c7702851db421f46f3a28f7d8ce070c02848ba01e24c871d79 WHIRLPOOL 872f060561828229c17e8bd13de519b87d44dc37d6eb080fae5bd0438f33e1e9478821dad7c04286eecade3a1db13421db39d8f41c7d3227e55d1fa399eb0fe6 +MISC ChangeLog 2620 SHA256 744acdb2c000f76eb30c0dd0fdfef9f0f240c4b375ad375a8f46e549b95fd0cc SHA512 d6d2cfa56476c7a35e5430e1ab19d8791a41b5cedc2d6b3e01f4d053a8c833fce526148fd6fe1789cef1b43d937f2d6ab0a226764cc38a8a0769ad02283fcdfe WHIRLPOOL d4bebb62dc002aa1cf7168a0a764f119b468327d8501f786435b8f9133205aa7c61db297f644e384e6b50cad8a792f6b191131160a089f7760a165b99ea92678 +MISC ChangeLog-2015 719 SHA256 0d636c30f392a1ca9995b34ca75759fc7b714b72affedd5194c27686d13e38a3 SHA512 d2be05fe3d6faf53b9cfe9065d4fe999210654154e0baad815d2baa8a7bd3d97a3229bea4ef5251a191ca251cd1aa1a7339c8c0e66df1706bdca5273f42ae4c2 WHIRLPOOL 4433e4128a70c1a36d42e17b5cfa3affe859f709c36d28b773b3b0b090030cb23d78c777e5e1525c36309c9bb4a1c4a6d849b9b1fa9fb952614c3067a4922d34 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/pymol-plugins-caver/metadata.xml b/sci-chemistry/pymol-plugins-caver/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/pymol-plugins-caver/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild b/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild new file mode 100644 index 000000000000..ffc1c59074aa --- /dev/null +++ b/sci-chemistry/pymol-plugins-caver/pymol-plugins-caver-2.1.2.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit multilib python-r1 eutils versionator java-utils-2 + +MY_PV="$(replace_all_version_separators _)" +MY_P="Caver${MY_PV}_pymol_plugin" + +DESCRIPTION="Calculation of pathways of proteins from buried cavities to outside solvent" +HOMEPAGE="http://loschmidt.chemi.muni.cz/caver/" +SRC_URI="${MY_P}.zip" + +LICENSE="CAVER" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + >=virtual/jre-1.6 + sci-chemistry/pymol[${PYTHON_USEDEP}] + ${PYTHON_DEPS}" +DEPEND="app-arch/unzip + ${PYTHON_DEPS}" + +RESTRICT="fetch" + +S="${WORKDIR}/${MY_P}"/linux_mac + +pkg_nofetch() { + elog "Download ${A}" + elog "from ${HOMEPAGE}. This requires registration." + elog "Place tarballs in ${DISTDIR}." +} + +src_install() { + java-pkg_dojar Caver${MY_PV}/*.jar + + java-pkg_jarinto /usr/share/${PN}/lib/lib/ + java-pkg_dojar Caver${MY_PV}/lib/*.jar + + installation() { + sed \ + -e "s:directory/where/jar/with/plugin/is/located:${EPREFIX}/usr/share/${PN}/lib/:g" \ + -i Caver${MY_PV}.py || die + + python_moduleinto pmg_tk/startup/ + python_domodule Caver${MY_PV}.py + python_optimize + } + python_foreach_impl installation +} diff --git a/sci-chemistry/pymol-plugins-dssp/Manifest b/sci-chemistry/pymol-plugins-dssp/Manifest new file mode 100644 index 000000000000..f7a3fe4c37bd --- /dev/null +++ b/sci-chemistry/pymol-plugins-dssp/Manifest @@ -0,0 +1,5 @@ +DIST pymol-plugins-dssp-110430.py.xz 6836 SHA256 8be8da803f5b3908b5918c8fd355bd7e37785d2eada3a92d6de15b362b9e3868 SHA512 521e0a32ca6d2c8c21c690815b0654bb44303bd7fb9a1eb76227030b2ad7311fadb0d748e49b8bbc16cd5e69acba375b5353de7bffef1ff69686e62021fe64f4 WHIRLPOOL bfe0edc2307b3879668095dbe8a9bb242a58c5f6e449f1a08d3a655e9383c7b5a273d7cae65d3067f8f06a0a9d251565cd7f047d741349876bbfdfd366ffe2a5 +EBUILD pymol-plugins-dssp-110430-r1.ebuild 885 SHA256 ad49eee0ec37d66701ac51bc7a0868303f053a7264709f243ba4a33d7178a127 SHA512 617949f73a08f3b53ceecbce15669202e935c18e4b052092a810b644c9d11e9b5cbf0663c4c830895d0f19c55d34a55c2e1bcf405d3ec0d1e4ec29c8a56c642c WHIRLPOOL a8d55545a707b3315fba7e6f7f0398b5f0444aaa940c1c608ec6dc75f9356124bf32d7264285b9c5af7d73136e984c4da5820603630c3f1ac3a9b204f8ba1af1 +MISC ChangeLog 3122 SHA256 7fc9e0ee47c0f007179c0143bb89837870522029c3caa40fc8bb275602db9564 SHA512 a241bdd67d903080aa05dbb1a73121cf7720636db4ef6f81c04ff1df1307febf85df4044751396757d572727daead57f3953530d64df4b5113b8bbf1ba471497 WHIRLPOOL 80c9daf6420cdde06c245edbc264de1b83e26d125893c1d48f0a0a222e8348dcf751bb71ff7d8ced6a2f57b71531f34decba4073ac3fb295ac7e6a06bad3c78e +MISC ChangeLog-2015 932 SHA256 6af4a21c96647f34105092a443d7f257a815cd8152956c65394d299faf2e9f1f SHA512 ba8a72329188133a5acfc5cc0448d8afe7011e7509888574e7545c398826c71abe4c3eee009a879a5b01774711fb5f421b6476a7d6a0b6d95461d295b89d1934 WHIRLPOOL a350a20f49275cf824fa8089eb43bfbfba8d444a6384a77ba98404a3e62fb26c141f51e4c07c6e26edc7b2541b10d91a2b683217c7afbb358aac6cedfb3c574f +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/pymol-plugins-dssp/metadata.xml b/sci-chemistry/pymol-plugins-dssp/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/pymol-plugins-dssp/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430-r1.ebuild b/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430-r1.ebuild new file mode 100644 index 000000000000..11269a75591f --- /dev/null +++ b/sci-chemistry/pymol-plugins-dssp/pymol-plugins-dssp-110430-r1.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-r1 + +DESCRIPTION="DSSP Plugin for PyMOL" +HOMEPAGE="http://www.biotec.tu-dresden.de/~hongboz/dssp_pymol/dssp_pymol.html" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.py.xz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="BSD pymol" +IUSE="" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND="${PYTHON_DEPS}" +RDEPEND="${DEPEND} + sci-chemistry/dssp + sci-biology/stride + sci-chemistry/pymol[${PYTHON_USEDEP}]" + +S="${WORKDIR}" + +src_prepare() { + sed \ + -e "s:GENTOO_DSSP:${EPREFIX}/usr/bin/dssp:g" \ + -e "s:GENTOO_STRIDE:${EPREFIX}/usr/bin/stride:g" \ + -i ${P}.py || die +} + +src_install() { + python_moduleinto pmg_tk/startup + python_foreach_impl python_domodule ${P}.py + python_foreach_impl python_optimize +} diff --git a/sci-chemistry/pymol-plugins-dynamics/Manifest b/sci-chemistry/pymol-plugins-dynamics/Manifest new file mode 100644 index 000000000000..ce57945fca8a --- /dev/null +++ b/sci-chemistry/pymol-plugins-dynamics/Manifest @@ -0,0 +1,7 @@ +DIST pymol-plugins-dynamics-2.0.7.tar.gz 822680 SHA256 282e806b088a8d059ff5c722bb1e4789591cc263e9911d9129d3c3863ed4a5e0 SHA512 0d57e3e90a86a59cb96b11371ff1227b2b3e8f5b82cce713f4a855d6e7f5a10524508d4cb4dad7d9f77562fc1753b1af3c9240d4333e0189dabeef07c40d78a1 WHIRLPOOL 51d866d45e172751151f4fd0bfb4d6cb102b0279e0c4a3aff68242a23fbaaaf9dfa347842192c1cef0d182708d6f17c383fc87707e543d9ccec6bc2d8aaa7d9d +DIST pymol-plugins-dynamics-2.1.1.tar.gz 816623 SHA256 31b7ebca39e4922af9a5d05d7e1e81688ba096e6ed4355291362a7bf94d6f5e9 SHA512 e872c131e7d4ae37bd0e33e56d5d51e83ad732a125a46802ad9fa08648906d49de166bf75fbeca1431726aa9df781671c29578a799f580a94dc1fd89fb398b3c WHIRLPOOL a8396f962bfd0571d09696aa2f1ee73e0da120db70beac6f871fcf971854320b3b07e03e926c192fc137765d0249197fc5ab432e845adbaac8f817245736e866 +EBUILD pymol-plugins-dynamics-2.0.7.ebuild 762 SHA256 fca78ddfadb3434d4e130ac5b8fad92c6e55c1fffc3b8f6fd3879e3c7b226456 SHA512 7d56fad6af90be0e978ce97867effc548ec1a0d268e6ba7e4e7bd4c1755ca7c7509d92b70c3a75724526aecf686aebe21cae3473515b5a1ebe928201783b06c5 WHIRLPOOL 7f2c6e4df8391be8d16851b784c4456d5b72038fbcf7775127b7eee5158e1743db20b6a0e85ba5ef44d320d37e0209ad76a2ec00dd24b7729aaa6be43b01f064 +EBUILD pymol-plugins-dynamics-2.1.1.ebuild 762 SHA256 fca78ddfadb3434d4e130ac5b8fad92c6e55c1fffc3b8f6fd3879e3c7b226456 SHA512 7d56fad6af90be0e978ce97867effc548ec1a0d268e6ba7e4e7bd4c1755ca7c7509d92b70c3a75724526aecf686aebe21cae3473515b5a1ebe928201783b06c5 WHIRLPOOL 7f2c6e4df8391be8d16851b784c4456d5b72038fbcf7775127b7eee5158e1743db20b6a0e85ba5ef44d320d37e0209ad76a2ec00dd24b7729aaa6be43b01f064 +MISC ChangeLog 3246 SHA256 d90881109bda15c6721c9905f9e7531e23e8fbfd99a25871444de50c8941d248 SHA512 77e68d4cc1bba5d281a5d7650019cd8ab4b46c8b3a9ef119850d57de41864e2c886409668e53ce4c6f764e7cd3e61118d9d26d3ad08b0fb6c3df5d088e9df153 WHIRLPOOL 85422a9c8dfb94598b3527e1337fcb4d12c4a7f0fec8a41e77b93f926e30b7874d95479eff568502fe79c2f62d93e6875c62080ebb3e2a5588453db0ba688be7 +MISC ChangeLog-2015 720 SHA256 7654ee0712eb3ff32ad6a9bc655b60c6f909b5d30dd154ed1a05d59cb78b5b58 SHA512 62d16a30d2194a372b4bfa792ed1b2c43f2126113ad0be27abbb4a1ab446316b731e3aa43e73d0001e16019c21d98d63292403407bb67d687d7a32155604586c WHIRLPOOL 402d766cc45d872bdf52c7431e146d173b82a83f629e40d2693fa527a60726a3dcfae17efdc802f872e65f852780d898864fbb3f1b9c227dd1884f81f5c62903 +MISC metadata.xml 365 SHA256 4e1fc937c4943dbc0ce761f1b9cac06ef7dfad7fcfd8248d0cb3c667838493a5 SHA512 470165dfdb7117d8a87f1a7fbb21d806c5ff5eca77d450aa2a3ca32bb32347a4014bfb205d139e9597d8d6da0eba97bb3acb662c63b2d5ce42fdc63e5366d82f WHIRLPOOL 734fb2fd2f92b33b13b0a67568c483bdb43501b0f4352a7703a15cb92742c61fd026e37eff2ba02d1e3c133c6c772c4a393d82f166a6f47e7ad7dd3cbe68c8a4 diff --git a/sci-chemistry/pymol-plugins-dynamics/metadata.xml b/sci-chemistry/pymol-plugins-dynamics/metadata.xml new file mode 100644 index 000000000000..d0be20ea989c --- /dev/null +++ b/sci-chemistry/pymol-plugins-dynamics/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="github">tomaszmakarewicz/Dynamics</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.7.ebuild b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.7.ebuild new file mode 100644 index 000000000000..a860012cf6ff --- /dev/null +++ b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.0.7.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-r1 + +MY_PN="Dynamics" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Molecular dynamics in Pymol" +HOMEPAGE="https://github.com/tomaszmakarewicz/Dynamics" +SRC_URI="https://github.com/tomaszmakarewicz/Dynamics/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND=" + ${PYTHON_DEPS} + sci-chemistry/prody[${PYTHON_USEDEP}] + " +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/${MY_P} + +DOCS=( manual.odt ) + +src_install() { + python_moduleinto pmg_tk/startup + python_foreach_impl python_domodule pymol_plugin_dynamics.py +} diff --git a/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.1.1.ebuild b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.1.1.ebuild new file mode 100644 index 000000000000..a860012cf6ff --- /dev/null +++ b/sci-chemistry/pymol-plugins-dynamics/pymol-plugins-dynamics-2.1.1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-r1 + +MY_PN="Dynamics" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Molecular dynamics in Pymol" +HOMEPAGE="https://github.com/tomaszmakarewicz/Dynamics" +SRC_URI="https://github.com/tomaszmakarewicz/Dynamics/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND=" + ${PYTHON_DEPS} + sci-chemistry/prody[${PYTHON_USEDEP}] + " +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/${MY_P} + +DOCS=( manual.odt ) + +src_install() { + python_moduleinto pmg_tk/startup + python_foreach_impl python_domodule pymol_plugin_dynamics.py +} diff --git a/sci-chemistry/pymol-plugins-emovie/Manifest b/sci-chemistry/pymol-plugins-emovie/Manifest new file mode 100644 index 000000000000..0b2013d64f5c --- /dev/null +++ b/sci-chemistry/pymol-plugins-emovie/Manifest @@ -0,0 +1,6 @@ +AUX 1.0.4-indent.patch 706 SHA256 b57d251335f97ab49386b0acc5b41c231ee56b1ad134eb85abd71a576e9ecc6b SHA512 6788795d177db8c7597376a364eed79cc40a2423c6d86b837f4378308515d6f41a6c352df775de309d363ec284997a688285f2f851d5d84e891e78a771580b0e WHIRLPOOL 617c5647a9f059ecfb3b9676290ce6f4c2e055722b001cd09b5f2668a44e5391fbdb5f0d6eacbc56f936d4a7bcf0b06d2758f9277e87c5eaf9a7fd52ccf36239 +DIST eMovie_package.zip 22840 SHA256 a899d08f43902f803a797ddbd1052c687db03add53b2f815c91ae83223cc7f82 SHA512 5d4af5f8bd6e7e0f24f33d769925bd0444389b1c0fbdd14776f4073fd3e1e818c4623791bcb0cff5496729dc55e0429c48c3c16cb5fdbb91c51f9c5445c7afe4 WHIRLPOOL c8b5eee268d1a4f835152265a5320fe3020f1b548da16a43f97aca1bc8ecf24063287322667627e8e9566e61bd83c8fb0a1f71e7de1f6fc89d8560c63ac916c2 +EBUILD pymol-plugins-emovie-1.0.4.ebuild 769 SHA256 9a1990e2d4244cece59b7210a8ff5edb31a585bf19f6be9592fc68ba71c2b6ce SHA512 cd0dd0ef466eb9706296985b39a1b9921bf128aab3e75a801c7e26ea050baac584a00f856f943e52fa0e11c28c3f9833b1105428d519b3011d5766e5f4c47aa5 WHIRLPOOL 41269a0478131309264b1fa7747c5d5f10215f7f9cad302ef9bc7a58fd4664770bda59cc18ff1d193fa6b2b844d695a09f446528e0307a62747421c60d5be00c +MISC ChangeLog 2923 SHA256 5f823348fb5719fe7cb4301ee2623935d04de3a548d3fff71d5cf05e75e1363e SHA512 ce61346fc558f1b0bfbb88d91407da1457e48b09c6896190d79c1a2e18bd236d297a04f11a171781ce5a0318c3c5c0b85541300b6629c0cabcbc30281da1919a WHIRLPOOL 159ec585d3f04cc390edee7400f94756e4c07e196c34b7bb2fccb127259bbe960634573abf05f39f4ed6a07c3750bd16c28c5529cb99118e9b6e17a25e931171 +MISC ChangeLog-2015 729 SHA256 57912dad75c24b30ba871deaa57f9a09d867e6ad41c7e75d364860c1905dddc3 SHA512 280c71fc89395e675759e370bdf1753a6f4fe30cd32b730b86d01b55f86b712413d89357c1d492a8f2052cda78596e6f37e4f5d27b8df3feb2d27c99a564db0f WHIRLPOOL 5963042015b0a1e7506939abe60be7c96bd7d43e56260c8ef1fc9a13bb97a3ad1c9f29aa2b06825789c3c56df7829fc62f80b493eba530fb9fc26794850a1bb5 +MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d diff --git a/sci-chemistry/pymol-plugins-emovie/files/1.0.4-indent.patch b/sci-chemistry/pymol-plugins-emovie/files/1.0.4-indent.patch new file mode 100644 index 000000000000..a9a77e5055dd --- /dev/null +++ b/sci-chemistry/pymol-plugins-emovie/files/1.0.4-indent.patch @@ -0,0 +1,22 @@ +diff --git a/eMovie.py b/eMovie.py +index a865732..8b5b068 100644 +--- a/eMovie.py ++++ b/eMovie.py +@@ -931,7 +931,7 @@ class Story(tkSimpleDialog.Dialog): + + if self.parent is not None: + self.geometry("+%d+%d" % (parent.winfo_rootx()+50,parent.winfo_rooty()+50)) +- self.initial_focus.focus_set() ++ self.initial_focus.focus_set() + + self.wait_window(self) + +@@ -2041,7 +2041,7 @@ class AddMorph(tkSimpleDialog.Dialog): + + if self.parent is not None: + self.geometry("+%d+%d" % (parent.winfo_rootx()+50,parent.winfo_rooty()+50)) +- self.initial_focus.focus_set() ++ self.initial_focus.focus_set() + + self.wait_window(self) + diff --git a/sci-chemistry/pymol-plugins-emovie/metadata.xml b/sci-chemistry/pymol-plugins-emovie/metadata.xml new file mode 100644 index 000000000000..da36ecbfcd6a --- /dev/null +++ b/sci-chemistry/pymol-plugins-emovie/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild b/sci-chemistry/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild new file mode 100644 index 000000000000..7c143bf877ba --- /dev/null +++ b/sci-chemistry/pymol-plugins-emovie/pymol-plugins-emovie-1.0.4.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils python-r1 + +DESCRIPTION="PyMOL plugin for convinient movie creation" +SRC_URI="http://www.weizmann.ac.il/ISPC/eMovie_package.zip" +HOMEPAGE="http://www.weizmann.ac.il/ISPC/eMovie.html" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~x86 ~amd64 ~x86-linux ~amd64-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + >sci-chemistry/pymol-0.99[${PYTHON_USEDEP}]" +DEPEND="app-arch/unzip" + +S="${WORKDIR}" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-indent.patch +} + +src_install(){ + python_moduleinto pmg_tk/startup + python_foreach_impl python_domodule eMovie.py + python_foreach_impl python_optimize +} diff --git a/sci-chemistry/pymol-plugins-msms/Manifest b/sci-chemistry/pymol-plugins-msms/Manifest new file mode 100644 index 000000000000..55aa0fb759c1 --- /dev/null +++ b/sci-chemistry/pymol-plugins-msms/Manifest @@ -0,0 +1,6 @@ +AUX 100415-msms.patch 1687 SHA256 50509fe85feb3e12d35d0a1aba8fe2edef5dc557d06617bb1fcaaff7dae3938a SHA512 52410d467c314578cd22e777ae45a0012203fd21d2afa6ff329fa67db6d7ee2cb381558ce6aef48a1305a572f9218cf962ab1fc552ebe1873f94a4d6d2db1bcf WHIRLPOOL e3dfc92ea73765e9a236ded4ceaa9d7b7f84b0a554e0b87a328b8f5ad1a703a024d02ed847d7d2ba2eaed38ae3f42bbe562f036b23cd2446d72f02ee5eb20b0d +DIST pymol-plugins-msms-100415.py 62320 SHA256 1452acdcf8b13f5af22da563d44d51aca9f8fdd108dd7a0548ec41941cb463a5 SHA512 924d89836f92d0be52d7534cbe6dc9338dac1c2263a51900ab62dbe96e4f54f565dbaa6bdf51236d8ea8e9042aa09283a117f5285561b252177a5a32f3876489 WHIRLPOOL c5889b3543ac554083b76c38bb53fad1f001bd46f6686b0cdc36c1a7e576de3dc9a9bba0b459e0d928e30aec21ab09b98a0a8eb128fa64fc5b4228ca9ad7c0e4 +EBUILD pymol-plugins-msms-100415-r1.ebuild 1045 SHA256 eb8cf86edd1fd93d666770c9488123b73b23bc277b0e5f99ffb14920b1564fd5 SHA512 20799591eee520158f5872748c58b5280ec2fa0c0292fc1f069f823b20b6c4134a5b82ac57f884ecd2f8da3add00034ecc961463eada3e503a07246b823c084b WHIRLPOOL f82ddd2befc51b2918edda8f5159f0af95a119682ae9281c5012d9b94f0ae39290625ee4a91913e51b64c17a6d0918dad2a64849fe609e1009f41d12977034dc +MISC ChangeLog 3077 SHA256 d5d21ab17ea4fb7edc7d0cd473374bca2b2bc0b9828e0e7cb259a36592370fe7 SHA512 ab0d687b9dca24a4a4e32168fa5cea4d3adf15a8cc4d0e6192bbd8053c8a81a034b454bb2fe9ec1369f6f93ea7b5bdb509a68f9607ae57d673bdf3e5cc99de31 WHIRLPOOL 9eac2336e2cc25268b1e52ab42927efb0a28085ee23ad0b6940931109bb0d88c2d48ecf649dc0a9d1e838e09dadea1ad9b9cfa5956929acde3e7fec888c4154a +MISC ChangeLog-2015 698 SHA256 a71a1b2f16845ce359ccab70e91abdf659fa82338c9340c518e584556ed9cedf SHA512 5bc4cc7d0269560998c3ab1f0e4883075f76b1046ffbf99bba6d5bde26fe36bef4cb49543cb386acc208ff239504e9a59e697cef9e859b7e217e3666b672d65b WHIRLPOOL 72251bb83ccf1d2ec3e899ac4a3b4daf4c21c4623f29f1bb728a23069048b7f2881def5f530da477499ffdac391b2300091844298aad10854fff23d5d4c2ab58 +MISC metadata.xml 705 SHA256 76b53706caf15631163debdc5f1b608ee89d7ac72ad4f6ddd1f8cd6cf55c63eb SHA512 e33e7c380ff1f99f62fc75871dd3f3d0bc98bd3629a5e46c9dcae83ad039f88450d83b46379a6da88636795fb8e7c73c72480c4054a64dedd9c6bb0b501cf210 WHIRLPOOL a0c94989bfc5ac3af677d47e96a9b2a1ec915d9a08160d7c170e359783b51b0519c33410798ad7d97ce60c8ecb82047b34970af6085a8fdf485bf6665ffeb73c diff --git a/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch b/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch new file mode 100644 index 000000000000..0d26fb31c5f1 --- /dev/null +++ b/sci-chemistry/pymol-plugins-msms/files/100415-msms.patch @@ -0,0 +1,33 @@ + pymol-plugins-msms-100415.py | 18 ++++++++++-------- + 1 files changed, 10 insertions(+), 8 deletions(-) + +diff --git a/pymol-plugins-msms-100415.py b/pymol-plugins-msms-100415.py +index 725934d..7ea00bf 100644 +--- a/pymol-plugins-msms-100415.py ++++ b/pymol-plugins-msms-100415.py +@@ -99,15 +99,17 @@ class MSMSPlugin: + self.cleanup_saved_pymol_sel.set(True) # by default, clean up + + self.pdb_fn.set('') +- if 'MSMS_BIN' in os.environ: +- if VERBOSE: print 'Found MSMS_BIN in environmental variables', os.environ['MSMS_BIN'] +- self.msms_bin.set(os.environ['MSMS_BIN']) +- else: +- if VERBOSE: print 'MSMS_BIN not found in environmental variables.' +- self.msms_bin.set('') ++ self.msms_bin.set('GENTOOMSMS') ++## if 'MSMS_BIN' in os.environ: ++## if VERBOSE: print 'Found MSMS_BIN in environmental variables', os.environ['MSMS_BIN'] ++## self.msms_bin.set(os.environ['MSMS_BIN']) ++## else: ++## if VERBOSE: print 'MSMS_BIN not found in environmental variables.' ++## self.msms_bin.set('') + ## self.pdb2xyzr_bin.set('') +- if 'PDB2XYZRN' in os.environ: self.pdb2xyzrn_bin.set(os.environ['PDB2XYZRN']) +- else: self.pdb2xyzrn_bin.set('') ++ self.pdb2xyzrn_bin.set('GENTOOXYZRN') ++## if 'PDB2XYZRN' in os.environ: self.pdb2xyzrn_bin.set(os.environ['PDB2XYZRN']) ++## else: self.pdb2xyzrn_bin.set('') + self.tmp_dir.set('/tmp') + self.cleanup_msms_output = Tkinter.BooleanVar() + self.cleanup_msms_output.set(True) # by default, clean up msms output diff --git a/sci-chemistry/pymol-plugins-msms/metadata.xml b/sci-chemistry/pymol-plugins-msms/metadata.xml new file mode 100644 index 000000000000..214696c4a1f7 --- /dev/null +++ b/sci-chemistry/pymol-plugins-msms/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +MSMS is an excellent tool for computing protein solvent excluded surface (SES). +MSMS Plugin for PyMOL provides a graphical user interface for running MSMS and +displaying its results in PyMOL. + +1. Citation for this plugin: + Hongbo Zhu. MSMS plugin for PyMOL, 2010, Biotechnology Center (BIOTEC), TU Dresden. +2. Citation for PyMOL can be found at: http://pymol.sourceforge.net/faq.html#CITE +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild b/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild new file mode 100644 index 000000000000..33c7dbf9be7d --- /dev/null +++ b/sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils python-r1 + +DESCRIPTION="GUI for MSMS and displaying its results in PyMOL" +HOMEPAGE="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/msms_pymol.html" +SRC_URI="http://www.biotec.tu-dresden.de/~hongboz/msms_pymol/pymol_script/msms_pymol.py -> ${P}.py" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="BSD pymol" +IUSE="" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + sci-chemistry/msms-bin + sci-chemistry/pymol[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND}" + +src_unpack() { + mkdir "${S}" || die + cp "${DISTDIR}"/${A} "${S}/" || die +} + +src_prepare() { + epatch "${FILESDIR}"/${PV}-msms.patch + sed \ + -e "s:GENTOOMSMS:${EPREFIX}/opt/bin/msms:g" \ + -e "s:GENTOOXYZRN:${EPREFIX}/usr/bin/pdb_to_xyzrn:g" \ + -i ${A} || die +} + +src_install() { + python_moduleinto pmg_tk/startup + python_foreach_impl python_domodule ${P}.py + python_foreach_impl python_optimize +} diff --git a/sci-chemistry/pymol-plugins-promol/Manifest b/sci-chemistry/pymol-plugins-promol/Manifest new file mode 100644 index 000000000000..0ce2a16748cd --- /dev/null +++ b/sci-chemistry/pymol-plugins-promol/Manifest @@ -0,0 +1,5 @@ +DIST pymol-plugins-promol-3.0.2.zip 2219295 SHA256 4281131ab5fc5568c1e3984aec4a7022b515334c66adfbc2682df5f0e6a4c2d6 SHA512 e40e9c08e2cb1b223390d751bb1f32069924f1c23aa2b4bdafb6689254e6aa673d4412aca587792f660869f97a389db8a9183033d8b2394c998d0f911104d8d7 WHIRLPOOL 83a3122aaa60b3d81ca8f19dcc4c8bce32190861893c712e517d48053d65009ff001b7bb1bb89b7bbd2504f1cea38999655ddd164defcba0231e805a5c590728 +EBUILD pymol-plugins-promol-3.0.2-r1.ebuild 1571 SHA256 7eb94ed66c2d0c1662ae84b91bab711fcf6404942ef65120824c77eef7c3bb2d SHA512 c44e71917dc976f39055537ce137ca06c5cbf2f58937a5b54bd5b19463b051b5f0fbfcac320d1fdf01a76e6d32ffdb651b33a2945bb3fc9c143babe79a4bd889 WHIRLPOOL 31add0d298c303cd84070c38b6e102ff0700828917061d4556cfe93b996fa8d186e5315af6291ee2d83f3a71603fd7bcaf6cd7f61f872d508aff80b144c40515 +MISC ChangeLog 2853 SHA256 cd94fb4a561dd89dfb033452545e61a3a736eefe2f783841908b2b6d8fd3d58d SHA512 288dd3891bbee36018489dd50c74c7a52b28c4283e0a75e1a63ceb1973c1e55251a213dbb6875dd8d84e8a28fce7f2dae12c3d3a44fc03298089f7357bd63c63 WHIRLPOOL f75f79a459db6f22c5dbfe62c64973e1fd356d527f3c1e57e85219b618d96370997595b3ed347e1b72d91e6c63618cb935fd8f54a8b41632b7d6d8621013d3e7 +MISC ChangeLog-2015 1460 SHA256 722ddf35af6168b3ab9cde796759d8efce7bedfe4d8ce634088f69e0df2c40f9 SHA512 2fb6eac3c74bdf0eca52b9c1a7ef1de06e7f5d87f13d892e70aed2fdc2a53e632d71ffb43412efebee191884e2fb4b8145935403fb778cb8cd6c52493c0df1c3 WHIRLPOOL c4b8ba9d714812ae49062c1414da2d4979310420fb1d975cb6208d0463d9f1fddfbc8f822547672f670a5bd022328e12310df495b5f8fbf64e4dc20b5e55f58b +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/pymol-plugins-promol/metadata.xml b/sci-chemistry/pymol-plugins-promol/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/pymol-plugins-promol/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild b/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild new file mode 100644 index 000000000000..bda6bd694819 --- /dev/null +++ b/sci-chemistry/pymol-plugins-promol/pymol-plugins-promol-3.0.2-r1.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-r1 + +DESCRIPTION="Fast and accurate regognition of active sites" +HOMEPAGE="http://www.rit.edu/cos/ezviz/ProMOL_dl.html" +SRC_URI="http://www.rit.edu/cos/ezviz/ProMOL.zip -> ${P}.zip" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +LICENSE="all-rights-reserved" +IUSE="" + +RESTRICT="mirror bindist" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + virtual/python-pmw[${PYTHON_USEDEP}] + sci-chemistry/pymol[${PYTHON_USEDEP}]" +DEPEND="" + +S="${WORKDIR}/ProMOL Folder" + +src_prepare() { + python_copy_sources + preparation() { + cd "${BUILD_DIR}" || die + sed \ + -e "s:./modules/pmg_tk/startup:${EPREFIX}/$(python_get_sitedir)/pmg_tk/startup/ProMol:g" \ + -i ProMOL_302.py || die + } + python_foreach_impl preparation +} + +src_install(){ + dodoc *doc + dohtml -r Thanks.html EDMHelp.htm Help + + installation() { + cd "${BUILD_DIR}" || die + python_moduleinto pmg_tk/startup/ProMol + python_domodule PDB_List AminoPics Motifs *GIF pdb_entry_type.txt Master.txt Scripts + python_moduleinto pmg_tk/startup + python_domodule *.py + dosym ../../../../../../share/doc/${PF}/html/Help \ + $(python_get_sitedir)/pmg_tk/startup/ProMol/Help + dosym ../../../../../../share/doc/${PF}/html/Thanks.html \ + $(python_get_sitedir)/pmg_tk/startup/ProMol/Thanks.html + dosym ../../../../../../share/doc/${PF}/html/EDMHelp.htm \ + $(python_get_sitedir)/pmg_tk/startup/ProMol/EDMHelp.htm + } + python_foreach_impl installation +} diff --git a/sci-chemistry/pymol-plugins-psico/Manifest b/sci-chemistry/pymol-plugins-psico/Manifest new file mode 100644 index 000000000000..929a07dd5b42 --- /dev/null +++ b/sci-chemistry/pymol-plugins-psico/Manifest @@ -0,0 +1,5 @@ +DIST pymol-plugins-psico-3.1.tar.gz 76136 SHA256 07bfb0cfc1ca4720180de0b462a8c210e933bfc75cec9823d8c89fa2007ce651 SHA512 b0f57049ea6fc290a5abd48e0c98d4fda3c3f947898597b80e11cb3ab9ac14038aade0a016b21a525bf0ab4cf68e3be35c64b8ec34422268058414c20a755b0e WHIRLPOOL 7f64fc7fbded6a5eeb1940725b7ab3488e9c94a1587040a8f072a5e38319a640fbcf9d71cb57d97cdd7ca83de0298a0d839221f3a850601785db869a0ce2e2ea +EBUILD pymol-plugins-psico-3.1-r1.ebuild 982 SHA256 feb0dbdcbde9cc83975017b76a6d34a307366308c7d558e7730c79d567c51068 SHA512 33c405c0e95a1f040c58c8ed68d314dd6fee488fd92a5acf45014c692a0fe5d2168f46799a918683543e2e285e6c0decd9b94daf26aee1d98bc3f15a6841bb5a WHIRLPOOL 606fe830ca54abcc3166d17adc33bcaaad3a46f5105bfa436097c81184520c35da2f9f3ac752e0dbedd23839fdce2d1d4ecf46d1e3f64de72a95d230cc97936f +MISC ChangeLog 2801 SHA256 12821a356cfeebda5f3a864f1a9d3becf4faa3918cb3a47b39742c0231584049 SHA512 c42ff0944617011c350a6069a106ccb0f9e26862981f8d8219c7aaa53bd6a818dd5386e8c8039703f1f9833161a95cbb3535a8baf07894986b7ef1212d3e2cd4 WHIRLPOOL 615391f4672b780bd484112b7d82d34fa43ec138013b8a106f5b7461d2baddda0374f0aebd7f849bad427e127d1d881ebf3a1e36bd2d6850dd0014cd05db9e47 +MISC ChangeLog-2015 1288 SHA256 a833d45f77368e1be8aeaf4c80218a22ee2c073d758a0fbacf2d06341c2fb1d5 SHA512 fefb1ca693915be9561276443d92b0d0d5fac84fa4596593be35a143cf710fffdd9145105ed834fb3155d3e81939d1194dfa1ba834b9d53f243fd7f7f620f679 WHIRLPOOL 584235e1c1037e02366666ebcfbc14729f0b8642dc7467f498f912b0ad1ac508a5ca4713540f2945e7d9366523d41a17c7c094e9c5b6b352e891582b824fa9da +MISC metadata.xml 359 SHA256 e62d74ddced00f8af097658b30f20e62534cd728a32d933e39b1d91d1bd42af4 SHA512 1c94755813187e50e66f575868d2deabf6448e39bc6829ecdb60a29a4de5a37c58d28bdc7b21551f906101469614b2672949658220e5edea0fc4f10bad8d4116 WHIRLPOOL 0809054912c0c85bf9558722ce6de2651648a66bddbff8fd491e3d212f3a357744b80a162f34d5dd1339298f6cc373554611fd11ac3b840065da4990a9cf704e diff --git a/sci-chemistry/pymol-plugins-psico/metadata.xml b/sci-chemistry/pymol-plugins-psico/metadata.xml new file mode 100644 index 000000000000..29f0c024a2f1 --- /dev/null +++ b/sci-chemistry/pymol-plugins-psico/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="github">speleo3/pymol-psico</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild new file mode 100644 index 000000000000..0fca945ebee8 --- /dev/null +++ b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.1-r1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 vcs-snapshot + +DESCRIPTION="Pymol ScrIpt COllection" +HOMEPAGE="https://github.com/speleo3/pymol-psico/" +SRC_URI="https://github.com/speleo3/pymol-psico/tarball/${PV} -> ${P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="BSD-2" +IUSE="minimal" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-biology/biopython[${PYTHON_USEDEP}] + sci-libs/mmtk[${PYTHON_USEDEP}] + sci-chemistry/pymol[${PYTHON_USEDEP}] + !minimal? ( + media-libs/qhull + media-video/mplayer + sci-biology/stride + sci-chemistry/dssp + sci-chemistry/mm-align + sci-chemistry/pdbmat + sci-chemistry/theseus + sci-chemistry/tm-align + sci-mathematics/diagrtb + )" + +pkg_postinst() { + if ! use minimal; then + elog "For full functionality you need to get DynDom from" + elog "http://fizz.cmp.uea.ac.uk/dyndom/dyndomMain.do" + fi +} diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest new file mode 100644 index 000000000000..bfc21a112425 --- /dev/null +++ b/sci-chemistry/pymol/Manifest @@ -0,0 +1,8 @@ +DIST pymol-1.8.4.0.png.xz 19528 SHA256 e2c956b39965130a3dc51c2c1b1090bee6bf591885069b2ddb77c0991e9e4928 SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c WHIRLPOOL 1336c20e068b71cdf35118c84b5df8485c86bc51eed7f542a483fb78ce374ca76e4aed3518aced0a6f8ea49e0b180004e567cc059ac52a27a3d616adb282cea2 +DIST pymol-v1.8.4.0.tar.bz2 8717344 SHA256 b6147befe74844dd23550461b831b2fa6d170d4456f0059cf93fb1e8cb43d279 SHA512 73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe WHIRLPOOL 3943a619ca00cc2bfb51ff4dffa0166856b4425c7518d91b1ff2a048caa53dcb7411c64b246014b860b7f036de582e9efdc09783b3918283f0a96ee5130c7287 +DIST pymol-v1.8.6.0.tar.bz2 8717164 SHA256 7eaaf90ac1e1be0969291cdb1154b3631b5b6403cce1d697133d90cd37a3c565 SHA512 bd08e6890382af1503d6af16b27b43af09b372a1229cc9d8e2de311873918b5e7b06e8a2365ce73a5f52cb31ac795f5d91b2ae6ef62890d9c2bf0ea25f856658 WHIRLPOOL 950d655a48b3801de2657b6d8935404ca0069525719b9c88a117ad819c37366a55e42dbe51a253b960b79413e5df9d781b9ada8839ca06e1e01dde965044efe4 +EBUILD pymol-1.8.4.0-r1.ebuild 3009 SHA256 a5f968aa75695834f878c9c18ed98c30461ea2d0f8ec70e0cb1b52b4eb9b19dc SHA512 c696905b2e28c28249bf458e37dfe05237b307e3af1727fe17ebfd6a818322e6f9dc947d720df7ee29d694fe6501791f3a2f6fdc554a8e7dd43adf9727c8ece8 WHIRLPOOL 65730bcce7ade5900a90fb5a24207cba2d2433ab1312ab91a9af9c48ca98bad216d2732d59ce5e4e95e5b0f5cf064a7b221ae2973f712ac47c1890c4574f43f9 +EBUILD pymol-1.8.6.0.ebuild 3052 SHA256 8b239353bac4386400100d0fcf889c16eef5f8323b03e62b938fe085ea1a08cb SHA512 f065ffbdade1cc02734a35f6f785670417e113299ec6b92d1b9c7ffdaaeba0ca5353dcc0ae09e206eb1a83474487db89234ab22c65c0a75e768e7b4cb5982f86 WHIRLPOOL f7aef767f1d264f14a93010385f8e0e4890f5dfe1619af0a2caf81e2b51d17fc93c35745bd44490c9e24b3476024bb1c073b6837fdc8fa5847b3b3f14957991e +MISC ChangeLog 5319 SHA256 e58797f1ec06da23cc79f421c1cf011d4ba4deff3198daa02c23b4aed4731ba0 SHA512 75974a75951abe5a2d9a0b615a4d2176f39dce7f06bbec2859efa08a9814f5fae299124529a8fd18eb6c983f62b1d9f91ba9cfc90596ecfcc413563d99a5001b WHIRLPOOL 8ee424fcf377c91456fabd4e54dca753d517019768a39a378f0d4f2f9b0320e937d56094982fc68dd7a8c7cf7f1bc6f8b79ae225ed5f94e0ea6e8f1dcda11560 +MISC ChangeLog-2015 9337 SHA256 c462188628a8604c4023b896438c60be3fadb47cae8259d22847ef5bb1cd8a8b SHA512 29c5ce09d595262a27750f13adf918ec0a0bfea21eb787c3f9048a4cc9cc8f053b53d9faf178be34ae9fe23d07933a0a3d5dcdf857ce9ae2cc70cec18b24dbcb WHIRLPOOL 4d8adb760612b09ac2cc823b156cfd0dfe6a6533d99b81eb56d7c0d83f79df52c993bf7f5cc93fa14007e0c306ffb955ebdcb7b9560c88c2a388193e6b6b9f25 +MISC metadata.xml 439 SHA256 ee9fdf7e53b518562aa334a006889f3a7ffd56cb635f54b18171f08700678cee SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4 WHIRLPOOL 88c38bd335bafc9105e94d743229edc6244d426ea040aa6fba7f33f01eea69268aa0963d79b2479a96457332dec8b4b60983915c6668d6c29fb32f81191fbac6 diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml new file mode 100644 index 000000000000..156735fe0d36 --- /dev/null +++ b/sci-chemistry/pymol/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="web">Install Pymodule needed for web app support</flag> + </use> + <upstream> + <remote-id type="sourceforge">pymol</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild new file mode 100644 index 000000000000..c2bedf7ca9db --- /dev/null +++ b/sci-chemistry/pymol/pymol-1.8.4.0-r1.ebuild @@ -0,0 +1,108 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="tk" + +inherit distutils-r1 eutils fdo-mime flag-o-matic versionator + +DESCRIPTION="A Python-extensible molecular graphics system" +HOMEPAGE="http://www.pymol.org/" +SRC_URI=" + https://dev.gentoo.org/~jlec/distfiles/${P}.png.xz + mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2 + " +# git archive -v --prefix=${P}/ master -o ${P}.tar.xz +RESTRICT="mirror" +LICENSE="PSF-2.2" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="web" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pyopengl[${PYTHON_USEDEP}] + media-libs/freeglut + media-libs/freetype:2 + media-libs/glew:0= + media-libs/libpng:0= + media-video/mpeg-tools + sys-libs/zlib + virtual/python-pmw[${PYTHON_USEDEP}] + !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}] + web? ( !dev-python/webpy[${PYTHON_USEDEP}] )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/${PN} + +python_prepare_all() { + sed \ + -e "s:\"/usr:\"${EPREFIX}/usr:g" \ + -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ + -e "/import/s:argparse:argparseX:g" \ + -i setup.py || die + + sed \ + -e "s:/opt/local:${EPREFIX}/usr:g" \ + -e '/ext_comp_args/s:\[.*\]:[]:g' \ + -i setup.py || die + + append-cxxflags -std=c++0x + + distutils-r1_python_prepare_all +} + +python_install() { + distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol" + + sed \ + -e '1d' \ + -e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \ + -e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \ + -e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \ + -i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die +} + +python_install_all() { + distutils-r1_python_install_all + + sed \ + -e '1i#!/usr/bin/env python' \ + "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die + + python_foreach_impl python_doscript "${T}"/${PN} + + # These environment variables should not go in the wrapper script, or else + # it will be impossible to use the PyMOL libraries from Python. + cat >> "${T}"/20pymol <<- EOF + PYMOL_PATH="${EPREFIX}/usr/share/pymol" + PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" + PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" + EOF + + doenvd "${T}"/20pymol + + newicon "${WORKDIR}"/${P}.png ${PN}.png + make_desktop_entry ${PN} PyMol ${PN} \ + "Graphics;Education;Science;Chemistry;" \ + "MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;" + + if ! use web; then + rm -rf "${D}/$(python_get_sitedir)/web" || die + fi + + rm -f "${ED}"/usr/share/${PN}/LICENSE || die +} + +pkg_postinst() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update + optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr +} + +pkg_postrm() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update +} diff --git a/sci-chemistry/pymol/pymol-1.8.6.0.ebuild b/sci-chemistry/pymol/pymol-1.8.6.0.ebuild new file mode 100644 index 000000000000..8fd0a78a12a1 --- /dev/null +++ b/sci-chemistry/pymol/pymol-1.8.6.0.ebuild @@ -0,0 +1,109 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="tk" + +inherit distutils-r1 eutils fdo-mime flag-o-matic versionator + +DESCRIPTION="A Python-extensible molecular graphics system" +HOMEPAGE="http://www.pymol.org/" +SRC_URI=" + https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz + mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2 + " +# git archive -v --prefix=${P}/ master -o ${P}.tar.xz +RESTRICT="mirror" +LICENSE="PSF-2.2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="web" + +DEPEND=" + dev-libs/msgpack[cxx] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pyopengl[${PYTHON_USEDEP}] + media-libs/freeglut + media-libs/freetype:2 + media-libs/glew:0= + media-libs/libpng:0= + media-video/mpeg-tools + sys-libs/zlib + virtual/python-pmw[${PYTHON_USEDEP}] + !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}] + web? ( !dev-python/webpy[${PYTHON_USEDEP}] )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/${PN} + +python_prepare_all() { + sed \ + -e "s:\"/usr:\"${EPREFIX}/usr:g" \ + -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ + -e "/import/s:argparse:argparseX:g" \ + -i setup.py || die + + sed \ + -e "s:/opt/local:${EPREFIX}/usr:g" \ + -e '/ext_comp_args/s:\[.*\]:[]:g' \ + -i setup.py || die + + append-cxxflags -std=c++0x + + distutils-r1_python_prepare_all +} + +python_install() { + distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol" + + sed \ + -e '1d' \ + -e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \ + -e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \ + -e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \ + -i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die +} + +python_install_all() { + distutils-r1_python_install_all + + sed \ + -e '1i#!/usr/bin/env python' \ + "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die + + python_foreach_impl python_doscript "${T}"/${PN} + + # These environment variables should not go in the wrapper script, or else + # it will be impossible to use the PyMOL libraries from Python. + cat >> "${T}"/20pymol <<- EOF + PYMOL_PATH="${EPREFIX}/usr/share/pymol" + PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" + PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" + EOF + + doenvd "${T}"/20pymol + + newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png + make_desktop_entry ${PN} PyMol ${PN} \ + "Graphics;Education;Science;Chemistry;" \ + "MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;" + + if ! use web; then + rm -rf "${D}/$(python_get_sitedir)/web" || die + fi + + rm -f "${ED}"/usr/share/${PN}/LICENSE || die +} + +pkg_postinst() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update + optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr +} + +pkg_postrm() { + fdo-mime_desktop_database_update + fdo-mime_mime_database_update +} diff --git a/sci-chemistry/rasmol/Manifest b/sci-chemistry/rasmol/Manifest new file mode 100644 index 000000000000..5672f0f3675c --- /dev/null +++ b/sci-chemistry/rasmol/Manifest @@ -0,0 +1,9 @@ +AUX 2.7.5-bundled-lib.patch 2513 SHA256 86fc627ae39fbc6d85063436b1e05e19745fd4690e6df70fd6111f99c1b90505 SHA512 940e85bbe35ed6055d8deb1d761e925aec3b60d63c3e91bcc3c08596f1b8269efd4c8a257ff9efdbe32888e987852e85ed19cba5566d8d610e8d625a23b0994a WHIRLPOOL ffbe6399b1176601459dafb8bed6267fbff60d859761a7e0ecbf55b4b0c2f607888a11c0ca9c66278e3cc514ed2b44b769cac3af8099a10efd8decd7bac37077 +AUX rasmol-2.7.5.2-format-security.patch 1617 SHA256 6171a944ac63bcbc18e8d4a1aabb03dca5297cedad00eef8a38cb78253f8c3c8 SHA512 cab29465d5830e669eca152880ae60c403f90668ee5bf97e3694b6e754e2e23086a520717c2df990c74fcfbafc761a460bea111d868a57ae63f13bce1603f074 WHIRLPOOL dcf0437e73150f0dc7ad5c7876a28d74e9d1df51033f6d9bb089876895dde97871b0f2e48bc2daa75cd35f9a5e2739df33d089e5fe556b238c8f7d64d4b4c42e +AUX rasmol-2.7.5.2-glib.h.patch 770 SHA256 4093621678676bdc7c517f6d6c260f495b9d946d57691d8e58371b627cd6c178 SHA512 d743b89817d0ed2aa551f3a6529e5bcc50c811d79c0deddd50d07a59614cb0c2d71500452ff9aec4b4b84e4985d9851f61aafa30196356aa1724212b5159375e WHIRLPOOL 250e59fbafe5d53f1dfd77bc2392cf085b07968578675e61635c8ca2e5de1dd60f060240f2a9afdb088285bac3a94cb695cecd3abbb93214f2d6fcf584fe8a16 +AUX rasmol-2.7.5.2-longlong.patch 396 SHA256 98503ec652d13e62443275536d86a8abefae6f6006441425026d400f40f25607 SHA512 4c3ce01ade36fe8a9512bdac62bcd47268bcc5a0448f4af69b26d8add9cc8495d376bac33a8ae5aeae42fa114a1cba980ce86559bf2d52334257f2e001c011d3 WHIRLPOOL 812ff6f3b2d3a6d5dc4ce1c0a9ebf627998b4df355bf435ff1a2e43b3ba369d29fed8cd8ffeef472a62735f71a4bfa2bf89812dafb7f11ec4be34716793f95a7 +DIST rasmol-2.7.5.2-13May11.tar.gz 9768769 SHA256 b975e6e69d5c6b161a81f04840945d2f220ac626245c61bcc6c56181b73a5718 SHA512 c4fd149c002a34d8ce7620a7eed37aa6020acd83fc352a4c16697eb94e6a0377c55455cb6da5fb3f492f879248a6707f677f4b35572f2295b23fc924ddf3128f WHIRLPOOL 261c5351e32a67807d2979b73fbdf83b947aa641568c08fd2f2b0e06115330541a56f7bbd8f05313c86554c321e59cfe11bf5ee613c09249b9e149411c61d5ca +EBUILD rasmol-2.7.5.2-r2.ebuild 2299 SHA256 736f1d571389b382043a3562397e04ce95fb9306b6dc6783cae826ad5abbafc2 SHA512 c725dde02ff311e385373f6125f254ff9ba3ab7e59164315edcfb852f587495fc1ca30e48a65eaad4c9756ba95c682100034808e8fbbc2a97de4f5c954f82e02 WHIRLPOOL d6571bbdebd614d6777d3405f9ceab7fb6fb9edf9ff8ea150a8946a7c40126270d1f10aad21d7779c933a178e07603227d8e4cbc9203b454563e8f1a0072456a +MISC ChangeLog 2594 SHA256 6e7e7df4aec74262f9a00545174147af18ee6e2b7ae0e41f1f8e13f35aecaa83 SHA512 930f250703285b0efc579ec45f71a2f1659cba72265788dcaf2fbd042b2c162c43916cfd215c2a853a5cacc61f3e8fb9b6de90045ff2c08e48fe39889de09105 WHIRLPOOL 56c528196574bb8002ad3947c48c43bc0331960d49d5cd0b58093c95ac770dbf7ab5c2a16513178fd8221fad541662896c12c9cf5c77c3056fe54e3a20f36da1 +MISC ChangeLog-2015 8025 SHA256 04c9b2b53016b1f3704e7b3b3c20149411a861054d16ab985b8b1df77ef0abe8 SHA512 1b38bdbd882c910e5127c2bbffd337c485415c82dea0f6208742b691e016ec6f058f8dcc0151cda4939527bf835cde83b105885a19c744ffe39a463f9f1d0439 WHIRLPOOL fe46f78161c4ef1637db917689a30f8ed0b4c934ec7c3d071d4305e03088fa387fd6d3e9f2565a16db659b70c96c8931ad60391a148bef8b0e46a8eafd864fd0 +MISC metadata.xml 355 SHA256 76c1dff8297a72d84445be9ede0d498e9bc76cb1c240da8cfeb2ae5ba394b645 SHA512 98822367149551ef6af6d75e4bd0b9104f1a625a5a17e1a2dad32e7ed83345870dc45392525cfe7e49514eae29f986e8ac2ed253ec22fec94d6152f96620b916 WHIRLPOOL d43bf1f6f203a892e4e3630d2101be9363c0dc970f4714678f9c53d99f94e95b6de5350cfc650e9c254bcaf4cba08bef04436764b5c3c26804c6eedfda3881c0 diff --git a/sci-chemistry/rasmol/files/2.7.5-bundled-lib.patch b/sci-chemistry/rasmol/files/2.7.5-bundled-lib.patch new file mode 100644 index 000000000000..10705165ad47 --- /dev/null +++ b/sci-chemistry/rasmol/files/2.7.5-bundled-lib.patch @@ -0,0 +1,80 @@ +diff --git a/src/Imakefile b/src/Imakefile +index 03be00e..a0c68f9 100755 +--- a/src/Imakefile ++++ b/src/Imakefile +@@ -176,7 +176,7 @@ XFORMSLIB_DIR = /usr/local + #endif + endif + XFORMSLIB_INCLUDE_DIR = $(XFORMSLIB_DIR)/include +-XFORMSLIB_LDLIB = -lXpm -L$(XFORMSLIB_DIR)/lib -lforms ++XFORMSLIB_LDLIB = -lXpm -L$(XFORMSLIB_DIR)/lib + #endif + #endif + #endif +@@ -281,17 +281,10 @@ RASMOLDIR = $(USRLIBDIR)/rasmol/ + + #ifndef USE_XFORMSLIB + DEFINES = $(GTKCFLAGS) $(GUIDEF) -DRASMOLDIR=\"$(RASMOLDIR)\" $(DEPTHDEF) $(LOCALEDEF) \ +- -D_USE_RASMOL_H_ $(GUIOPTION) -I$(CBFLIB_INCLUDE_DIR) \ +- -I$(CQRLIB_INCLUDE_DIR) \ +- -I$(CVECTOR_INCLUDE_DIR) \ +- -I$(NEARTREE_INCLUDE_DIR) ++ -D_USE_RASMOL_H_ $(GUIOPTION) -I@GENTOO_PORTAGE_EPREFIX@/usr/include -I@GENTOO_PORTAGE_EPREFIX@/usr/include/cbflib + #else + DEFINES = $(GTKCFLAGS) $(GUIDEF) -DRASMOLDIR=\"$(RASMOLDIR)\" $(DEPTHDEF) $(LOCALEDEF) \ +- -D_USE_RASMOL_H_ $(GUIOPTION) -I$(CBFLIB_INCLUDE_DIR) \ +- -I$(CQRLIB_INCLUDE_DIR) \ +- -I$(CVECTOR_INCLUDE_DIR) \ +- -I$(NEARTREE_INCLUDE_DIR) \ +- -I$(XFORMSLIB_INCLUDE_DIR) ++ -D_USE_RASMOL_H_ $(GUIOPTION) -I@GENTOO_PORTAGE_EPREFIX@/usr/include -I@GENTOO_PORTAGE_EPREFIX@/usr/include/cbflib + #endif + + +@@ -317,11 +310,11 @@ OBJS = rasmol.o molecule.o abstree.o cmndline.o command.o transfor.o \ + # Additional RS6000 AIX MITSHM Library + # LDLIBS = -lm -lXi -lXextSam $(XLIB) + +-LDLIBS = -lm -lXi $(XLIB) $(EXTRA_LIBRARIES) $(XFORMSLIB) $(GTKLIBS) \ +- $(CBFLIB_LDLIB) \ +- $(CQRLIB_LDLIB) \ +- $(CVECTOR_LDLIB) \ +- $(NEARTREE_LDLIB) $(XFORMSLIB_LDLIB) ++LDLIBS = -lm -lXi $(XLIB) $(EXTRA_LIBRARIES) $(GTKLIBS) \ ++ -lcbf \ ++ -lCQRlib \ ++ -lCVector \ ++ -lCNearTree -lgfortran + + + # +@@ -425,11 +418,11 @@ $(NEARTREE_DIR): + $(NEARTREE_DIR)/CNearTree.c: $(NEARTREE_DIR) + #endif + +-$(OBJS): $(EXTPKGDIR) $(CBFLIB_OBJDEP) \ +- $(CQRLIB_OBJDEP) \ +- $(CVECTOR_OBJDEP) \ +- $(NEARTREE_OBJDEP) \ +- $(XFORMSLIB_OBJDEP) ++# $(OBJS): $(EXTPKGDIR) $(CBFLIB_OBJDEP) \ ++# $(CQRLIB_OBJDEP) \ ++# $(CVECTOR_OBJDEP) \ ++# $(NEARTREE_OBJDEP) \ ++# $(XFORMSLIB_OBJDEP) + + + gtkwin.c: gtkui.h +diff --git a/src/Makefile.in b/src/Makefile.in +index fc6d0af..bad90fc 100755 +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -165,7 +165,7 @@ $(CBFLIBDIR)/lib/libcbf.a: $(CBFLIBDIR) + + all: postdownload rasmol rastxt + +-rasmol: postdownload $(X11OBJS) $(CBFLIBDIR)/lib/libcbf.a ++rasmol: postdownload $(X11OBJS) + $(CC) -o rasmol $(LFLAGS) $(X11OBJS) $(X11LIBS) + chmod 755 rasmol + diff --git a/sci-chemistry/rasmol/files/rasmol-2.7.5.2-format-security.patch b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-format-security.patch new file mode 100644 index 000000000000..22eb229d8a3d --- /dev/null +++ b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-format-security.patch @@ -0,0 +1,39 @@ +diff -urp RasMol-2.7.5.2/src/command.c RasMol-2.7.5.2_sprintf/src/command.c +--- RasMol-2.7.5.2/src/command.c 2011-05-15 01:23:49.000000000 +0700 ++++ RasMol-2.7.5.2_sprintf/src/command.c 2014-02-12 18:02:24.633489549 +0700 +@@ -1286,7 +1286,7 @@ void ShowRecordCommand( void ) { + if (record_on[1]) WriteString("record appearance on\n"); + else WriteString("record apperance off\n"); + if (RecordMaxMS == 1.) { +- sprintf(param,RecordTemplate); ++ sprintf(param, "%s", RecordTemplate); + } else{ + sprintf(param,RecordTemplate,millisec<0?0:millisec); + } +@@ -1381,7 +1381,7 @@ void ShowPlayCommand( void ) { + WriteString(param); + } + if (PlayMaxMS == 1.) { +- sprintf(param,PlayTemplate); ++ sprintf(param, "%s", PlayTemplate); + } else{ + sprintf(param,PlayTemplate,millisec<0?0:millisec); + } +@@ -1469,7 +1469,7 @@ void WriteMovieFrame( void ) { + RecordPause = True; + } else { + if (RecordMaxMS == 1.) { +- sprintf(param,RecordTemplate); ++ sprintf(param, "%s", RecordTemplate); + } else{ + sprintf(param,RecordTemplate,millisec); + } +@@ -1505,7 +1505,7 @@ static int PlayMovieFrame( void ) { + for (play_frame[1] = 0;play_frame[1]<=millisec; play_frame[1]++) + { + if (RecordMaxMS == 1.) { +- sprintf(param,PlayTemplate); ++ sprintf(param, "%s", PlayTemplate); + } else{ + sprintf(param,PlayTemplate,millisec-play_frame[1]); + } diff --git a/sci-chemistry/rasmol/files/rasmol-2.7.5.2-glib.h.patch b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-glib.h.patch new file mode 100644 index 000000000000..69c19dae5e8d --- /dev/null +++ b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-glib.h.patch @@ -0,0 +1,31 @@ + src/egg-macros.h | 3 ++- + src/eggfileformatchooser.c | 2 ++ + 2 files changed, 4 insertions(+), 1 deletions(-) + +diff --git a/src/egg-macros.h b/src/egg-macros.h +index 9a7caad..1a6bce0 100644 +--- a/src/egg-macros.h ++++ b/src/egg-macros.h +@@ -9,7 +9,8 @@ + #ifndef _EGG_MACROS_H_ + #define _EGG_MACROS_H_ + +-#include <glib/gmacros.h> ++#include <glib.h> ++#include <glib/gprintf.h> + + G_BEGIN_DECLS + +diff --git a/src/eggfileformatchooser.c b/src/eggfileformatchooser.c +index 32ce2ab..febfc2e 100644 +--- a/src/eggfileformatchooser.c ++++ b/src/eggfileformatchooser.c +@@ -19,6 +19,8 @@ + #include "eggfileformatchooser.h" + #include "egg-macros.h" + ++#include <glib.h> ++#include <glib/gprintf.h> + #include <glib/gi18n.h> + #include <gtk/gtk.h> + #include <string.h> diff --git a/sci-chemistry/rasmol/files/rasmol-2.7.5.2-longlong.patch b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-longlong.patch new file mode 100644 index 000000000000..3cff0fa2f98f --- /dev/null +++ b/sci-chemistry/rasmol/files/rasmol-2.7.5.2-longlong.patch @@ -0,0 +1,12 @@ +diff -urp rasmol-2.7.5-23Jul09/src/rasmol.h rasmol-2.7.5-23Jul09-64b/src/rasmol.h +--- rasmol-2.7.5-23Jul09/src/rasmol.h 2009-07-20 21:08:43.000000000 +0700 ++++ rasmol-2.7.5-23Jul09-64b/src/rasmol.h 2013-02-22 14:40:00.378574163 +0700 +@@ -125,6 +125,8 @@ + #define VECTOR_FAR + #endif + ++#define _LONGLONG ++ + /*========================*/ + /* Default User Options! */ + /*========================*/ diff --git a/sci-chemistry/rasmol/metadata.xml b/sci-chemistry/rasmol/metadata.xml new file mode 100644 index 000000000000..59ea086025a2 --- /dev/null +++ b/sci-chemistry/rasmol/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">openrasmol</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild b/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild new file mode 100644 index 000000000000..3335b5ae5a47 --- /dev/null +++ b/sci-chemistry/rasmol/rasmol-2.7.5.2-r2.ebuild @@ -0,0 +1,106 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils fortran-2 multilib prefix toolchain-funcs + +MY_P="RasMol_${PV}" +VERS="13May11" + +DESCRIPTION="Molecular Graphics Visualisation Tool" +HOMEPAGE="http://www.openrasmol.org/" +#SRC_URI="http://www.rasmol.org/software/${MY_P}.tar.gz" +SRC_URI="mirror://sourceforge/open${PN}/RasMol/RasMol_2.7.5/${P}-${VERS}.tar.gz" +#SRC_URI="mirror://sourceforge/open${PN}/RasMol/RasMol_2.7.5/RasMol.tar.gz" + +LICENSE="|| ( GPL-2 RASLIC )" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-libs/cvector + dev-util/gtk-builder-convert + >=sci-libs/cbflib-0.9.2 + >=sci-libs/cqrlib-1.1.2 + >=sci-libs/neartree-3.1.1 + x11-libs/cairo + x11-libs/gtk+:2 + x11-libs/libXext + x11-libs/libXi + x11-libs/vte:0" +DEPEND="${RDEPEND} + app-text/rman + x11-misc/imake + x11-proto/inputproto + x11-proto/xextproto" + +#S="${WORKDIR}/${PN}-2.7.5-${VERS}" +S="${WORKDIR}/RasMol-${PV}" + +src_prepare() { + cd src || die + + epatch \ + "${FILESDIR}"/${P}-glib.h.patch \ + "${FILESDIR}"/${P}-format-security.patch \ + "${FILESDIR}"/${P}-longlong.patch + + if use amd64 || use amd64-linux; then + mv rasmol.h rasmol_amd64_save.h && \ + echo "#define _LONGLONG"|cat - rasmol_amd64_save.h > rasmol.h + fi + + sed \ + -e 's:-traditional::g' \ + -i Makefile* || die + + cat > Imakefile <<- EOF + #define PIXELDEPTH 32 + #define GTKWIN + EOF + + cat Imakefile_base >> Imakefile || die + epatch "${FILESDIR}"/2.7.5-bundled-lib.patch + + eprefixify Imakefile + + sed \ + -e 's:vector.c:v_ector.c:g' \ + -e 's:vector.o:v_ector.o:g' \ + -e 's:vector.h:v_ector.h:g' \ + -i *akefile* || die + + sed \ + -e 's:vector.h:v_ector.h:g' \ + -i *.c *.h || die + + mv vector.c v_ector.c || die + mv vector.h v_ector.h || die + + xmkmf -DGTKWIN || die "xmkmf failed with ${myconf}" +} + +src_compile() { + emake -C src clean + emake \ + -C src \ + DEPTHDEF=-DTHIRTYTWOBIT \ + CC="$(tc-getCC)" \ + CDEBUGFLAGS="${CFLAGS}" \ + EXTRA_LDOPTIONS="${LDFLAGS}" +} + +src_install () { + libdir=$(get_libdir) + insinto /usr/${libdir}/${PN} + doins doc/rasmol.hlp + dobin src/rasmol + dodoc PROJECTS {README,TODO}.txt doc/*.{ps,pdf}.gz doc/rasmol.txt.gz + doman doc/rasmol.1 + insinto /usr/${libdir}/${PN}/databases + doins data/* + + dohtml -r *html doc/*.html html_graphics +} diff --git a/sci-chemistry/raster3d/Manifest b/sci-chemistry/raster3d/Manifest new file mode 100644 index 000000000000..e3a841c1f33f --- /dev/null +++ b/sci-chemistry/raster3d/Manifest @@ -0,0 +1,9 @@ +AUX 3.0.2-as-needed.patch 1579 SHA256 9348541ca30f28466690e53e3fc94efdcbb4f9dec4cb25d5e959ea1c2c4722f4 SHA512 2898b55dca4e8d8d353922c36f44a9bb1dece19fa4c1de3f13ea5a09202004c10fbab6c2df2a39b71a65de3f30c19cd2724703b22b7ef978f366c69894761ce9 WHIRLPOOL e0205f149fd224e0164b51ea81b0c25700bbf915e77cca20510a76035c32a48301f4ac2552983b8608bff407b9997c77994ecf628a1df178329fa13ba73f0c69 +AUX 3.0.2-gentoo-prefix.patch 738 SHA256 4d7f94ad57280254177cfecec0f0a6f5610f1d3b4c7c4b7439ab68262e285515 SHA512 5cb22fdff116c6a84a9f570af99062c08463d391cb0460d06e64990eaab2c945e86f0b3f5a378144c49014c0c41dc70cafb102c5feba500c43c8555ce41612a0 WHIRLPOOL 32c239f5704ad67e87ca24313e15d70d1b5a395637f64191deb597787596ae47172373c78b5310ce1bb08aad5384c466a713f0738676e50deb1f0140a1165613 +DIST Raster3D_3.0-2.tar 1743034 SHA256 a89bdfda61fae8d189820941f1b5685b40743b817128f57bc1225f983a47d984 SHA512 f8f73cc91eae521839a9db8ee1a7a9d8727ed510cb574116d89e918480700d844691a6fc3c4a28cb54312b0133cc610422e55d99716803cf3e8bb5d9d934e37f WHIRLPOOL 58fc31cc438538715b1f0ea17a28b44294d78db32e40fa16f8ab5a5781e26198227c534f06b8d25072e6c6101a4c9255fa906b9fee57b128d0e767bc0e04db83 +DIST Raster3D_3.0-3.tar 1729356 SHA256 1e7d02cf17f2d14855b8d241269948b37ed4d3ae6395914b66ff9f95c3a7fecf SHA512 bd372c4ba8d40db38e19f520883ca71ab7c5ef7a451b67150894e229b45167dfe00b77c19e118afc6abdb9ac07800cc16de5d2dc82c3ef9baa751200490e40fa WHIRLPOOL ad7c11cfd42543845420dcffbc87024c60b3058a51663076ace63b2e2fc0fec81a342f7b4e54f535e03de14fb9e76eace65259cdd2e83a6e0e83810ac8280c10 +EBUILD raster3d-3.0.2.ebuild 2465 SHA256 660b7fcd0ffec71b3ae85a89624e67a8894df802149ac9864baa7c229ca861b8 SHA512 4e8a30469d18f14da0b8258622adaa17c8ac6ff06229dfa59efdf1ec4ba5386c23a594317d059a53d21160d229c17b2fb0db8b8cfc02c36d257230ec641ba9db WHIRLPOOL 0c4af280676e8f020a78313373fb8b7a9ec0ce10d22167c8e20dcd9384fbce4c692dc8e0a4d09b2db1ade579ee9e4e1486bb4c8eea4122e71b1c0235ec711773 +EBUILD raster3d-3.0.3.ebuild 2468 SHA256 bfee09542d343481da0f70a09281408af0fd1cc59eed0b8a16755640cf9180e7 SHA512 3cb278b220520dec632ed9c15c33df8774e4c99b327cd0e895307f9b61c427a8da31d321e27df04985b780957470b739d5202d4d8544c8864ebaeaa50dd0df38 WHIRLPOOL 10167f2c5dcaeebfe38c346b7a9ff5deb2f3233490e0e747384b4cba47214533bac0270879adb4e2b25d19abaaa80b14f5efa97092ccff6d21ed8b416853a70b +MISC ChangeLog 2625 SHA256 c63500406a45299d211690fedfb6a20193d6b195d72dde2d361d7067f93a1c3f SHA512 f87516d6a6fad91d6af0eab2b10c603a349298a45f1a7f96981fbe35e8674a58bc2733a06f98bfdd7518c8ccb85339fcbc7ff1e0224824137b7615bbb5af0439 WHIRLPOOL 870b5dc25e5911a568d9566421d7e8985808aaaac323bc90525c0e38798e3f13b6f054c234b78cc07ea985d55a0edd8386cae5651f543ff6280cc2c3582e9266 +MISC ChangeLog-2015 5814 SHA256 5b0aeacb31004d6b68ec8011ee2c27fd2253b24f6fd84930fbeeb795f6ce873b SHA512 6ab7c5d962850530fe8dda285150811a186b79993fcf400fd34fb2fb7fc9f0ff5c3d72ed99825f1b38fdf4ac2de627c8ff9672eee43ef6374277e7bc94c1926b WHIRLPOOL 7b92093a1660ba87306253e5c2bf499a5bc71e80b86376491ecb6252e6faf417a2e758d626c9427dd118bd878775ad02ed2f21f59f14d7704cb5f8c5e205ffd7 +MISC metadata.xml 459 SHA256 93bb5dee2c50eafdebc0d48e755eaedaeb86ca16d72e757fa1b79f9fecc4e66c SHA512 fe5bb2f873ea63f4c7185601842757cb0f791cecd8651fb4e15ea4992898ae60508e4a4c7bc161bddcfa3cf4125577da029b04cf06c900d6269af3f5b63bd916 WHIRLPOOL ae59b378f1fd7399922b683977d8669c1660ad6fed887c5088b69f3dc75863a6d6ab587d76d6187622b95e05dbdf38451f6ef1871df252496676b19c4c0bc4b9 diff --git a/sci-chemistry/raster3d/files/3.0.2-as-needed.patch b/sci-chemistry/raster3d/files/3.0.2-as-needed.patch new file mode 100644 index 000000000000..9e0961952535 --- /dev/null +++ b/sci-chemistry/raster3d/files/3.0.2-as-needed.patch @@ -0,0 +1,50 @@ +diff --git a/Makefile b/Makefile +index 1a1c549..4d74dd0 100644 +--- a/Makefile ++++ b/Makefile +@@ -58,7 +58,7 @@ linux: + @echo OSDEFS = -DLINUX -DNETWORKBYTEORDER >> Makefile.incl + @echo include Makefile.package >> Makefile.incl + @echo >> Makefile.incl +- @echo qinp.o: qinp.f >> Makefile.incl ++ @echo qinp.o: qinp.f normal3d.o render.o >> Makefile.incl + @echo " \$$(FC) -g -O0 -Wall -Wtabs -c -o qinp.o qinp.f" >> Makefile.incl + @echo >> Makefile.incl + +@@ -214,20 +214,20 @@ ribbon: ribbon.f ribbon1.f modsubs.f + ribbon.f ribbon1.f modsubs.f -o ribbon + + rastep: rastep.f quadric.o suv.o +- $(FC) $(FFLAGS) \ +- rastep.f quadric.o suv.o $(LDFLAGS) \ ++ $(FC) $(FFLAGS) $(LDFLAGS) \ ++ rastep.f quadric.o suv.o \ + -o rastep + + render: render.o local.o quadric.o parse.o r3dtogd.o ungz.o qinp.o +- $(FC) $(FFLAGS) \ ++ $(FC) $(FFLAGS) $(LDFLAGS) \ + render.o local.o quadric.o parse.o r3dtogd.o ungz.o \ + qinp.o \ +- $(LIBS) $(LDFLAGS) \ +- -o render ++ -o render \ ++ $(LIBS) + + normal3d: normal3d.o quadric.o qinp.o ungz.o parameters.incl +- $(FC) $(FFLAGS) \ +- normal3d.o quadric.o ungz.o qinp.o $(LDFLAGS) \ ++ $(FC) $(FFLAGS) $(LDFLAGS) \ ++ normal3d.o quadric.o ungz.o qinp.o \ + -o normal3d + + stereo3d: +@@ -264,7 +264,7 @@ example1.png: render_small + ./render_small + + render_small: render_small.o local.o quadric.o parse_small.o r3dtogd.o ungz.o qinp_small.o +- $(FC) $(FFLAGS) $^ $(LIBS) $(LDFLAGS) -o $@ ++ $(FC) $(FFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) + + .SUFFIXES: .incl + SMALL=10 diff --git a/sci-chemistry/raster3d/files/3.0.2-gentoo-prefix.patch b/sci-chemistry/raster3d/files/3.0.2-gentoo-prefix.patch new file mode 100644 index 000000000000..19b6cac3a6fe --- /dev/null +++ b/sci-chemistry/raster3d/files/3.0.2-gentoo-prefix.patch @@ -0,0 +1,24 @@ +diff --git a/Makefile.template b/Makefile.template +index 59de553..0ed283d 100644 +--- a/Makefile.template ++++ b/Makefile.template +@@ -8,15 +8,15 @@ include VERSION + # + # Where to install the program, data files, and manuals + # +-prefix = /usr/local ++prefix = @GENTOO_PORTAGE_EPREFIX@/usr/ + bindir = $(prefix)/bin + datadir = $(prefix)/share/Raster3D/materials + mandir = $(prefix)/man/manl +-htmldir = $(prefix)/share/Raster3D/html ++htmldir = $(prefix)/share/doc/MYPF/html + examdir = $(prefix)/share/Raster3D/examples + +-INCDIRS = -I/usr/include -I/usr/local/include +-LIBDIRS = -L/usr/local/lib ++INCDIRS = -I@GENTOO_PORTAGE_EPREFIX@/usr/include ++LIBDIRS = -L@GENTOO_PORTAGE_EPREFIX@/usr/MYLIB + + # + # TIFF support (enabled by default) diff --git a/sci-chemistry/raster3d/metadata.xml b/sci-chemistry/raster3d/metadata.xml new file mode 100644 index 000000000000..59d8b8360b0f --- /dev/null +++ b/sci-chemistry/raster3d/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <changelog>http://skuld.bmsc.washington.edu/raster3d/CHANGELOG</changelog> + </upstream> + <use> + <flag name="gd">libgd support for PNG and JPEG output</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/raster3d/raster3d-3.0.2.ebuild b/sci-chemistry/raster3d/raster3d-3.0.2.ebuild new file mode 100644 index 000000000000..a83e43ba57cf --- /dev/null +++ b/sci-chemistry/raster3d/raster3d-3.0.2.ebuild @@ -0,0 +1,106 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils fortran-2 flag-o-matic multilib toolchain-funcs versionator prefix + +MY_PN="Raster3D" +MY_PV=$(replace_version_separator 2 -) +MY_P="${MY_PN}_${MY_PV}" + +DESCRIPTION="Generation high quality raster images of proteins or other molecules" +HOMEPAGE="http://www.bmsc.washington.edu/raster3d/raster3d.html" +SRC_URI="http://www.bmsc.washington.edu/${PN}/${MY_P}.tar.gz -> ${MY_P}.tar" + +LICENSE="Artistic-2" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="gd tiff" + +RDEPEND=" + tiff? ( media-libs/tiff:0 ) + gd? ( media-libs/gd[jpeg,png] )" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}-as-needed.patch \ + "${FILESDIR}"/${PV}-gentoo-prefix.patch + + sed \ + -e "s:MYPF:${PF}:" \ + -e "s:MYLIB:$(get_libdir):g" \ + -i Makefile.template || \ + die "Failed to patch makefile.template" + + if ! use gd; then + sed \ + -e "/GDLIBS/s:^:#:g" \ + -e "/GDDEFS/s:^:#:g" \ + -i Makefile.template || die + fi + + if ! use tiff; then + sed \ + -e "/TLIBS/s:^:#:g" \ + -e "/TDEFS/s:^:#:g" \ + -i Makefile.template || die + fi + + if [[ $(tc-getFC) =~ gfortran ]]; then + append-cflags -Dgfortran + fi + + append-fflags -ffixed-line-length-132 + + eprefixify Makefile.template + cp Makefile.template Makefile.incl || die +} + +src_compile() { + local target + local i + + if [[ $(tc-getFC) =~ gfortran ]]; then + target="linux" + else + target="linux-$(tc-getFC)" + fi + + for i in render.o ${target} all; do + emake \ + CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + FFLAGS="${FFLAGS}" \ + CC="$(tc-getCC)"\ + FC="$(tc-getFC)" \ + INCDIRS="-I${EPREFIX}/usr/include" \ + LIBDIRS="-L${EPREFIX}/usr/$(get_libdir)" \ + ${i} + done +} + +src_install() { + emake prefix="${ED}"/usr \ + bindir="${ED}"/usr/bin \ + datadir="${ED}"/usr/share/Raster3D/materials \ + mandir="${ED}"/usr/share/man/man1 \ + htmldir="${ED}"/usr/share/doc/${PF}/html \ + examdir="${ED}"/usr/share/Raster3D/examples \ + install + + dodir /etc/env.d + echo -e "R3D_LIB=${EPREFIX}/usr/share/${NAME}/materials" > \ + "${ED}"/etc/env.d/10raster3d || \ + die "Failed to install env file." +} + +pkg_postinst() { + elog "Add following line:" + elog "<delegate decode=\"r3d\" command='\"render\" < \"%i\" > \"%o\"' />" + elog "to ${EPREFIX}/usr/$(get_libdir)/ImageMagick-6.5.8/config/delegates.xml" + elog "to make imagemagick use raster3d for .r3d files" +} diff --git a/sci-chemistry/raster3d/raster3d-3.0.3.ebuild b/sci-chemistry/raster3d/raster3d-3.0.3.ebuild new file mode 100644 index 000000000000..309e0dfc1ba5 --- /dev/null +++ b/sci-chemistry/raster3d/raster3d-3.0.3.ebuild @@ -0,0 +1,106 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils fortran-2 flag-o-matic multilib toolchain-funcs versionator prefix + +MY_PN="Raster3D" +MY_PV=$(replace_version_separator 2 -) +MY_P="${MY_PN}_${MY_PV}" + +DESCRIPTION="Generation high quality raster images of proteins or other molecules" +HOMEPAGE="http://www.bmsc.washington.edu/raster3d/raster3d.html" +SRC_URI="http://www.bmsc.washington.edu/${PN}/${MY_P}.tar.gz -> ${MY_P}.tar" + +LICENSE="Artistic-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="gd tiff" + +RDEPEND=" + tiff? ( media-libs/tiff:0 ) + gd? ( media-libs/gd[jpeg,png] )" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch \ + "${FILESDIR}"/3.0.2-as-needed.patch \ + "${FILESDIR}"/3.0.2-gentoo-prefix.patch + + sed \ + -e "s:MYPF:${PF}:" \ + -e "s:MYLIB:$(get_libdir):g" \ + -i Makefile.template || \ + die "Failed to patch makefile.template" + + if ! use gd; then + sed \ + -e "/GDLIBS/s:^:#:g" \ + -e "/GDDEFS/s:^:#:g" \ + -i Makefile.template || die + fi + + if ! use tiff; then + sed \ + -e "/TLIBS/s:^:#:g" \ + -e "/TDEFS/s:^:#:g" \ + -i Makefile.template || die + fi + + if [[ $(tc-getFC) =~ gfortran ]]; then + append-cflags -Dgfortran + fi + + append-fflags -ffixed-line-length-132 + + eprefixify Makefile.template + cp Makefile.template Makefile.incl || die +} + +src_compile() { + local target + local i + + if [[ $(tc-getFC) =~ gfortran ]]; then + target="linux" + else + target="linux-$(tc-getFC)" + fi + + for i in render.o ${target} all; do + emake \ + CFLAGS="${CFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + FFLAGS="${FFLAGS}" \ + CC="$(tc-getCC)"\ + FC="$(tc-getFC)" \ + INCDIRS="-I${EPREFIX}/usr/include" \ + LIBDIRS="-L${EPREFIX}/usr/$(get_libdir)" \ + ${i} + done +} + +src_install() { + emake prefix="${ED}"/usr \ + bindir="${ED}"/usr/bin \ + datadir="${ED}"/usr/share/Raster3D/materials \ + mandir="${ED}"/usr/share/man/man1 \ + htmldir="${ED}"/usr/share/doc/${PF}/html \ + examdir="${ED}"/usr/share/Raster3D/examples \ + install + + dodir /etc/env.d + echo -e "R3D_LIB=${EPREFIX}/usr/share/${NAME}/materials" > \ + "${ED}"/etc/env.d/10raster3d || \ + die "Failed to install env file." +} + +pkg_postinst() { + elog "Add following line:" + elog "<delegate decode=\"r3d\" command='\"render\" < \"%i\" > \"%o\"' />" + elog "to ${EPREFIX}/usr/$(get_libdir)/ImageMagick-6.5.8/config/delegates.xml" + elog "to make imagemagick use raster3d for .r3d files" +} diff --git a/sci-chemistry/reduce/Manifest b/sci-chemistry/reduce/Manifest new file mode 100644 index 000000000000..d1a6f3611091 --- /dev/null +++ b/sci-chemistry/reduce/Manifest @@ -0,0 +1,9 @@ +AUX 3.13.080428-CFLAGS.patch 706 SHA256 ce2b82b16421d58bf5de67703f5e9b718f73176891408867460c560ece42cf63 SHA512 849f0ccb7e452a93e4534b232e0ac89a08fcf1c5c34e74910f76e485f12b96ee0aee04728efd8d6a888538ba8a83d4e1604d1a02cdaeeb23aa0d21a80e7b2be9 WHIRLPOOL abfdcd1f5352c282be497a13dd4295fd3bb66267f88f8642fbda14e909d6c52c67d944ff3d0e4c4a27fe57995009290a7a9870ed589c66803890654addbad1a6 +AUX 3.13.080428-LDFLAGS.patch 230 SHA256 9cdcab6d020e8bed56b6938e77c78c66dda91789a29761548511f1ec3220c013 SHA512 f7b471998c1fa5bb5c4eba7fd3f0900469b3ce1d90399413a18b736e5d35d93875c2b1666afe307935c9e71c516a7bd2db7eee1fba9640d403a2401a4427a539 WHIRLPOOL 7d932a12731035f0a3349aaa053f059f83db71d004711c41c33869df7afaeef6fce643f38285ad3ff7215183907be7b42c331d0c8118d11b49d53e90dea11f94 +AUX 3.14.080821-CFLAGS.patch 736 SHA256 18c5e5e6a20f82b0bcfbc3875742fd3de6ac5ae34c4e2aa194aac5515323fc24 SHA512 f435a889845065374753841a0ba5de64e5be0d73935bd145d2e69980671cb3620441e99ec68bedbd876f45a0d61f406dc1a98f1ed7affaf4c923105d7540530a WHIRLPOOL 76b5aad71c1ccef0d0e73159da768f76fee1aea5d07899b82944ef89da3e8f6e44ce40d1f0121b105880279ae9c64af5132485041aaa776aab636ad2e7f5119c +AUX reduce-3.16.111118-fix-c++14.patch 565 SHA256 785e4d0580150889303f868f630a61a137143f0ef653d00c81912af44774b60a SHA512 8b38d5cbcc76318bb1309185858000daf8cca15a466ce0d4174126c9a5caa50e79d8198d3e3ff3427aa4629d51d0e50773d96b7bce7d94e16cace4bb80f4eed0 WHIRLPOOL 9b9a7622a98b72f099840443d7af8a059af87c98d6c6f599259bcb9ef44369803b71443c3f09678340657a5b4396ef2a941066c5c2af80712c9da194fac19295 +DIST reduce.3.16.111118.src.zip 20342632 SHA256 a9f45dd31eb7022e056cdab1efbbed17fd8be7453396313904c95c839d41dbb3 SHA512 f7b4d8d91f1f57e9e96c91139fa919c570aebd07f3a440faf3df54bf5deb3a05ad998996a24b5fe9aff6280e00329c9914e338cbfe802c047c055f52ce8312a9 WHIRLPOOL 5d5e3c988e39986888eb23907e87ad180a2a441cf236c53406fc43f1cddd25e9e9051ae41d287f35bcf17f3882d720f9cee4c925cbae32139de5848c1fbcccdd +EBUILD reduce-3.16.111118.ebuild 1149 SHA256 c55852f2a650f91389f1ceb9d044ddde7f18c76f524e51a4d82e882d5f1464be SHA512 18b7e9573b1364de97bc7ed54a7ff4480cc79a80dd2a6b1de551d22ef3bc7c0011ac99cc5d5c98f0a434ae99905d982e6f481e14a5a9cf0f43fa82cc0a522a55 WHIRLPOOL f61a7e7772e9695679c7979b6ae637956106742d7d99b9410cddd246c19980f19d0851cf71efb4749da4c3245c525fb4d504958f724e31d72bb172244ceb1ef0 +MISC ChangeLog 2963 SHA256 f13e554a6c19751903ae5d573d1cab3ff263b41a8b7af27f2b7fb2531724f104 SHA512 eac795843f4184ae0a41b593b88b8780a9a52be9786192c1f3d8ba17152e9b9902ff0fc63f65dd283d231216cb7942f8290cfe438b76dc3f743f9f1519664114 WHIRLPOOL ea364ef7d3e3d0aa6f2ded256a5eb4fb74db1e51d040e3a5b5c3019c78d7ca915acb90ff7776f7de32663640cfbae1504a80f1809f978b69a8cf4a4d23cea15f +MISC ChangeLog-2015 3431 SHA256 4e4134fd5228f79a992f412589249f59d44d3ea6f5e66c62591c4ad53b10332c SHA512 6f4fea6138798282e846916b824a105151d703ec2209531d5ca1842b93a62a42f8d9eea1510f4d3a94020881f7831cf2161d19065d83970a9f6fd66287f45260 WHIRLPOOL b77b26ae8d476f222a3a9829d55949c326e03622c64565b4964c44865152dd0a679f0d4ed24a6a86b1521b2bbdfbb7349a08f156b2d758c335ad4fffc8861afe +MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d diff --git a/sci-chemistry/reduce/files/3.13.080428-CFLAGS.patch b/sci-chemistry/reduce/files/3.13.080428-CFLAGS.patch new file mode 100644 index 000000000000..7daa5336f689 --- /dev/null +++ b/sci-chemistry/reduce/files/3.13.080428-CFLAGS.patch @@ -0,0 +1,22 @@ +diff --git a/reduce_src/Makefile b/reduce_src/Makefile +index 598e367..067ace4 100644 +--- a/reduce_src/Makefile ++++ b/reduce_src/Makefile +@@ -12,7 +12,7 @@ PROG_FLGS = -DAROMATICS_ACCEPT_HBONDS \ + # -DDEBUGMOVABLENODE -DDEBUGDOTCOUNTS + # -DMINPREDEFINED -DMAXPREDEFINED\ + +-CFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC)\ ++CXXFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC)\ + -I$(PDBHOME) -I$(TOOLHOME) + # -Wall + +@@ -26,7 +26,7 @@ OBJLIST = GraphToHoldScores.o reduce.o CTab.o ElementInfo.o StdResH.o ResBlk.o A + CXX = g++ + + .cpp.o: +- $(CXX) -c $*.cpp $(CFLAGS) ++ $(CXX) -c $*.cpp $(CXXFLAGS) + + OPT = -O3 + DEBUG = $(CXXDEBUGFLAGS) diff --git a/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch b/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch new file mode 100644 index 000000000000..a615be088b24 --- /dev/null +++ b/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch @@ -0,0 +1,11 @@ +--- a/reduce_src/Makefile ++++ b/reduce_src/Makefile +@@ -34,7 +34,7 @@ + all: reduce + + reduce: $(OBJLIST) +- $(CXX) -o $@ $(OBJLIST) $(LFLAGS) ++ $(CXX) $(LDFLAGS) -o $@ $(OBJLIST) $(LFLAGS) + + clean: + @rm -rf *.o *.ckp ii_files diff --git a/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch b/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch new file mode 100644 index 000000000000..8294c8ca385d --- /dev/null +++ b/sci-chemistry/reduce/files/3.14.080821-CFLAGS.patch @@ -0,0 +1,22 @@ +diff --git a/reduce_src/Makefile b/reduce_src/Makefile +index 598e367..067ace4 100644 +--- a/reduce_src/Makefile ++++ b/reduce_src/Makefile +@@ -12,7 +12,7 @@ PROG_FLGS = -DAROMATICS_ACCEPT_HBONDS \ + # -DDEBUGMOVABLENODE -DDEBUGDOTCOUNTS + # -DMINPREDEFINED -DMAXPREDEFINED\ + +-CFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC) $(DICT_LOCOLD)\ ++CXXFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS) $(DICT_LOC) $(DICT_LOCOLD)\ + -I$(PDBHOME) -I$(TOOLHOME) + # -Wall + +@@ -26,7 +26,7 @@ OBJLIST = GraphToHoldScores.o reduce.o CTab.o ElementInfo.o StdResH.o ResBlk.o A + CXX = g++ + + .cpp.o: +- $(CXX) -c $*.cpp $(CFLAGS) ++ $(CXX) -c $*.cpp $(CXXFLAGS) + + OPT = -O3 + DEBUG = $(CXXDEBUGFLAGS) diff --git a/sci-chemistry/reduce/files/reduce-3.16.111118-fix-c++14.patch b/sci-chemistry/reduce/files/reduce-3.16.111118-fix-c++14.patch new file mode 100644 index 000000000000..5a45b7cef49c --- /dev/null +++ b/sci-chemistry/reduce/files/reduce-3.16.111118-fix-c++14.patch @@ -0,0 +1,14 @@ +Fix building with C++14, which errors out due to an erroneous std::cerr. +See also: https://bugs.gentoo.org/show_bug.cgi?id=594202 + +--- a/reduce_src/GraphToHoldScores.cpp ++++ b/reduce_src/GraphToHoldScores.cpp +@@ -1150,7 +1150,7 @@ + } + } + std::cerr << "CRITICAL ERROR IN whichVertex(" << vertex_index << ") called on edge [" << +- std::cerr << vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl; ++ vertex_indices_[ 0 ] << ", " << vertex_indices_[ 1 ] << "]" << std::endl; + assert(false); + exit(1); + return 0; // to avoid warnings diff --git a/sci-chemistry/reduce/metadata.xml b/sci-chemistry/reduce/metadata.xml new file mode 100644 index 000000000000..da36ecbfcd6a --- /dev/null +++ b/sci-chemistry/reduce/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/reduce/reduce-3.16.111118.ebuild b/sci-chemistry/reduce/reduce-3.16.111118.ebuild new file mode 100644 index 000000000000..ef1349e6adef --- /dev/null +++ b/sci-chemistry/reduce/reduce-3.16.111118.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +MY_P="${PN}.${PV}.src" + +DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/reduce31/${MY_P}.zip" + +LICENSE="richardson" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND} + app-arch/unzip" + +S="${WORKDIR}/" +PATCHES=( + "${FILESDIR}"/3.13.080428-LDFLAGS.patch + "${FILESDIR}"/3.14.080821-CFLAGS.patch + "${FILESDIR}"/${PN}-3.16.111118-fix-c++14.patch +) + +src_compile() { + DICT_DIR="/usr/share/reduce" + DICT_FOLD="reduce_het_dict.txt" + DICT_FNEW="reduce_wwPDB_het_dict.txt" + + emake clean + emake \ + CC="$(tc-getCC)" \ + CXX="$(tc-getCXX)" \ + OPT="${CXXFLAGS}" \ + DICT_HOME="${EPREFIX}/${DICT_DIR}/${DICT_FNEW}" \ + DICT_OLD="${EPREFIX}/${DICT_DIR}/${DICT_FOLD}" +} + +src_install() { + dobin "${S}"/reduce_src/reduce + insinto ${DICT_DIR} + doins "${S}"/${DICT_FOLD} "${S}"/${DICT_FNEW} + dodoc README.usingReduce.txt +} diff --git a/sci-chemistry/relax/Manifest b/sci-chemistry/relax/Manifest new file mode 100644 index 000000000000..1f814f2bbae5 --- /dev/null +++ b/sci-chemistry/relax/Manifest @@ -0,0 +1,5 @@ +DIST relax-4.0.0.src.tar.bz2 105659752 SHA256 4bd27341196d7bf963b269ef41d89b9ac1e1a21200f7911e7c27900d2c0f16d9 SHA512 28b5ddab2c83f95d7e1a502d05b5d3c93337fece68a1fef95ec8978f61fccf24cb37528cfef27cb20d132033535f4120b23cc76a75f34f52b27df17116351f8e WHIRLPOOL 438859c8970f4f16fa9fdf59f7630e3cb07eb0279971b53fa29f6da081c8b3965db0e3f9000efa47d285e44579641222fd74d04b837e453847a1b4dd72acf479 +EBUILD relax-4.0.0-r1.ebuild 1567 SHA256 6987d7acbafc202ec42d7633982589d1aaa2c66d4e5bf7e2586f3ddec72e714c SHA512 4b334b6c1c64a8495d716e4d9032f79c24201e07b87a8a555412677c70e5794456c662364c9b3d839b65248cf8f31f091540575f6ba5a72518964e9078a3ab32 WHIRLPOOL d8b527988dde4978933861e7553054c723193c9b83212088141d9a7872d20913d2e2caebc649ee2bcb9b3e2a9b94e301d60d98e4946459b62330adbc6621e43b +MISC ChangeLog 3538 SHA256 bb2b7ec4fd34c23d1f7b62b4c92366193c74f884a0466c2932df786e9ac2d11f SHA512 3b7572ca6194977e2a28791aa730c153262b26d4a96a8a78b772dcca302a2e450c0e69a6666973d96c592cf38bddbddb18d0e76bb3c373ad7ff4d59d7161229a WHIRLPOOL 524cbf1e96befab2491753eb29336922baaba9bf63b3134dd652e2c6d90b994c31c2543e25d5a5a01c468be4620b8f4b5fc9f3c11df4603f7f69e1120681b6af +MISC ChangeLog-2015 5910 SHA256 ca1e61f25d122fcfab4dcce6a54eab30fa2478303cd3731084fccc4dd9ec5bef SHA512 451b1db88327f0cbf9d8f94e37bd85c4e322165896ced5ce6897547a5600462c0fd01353f55376fc16cebede70379e6084672faf14c54aba24793a19d9066301 WHIRLPOOL 94148badb0db4e84134b38a184b075122fcfc8e6a0c3ee1771f84d6dd0fb2253553b4b31cb27c0cadf10a3ec2b173b4ac8496933033f855608ee0cfd336fed28 +MISC metadata.xml 1352 SHA256 930b174d7d5effaac775b58fc5784d05174ea87bb7a511121d272142290474fd SHA512 eec9d6ca6355a21224554e166ea618a25c1c80fdfe65b66d64437a8824f412d98c29a9f1fa8492175843ed635c78e541841af52a3620c856e73c5d30cce113f5 WHIRLPOOL cc5ff0846acdb5311958d9d79d5e746f09fdb19e1c62785df7e048dd908a749bd49ccbb9a09ec37761e7d685206992de8c6bcf101c0a579430ee8c6ed0b64232 diff --git a/sci-chemistry/relax/metadata.xml b/sci-chemistry/relax/metadata.xml new file mode 100644 index 000000000000..b9c92032837c --- /dev/null +++ b/sci-chemistry/relax/metadata.xml @@ -0,0 +1,30 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +The program relax is a software package designed for the study of molecular +dynamics through the analysis of experimental NMR data. Organic molecules, +proteins, RNA, DNA, sugars, and other biomolecules are all supported. It +was originally written for the model-free analysis of protein dynamics, +though its scope has been significantly expanded. + +relax is a community driven project created by NMR spectroscopists for +NMR spectroscopists. It supports a diverse range of analyses: + +Model-free analysis - the Lipari and Szabo model-free analysis of NMR + relaxation data. +R1 and R2 - the exponential curve fitting for the calculation of the + Rx NMR relaxation rates. +NOE - the calculation of the steady-state NOE NMR relaxation data. +Consistency testing of multiple field NMR relaxation data. +RSDM - Reduced Spectral Density Mapping. +Frame order and N-state model - study of domain motions via the N-state + model and frame order dynamics theories using anisotropic + NMR parameters such as RDCs and PCSs. +Stereochemistry investigations. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/relax/relax-4.0.0-r1.ebuild b/sci-chemistry/relax/relax-4.0.0-r1.ebuild new file mode 100644 index 000000000000..c08c298b59f4 --- /dev/null +++ b/sci-chemistry/relax/relax-4.0.0-r1.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +WX_GTK_VER="3.0" + +inherit eutils multiprocessing python-single-r1 scons-utils toolchain-funcs wxwidgets virtualx + +DESCRIPTION="Molecular dynamics by NMR data analysis" +HOMEPAGE="http://www.nmr-relax.com/" +SRC_URI="http://download.gna.org/relax/${P}.src.tar.bz2" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-python/Numdifftools[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/wxpython:${WX_GTK_VER}[${PYTHON_USEDEP}] + sci-chemistry/molmol + sci-chemistry/pymol[${PYTHON_USEDEP}] + sci-chemistry/vmd + >=sci-libs/bmrblib-1.0.3[${PYTHON_USEDEP}] + >=sci-libs/minfx-1.0.11[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + sci-visualization/grace + sci-visualization/opendx + x11-libs/wxGTK:${WX_GTK_VER}[X]" +DEPEND="${RDEPEND} + media-gfx/pngcrush + test? ( ${RDEPEND} ) + " + +pkg_setup() { + python-single-r1_pkg_setup +} + +src_prepare() { + rm -rf minfx bmrblib extern/numdifftools || die + tc-export CC + need-wxwidgets unicode +} + +src_compile() { + escons +} + +src_test() { + VIRTUALX_COMMAND="${EPYTHON} ./${PN}.py -x --traceback" + virtualmake +} + +src_install() { + dodoc README docs/{CHANGES,COMMITTERS,JOBS,relax.pdf} + + python_moduleinto ${PN} + python_domodule * + + rm ${PN} README || die + + make_wrapper ${PN}-nmr "${EPYTHON} $(python_get_sitedir)/${PN}/${PN}.py $@" +} diff --git a/sci-chemistry/shelx/Manifest b/sci-chemistry/shelx/Manifest new file mode 100644 index 000000000000..85a1591e2224 --- /dev/null +++ b/sci-chemistry/shelx/Manifest @@ -0,0 +1,22 @@ +DIST anode_amd64.bz2 8758937 SHA256 01568fd23b0abe280de7a286b9885182f10f06829f139e46bac75846276f60c7 SHA512 6d9f0e506531e14956a95ed23c4c5ccfabaf79b92feba237923db2731e9f3861163f6039e556a6976d910075558fae120088c4805f09880ff33955eff86cc2e1 WHIRLPOOL af181735822c8d04187f98d06f3be2d563cb3e81571fb81139e384a38b54ca7cc83d10a10564456fffb6eead5ab52833f9002882632634fd5a2f8f450d99ca8c +DIST anode_x86.bz2 4310241 SHA256 520f96803bb0ae7d2e7411187968bb38edadad42f06c22af4f89ee2fd4c95886 SHA512 344e25564d4e0d94764c536625c9be3f4a4b8be74153f17f07254f798e9ebbfe416d069a082906187ba0ec7ab958adf8c7c1ec0afab7a6b146fe02a0b5b88505 WHIRLPOOL 3f349040d1ac9af4323cb091e1b2eb37aff6fe5a1202e65adc9119d1ed141406b5a6792852050061e06253411cb409aebc07c3eb50a26bfa5064ed897ba8da9f +DIST ciftab_amd64.bz2 1409694 SHA256 47c4b4349b2534e5d98d499fb92322bfc0ded5c893a7f6c58c58dbcfb84d1b86 SHA512 7f2439cf5d7afefaf9df0a2e0ab970076ea3f65d1e394aa0a81340e4cae0cbcbd25169a5e490c8269cfdc92fe9d1240d9d0a2949322b48c339f7556173e83428 WHIRLPOOL 68dc54ee8c1f8ab5b84f0857fd1e21afd6e5417c949bcae74e9b76e3e13aeae0318c200f5716f02759a8a9b45089d6810d6bba658f43e7f300a28c7f010c224f +DIST ciftab_x86.bz2 510941 SHA256 d27dd5b21e85f77508f01da71c7f8e2cdadc75169eed362324a697938c02e992 SHA512 185628c888e74e7f7ae69eccb3195d841eab83616449c3358dd3fb49605f6bb9e86e97959cf6d20b424037746b67332ad98b9a41ca2a7fae7e3cbe503bf71127 WHIRLPOOL c121e9350b8bbfcb8cf87c4404e9485b678603943702eebfd07627441c47af95a00d457a49440c8fd65ac8fe625e09e35bd1ce8ead6c12af900dc5fbc56188a7 +DIST shelxc_amd64.bz2 1512555 SHA256 e4da94ecc95a8636b28e50254497a7e519313628106f4fe92869e238f659019f SHA512 11b382c6a8440052ffaf136f5c4695d7f6d10e184334810d0f9b7ff25a782c424ae3509a0bbacabddb152b56e6fdfea7266f9c395d0a39994a8c02bd650625ca WHIRLPOOL f6a7f92278741f19e4a19d4a278588770d50d1d9eac30ba96a285ba10add72613532b1cd5f3ffa28e270e654f252e4cf12939abb1458c70d166569e1dd36fbd4 +DIST shelxc_x86.bz2 614564 SHA256 0e8a4fd16a73f28b77e53225d3d6f1038aae1971dca5910043fa04a5818c6e61 SHA512 5be05948e5b79a44e4ead25deba9b1b08857a4636e4c2f8cdc832f6bb2c2407122adff393035f91ce24b48b025191582b919771052f56ebd7a06aaf66dc82115 WHIRLPOOL 6292394d47017524ecd8d3b809ff87793f718e8e3303e6b221c6b27ae4c7da562cff9945d23dd4112509f34f7c3e83cd4d73728c6ee26ffb7efc7b85a3f19aa0 +DIST shelxd_amd64.bz2 8773698 SHA256 fa7c103c0156ad060e7b66b6f39de8982d660a715a07584d2c1a1853d171d3c0 SHA512 6cb881a937e461edf9c9e7736bfab164e6dc16c4df4291b8dce69b3abf98ce27fadb8079cc5142d2b77eb94ac42c0bb375f3ac21b45f590d535839cc7f8cd762 WHIRLPOOL c4b3b8b7f9d78e15153b4f3678ef8766cdc97cc3c03686b528a40b98d45233612c0104aaa3ec491cd20e787d834965056b10bfa3fc247fc1a4aaee4c0739162d +DIST shelxd_x86.bz2 4406371 SHA256 0b0da50c0907f97e93b46bbd01e63737c007b1b93aa3a79d471621d39557e74f SHA512 68d11983f98984bfaca089b839d38cc9607857d2bb6d2cff306d9efa2f34ea8d741220eb01a99d2ecdd832dde1794b4bb228ceae3fc0e87e3210dfa491e6a402 WHIRLPOOL 6cb3343aa878a5703a65b93f6dd1255ebc668afad92117441a785a91dd39d1736a10411655b08da7ff714bed7ed423e30555b8436c9a7df9f49f8ea3351f651e +DIST shelxe_amd64.bz2 8302570 SHA256 fac87ba983a454cb32f76076318dabbf6ae2f98415cf2428a0154765b3401915 SHA512 cbafde59ba1d9943f74e8c66cc012168f1f8062e978d2f9103adb4d130c9a024e3e8b170af5b5207168f23db4742b4a99ce3b550e897c59e1dfd3631d7d6c6ab WHIRLPOOL 0007c53e4a9bb8e546b625a2565a9e5d01d60b35c8565e34ab753033c16f1c1b61cdfbe2129ff4981cb595cf637f08342b0d77c22ea8836e08df6b671ac6d2e4 +DIST shelxe_x86.bz2 4177233 SHA256 b2bff78b9b51b72e545d23ce76f6b93e016c2cd583aee9d7236b99fd1722d280 SHA512 67d56beef36918ec6b5d86109d2e61a0dc5a34ed73174ba5cdf96e0db8d8d41cdf20bffdee138f6f177e30a9df32aa1494c18221139538e5c778d61d5f558c51 WHIRLPOOL d8e4be4f7b7a313f5586c23a3d5c94dc2b177b36b47025219c5d54985fd41d7ffb902db4d2a1060ae0ce0448d59032782309029096449af76b5df6253db52e81 +DIST shelxl_amd64.bz2 2985452 SHA256 7e7bf32d5dcfa0e8bb0390add8dcc1d0e722012188dd3d124f255ed9e9c13208 SHA512 0c5b5e4bf6041399221a2f321a3e8f3def952a6eb9af26652a8af04c4bedf5cb98aa529c11e84da20c061028701a49af960135ac697ae157609ca8ae8acde219 WHIRLPOOL a5f7a2e118d5582cafa76c1abea86b614e48e1e8ed217e1280b770124eb16f247ef668112031b5a7660af098b51be94b2f53d0fb506dc090e1615ec7204ce712 +DIST shelxl_x86.bz2 1610822 SHA256 b7a28fb6318cb16948c06e7aed8ee7a7c6a5d3a8863c57f657fbbd2007b25955 SHA512 deaeed15676f294088ce07dc3760e2eecca503f87a537e3e9598d1de6102e82f25b2bd46c080e5140a35046847c345845a88adf159197be640ba52b1a790cfec WHIRLPOOL 5998b3909232016e4cfb99a112090e07a926e36442d47e6c7aa09d50d830eeeb21d2732cd962d01672b76b120cca51df400532805e971ee6b2a6c9d13692582d +DIST shelxs_amd64.bz2 1606403 SHA256 9b180574ee2b828123f622d42e307778d8d4a1f4c32d5741ba065ad2b7751e60 SHA512 3d26e8bc10f0004ee52a564be567db0cdf41f7d05d457e66c12e117bb82550066bf7333830f8dcd56ea987de677f365db25a51f4c22efda9c911fda03d49086e WHIRLPOOL 7e02ede8528e752f1a01d3109064914d42d6c83e4d8c0e901e13e9e1345160d087f35568d1f7ff7f61f54fdbf838a6e8b2d8ab9482df27fd561cc7f4dad610d7 +DIST shelxs_x86.bz2 746352 SHA256 3eea6b363f7e2ff90965a01b65f3aa5d4ac5642a1528a7824c3ea8398c272d2b SHA512 9ecf1e8da8df2280a1982c210dea5418004492047fdd3ab004eade39d247199f3c757d00a56d179eadc7a1ce434c8019c39af865b641ae3c370a8461a950140c WHIRLPOOL 5120481aefcaa3871e61dc2f9230095506386de83741e3e5fc7cdf29f2835509ae369276b55252b981907a76b59f3829e0c4ab1738605e5c6f72ff58401157d2 +DIST shelxt_amd64.bz2 8862210 SHA256 519c695b8f6c0425f2635dc021be8138ef029761a43d64133a5d736cccc031b8 SHA512 49cb7b5e9f3a1cab153dd04ce4ab424f3331790df2e4acf0584263edcd28e20f6225a6f48161469e1569ae0d6eeed5389db0c9a66d7853ea34b798364a346e27 WHIRLPOOL 11a821502863cddedb14377f8881b7a7931970f8ce9da668106a5dee6e7113fa6f41f69c9381e7ea4c93aa21a6c3498ba4c836df9289db7295c54e6267faa92c +DIST shelxt_x86.bz2 4441488 SHA256 ca64d86718d306d8d5269f0d7ca92fc2921f1a199afa1bc181b5f6cc339a012c SHA512 83027d24d58863030a284e5e573df27db760ce61f7c8d7da5741471bd814256ae5ade1316aa3e262a54c4c4fb6ad231dacfcef043c3279d381d2969e0b73dd14 WHIRLPOOL ec91f0e6d192507854cbcc2baa751c17185df70f2220eab8f487a1db082bc055aefe2b5f437e144fbbf60c01f1d735057c07ff2f71ab77c88c13a1a19ffe7a65 +DIST shredcif_amd64.bz2 1371002 SHA256 eddf6237b70114bab99845c228d5ba6240a2a9e019bf59678f2222e2ddc52cfe SHA512 5846f7a14936ae4c710ead752a83dd8d73bbcd6037c38f2c566156f87678a84c1db3fd5d0a6e3c6dfb04a2ed7c96c8497c36faaf2bf2ca99ace74f98152ba3be WHIRLPOOL 11b82847cd4f3529c7708de7d0ae7da4e741a58da58ac01954e7136ca2f02c599a81485c70ff36916cdce97e86ab67efe61ec544231db9d7ad903edfd68e232b +DIST shredcif_x86.bz2 461442 SHA256 aa06e0b3f2b7face7f486029d4c83e9fd591c46b2a41db6ce8e3014f6a713d78 SHA512 8097b6285d3e9269989663e52a4d903b279f9cdd0a5650c91d605dd324c62361de619c0873968a3178d3c125f59a9b448465a09542e2582779fbb8cca1f9ebf7 WHIRLPOOL 37f9410d1fcf2881b3e83b752d5170859ebab2063da8124715d5f627a83b9ef2ba4694a2a77a213e8c1b92d474304a7aea83b1f03111fd2abbb3fcd13d054052 +EBUILD shelx-20141228.ebuild 1106 SHA256 f44daa6079f2212bfbd1711d09b35d8206062134274d321fc630eabb028dad9f SHA512 b50a1b7db705633d9eb6654fd8485164c4f16dbe4f632ce834018b9dee9e605fb63c8fa04b4bb8f6a8689b73ab2481df8b0a9ba8ed858b69094f39c653775419 WHIRLPOOL 487936ae982520107f648e87929c60c2c1eac9d0875f971436e46ba61cbeb3f255c1d55cdc6ca30842fe6a05c1bb1bc267d2059b03188959f3bd4b841f93786c +MISC ChangeLog 2498 SHA256 c6f92ce1020d9d82b7a880efbfe5a264c0f7d397dc89942135a1ce525621c7f2 SHA512 e8c95dc38fa9b5501136db3afeb83da794e9b020cb686231ef590f726cdfb6d794ce966f197553d89d49426b3a79bbf5eb9988b9720cb385c9dfb40442104516 WHIRLPOOL f3c6b1bb75aa0e28ccf2270ace939ec29ce0d08984124e09ea528f3c829848ba9cbfd4af4228f95c680196159bc6df9144c9e0d6a3b607362f889b5ac1202ca5 +MISC ChangeLog-2015 3948 SHA256 7027a59f9fa7a23e56b7605991a54a9f1ce72fc9b0c01772e28d826e9d9b17a3 SHA512 059905e3fdd93429fc73bfe90d57d129eba9cf491fded18a49bff3370e81ad28fa11f9360c5983270a1a9e9c843dc4626f319c4a3d4302f0667135a01cff35b7 WHIRLPOOL 80b5cb4de4dd2af0d0f537b550e4881ce99e267eec089c70234e3df482cb0f702ecf6a0b8caa742c303cc61aec47d8c9c72317e6aa178f0080a3798daf0bb1b6 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/shelx/metadata.xml b/sci-chemistry/shelx/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/shelx/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/shelx/shelx-20141228.ebuild b/sci-chemistry/shelx/shelx-20141228.ebuild new file mode 100644 index 000000000000..541cbfb83802 --- /dev/null +++ b/sci-chemistry/shelx/shelx-20141228.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +DESCRIPTION="Programs for crystal structure determination from single-crystal diffraction data" +HOMEPAGE="http://shelx.uni-ac.gwdg.de/SHELX/" +SRC_URI=" + amd64? ( + anode_amd64.bz2 + ciftab_amd64.bz2 + shelxc_amd64.bz2 + shelxd_amd64.bz2 + shelxe_amd64.bz2 + shelxl_amd64.bz2 + shelxs_amd64.bz2 + shelxt_amd64.bz2 + shredcif_amd64.bz2 + ) + x86? ( + anode_x86.bz2 + ciftab_x86.bz2 + shelxc_x86.bz2 + shelxd_x86.bz2 + shelxe_x86.bz2 + shelxl_x86.bz2 + shelxs_x86.bz2 + shelxt_x86.bz2 + shredcif_x86.bz2 + ) +" + +SLOT="0" +LICENSE="free-noncomm" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}" + +RESTRICT="fetch" + +QA_PREBUILT="opt/bin/*" + +pkg_nofetch() { + elog "Go to ${HOMEPAGE}" + elog "Fill out the application form, and send it in." + elog "Download ${A} and rename them to" + use amd64 && elog "*_amd64.bz2" + use x86 && elog "*_x86.bz2" + elog "and place renamed tarballs in ${DISTDIR}." +} + +src_install() { + local i + into /opt + for i in *; do + newbin ${i} ${i/_*/} + done +} diff --git a/sci-chemistry/sparky/Manifest b/sci-chemistry/sparky/Manifest new file mode 100644 index 000000000000..97fa4139999e --- /dev/null +++ b/sci-chemistry/sparky/Manifest @@ -0,0 +1,10 @@ +AUX 3.115-fix-c++14.patch 849 SHA256 69498ca78090e575aa1e8637cc0d6dd12298cdc66fdbcbad02bbc3a73672f664 SHA512 80bbfe8a2e853f8be84ed48da99605805a42bb05b091c851ddbefb5513745cdf51c5396e97ad4e3be7dd199270fb069e239e0c24f6642d956fd6571d8b14a7e1 WHIRLPOOL ca4c9f6940808207fb5d411395ef13a528d5e698f3d1511b400271ba765e5b299d2ac48913f457bfc8839a510bfac608ca8bc0fa513bd0db2becfabb78532374 +AUX 3.115-ldflags.patch 2713 SHA256 227c4ca0deb0a98a6ce40f03065c68a8ac433772ef3d318adb6d69705fedfefe SHA512 1c439cc04af3e8e403257ccd45eecb16f0e36d4b51a28ab5ddda269bde271d23a20bb453cda48e03f58c31a9a614d4b19ca2b6aa7f75bdfec1f79b70e8c361de WHIRLPOOL d5d96703d1450abfca4a70c5dae6971664bc9e844d869d83928b1e21f4da4bce2093b9478c4d23ac47f711d0a412a85c13c4c55f02eeabfdb0b6a91fff37cf49 +AUX 3.115-makefile.patch 580 SHA256 c265b6114c826c8c88b7e7256ef281cfefba00997f8c719146000f95017139a5 SHA512 9ddd99de93656301f307aabb3284e86fe68f4c7957f0b5ff81da4615f850fc36b686908de84816f0ff8a3d75169ccd0d4d7cb5bb8afd88d96c913f766e7ee19a WHIRLPOOL ac85d055252a82373b781ebb60eca7cf33e3d40e248c866238bb9395555679d20e88a81b307962e89654660a24290274fac45e5257a1fb915be6437e62919c8c +AUX 3.115-paths.patch 415 SHA256 8a38226eb0b6cbf1cd5af9d4aad2a17da11897e8c8c027bfb18d9dac24d87b47 SHA512 44c44c99cf2c5c51c8e506267efc4efc50eb2277ccdab362943da0c45c63f9e797ae699e99eda3ce6ca0b4e0a886393d1917ce8614eea3086e97446fc3c0c674 WHIRLPOOL d7f1fad28bb51b03c30e61a6fbde8725cfb9602f78f3e494184beee1398d177b9d48ef024cd024554066e13eefbe5397221aff245e62f6fa11848a0f7f972ec2 +AUX 3.115-wrapper-r1.patch 1518 SHA256 e99acd1e5d735ee027361fda5d4c0652c729e2a02eedc80253fbc8b3654e89ea SHA512 be2c18a40ceabdb1c25a7849e1ee00438092f264c486e93b3bfb412fc417902a3b22b672d28a6cc104fedc5477ea2c0de66bc40dd5d4d607ed0201eee4d368a7 WHIRLPOOL 731d9511f3224399db3f108b9c8de8dfdda30a333389766d67610eb15c0196cda26464bc164aff3757c5af0bcb0414cf50b73b49dc9027bedae67360a46e395e +DIST sparky-source-3.115.tar.gz 4103686 SHA256 c187546aaec3d6489c533c3a778e1fe6fa634a931dcaf245c1e13f5720a002b6 SHA512 33b0fd368f15bf4d091d7152a189f57279aea54fb89a12f15314f2a1414b073f7bd282afedeb72e79192195b0b6ac212ca74da3def513592af5400c118ac8e89 WHIRLPOOL 8557a525eab51150da437f78cb8e404adad4f41ed0884498601887e832f78bb316e4847cc3b3a7147ec66bcddd4e06064323bb2ce76452b37d504a809feee7ff +EBUILD sparky-3.115-r2.ebuild 3192 SHA256 7f6a628c6056e9813558755f0298c47dd5a085658d7f177c429ffa86f19b0627 SHA512 f2f5fe11666e85feca9d90c5fb6c9d93f42b9bde269f311a943c37b334d617d7dcdbc5ee45cb555fb6af278a648c0c0ab4ec28027143675ee0cc2c77dc41c10a WHIRLPOOL 4b5fae4301f184c8c041f39a7c86b3c5d197ff0b2249cb1fc24ad3a5e2c2928e72fb51c61f799ac0a7a09a1460832639abc5b91effa5e5a5e5d60ed6ceb7e60b +MISC ChangeLog 3430 SHA256 fb5967bd22cef4fab1fa90f3e1a3e172b04fcbe992ac15c770a8a2bc824730b0 SHA512 14176a5d6f72e01337637ccdf402861638aecbba820c081c0aa6b350046cb60c0440378095db0686654434a3a432f6fc2ffc3944d1616868e48011e8ca7f52ab WHIRLPOOL 0d388824720b03aa771ae240a3595d58009f6b388806011752af7fb84e479e5928f99170e3e4b3dab0aa6181d115c050af93acc79b8161f5572d24dc22f1e406 +MISC ChangeLog-2015 3615 SHA256 ca930454305a6c0a819f94c74357aa75f93971b0427880550a7a3c0cc9b01d42 SHA512 ba7e788c591eed7e3a61ac8650757557ba44adf5265e0dabad54e0802dc68a5091f15300f6dd5e6f08aacc4b6b66f2b65f815acd14504c624dc5c60b9b0a3ec2 WHIRLPOOL 357f7369e9a0eae7d9f23c92fced2f8da8b63f598e6218f87b2405c76993800bfc6a07867e30cd3e9ffebc0a906c06108667db0aa736fee8e92f74dc5c37fa42 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/sparky/files/3.115-fix-c++14.patch b/sci-chemistry/sparky/files/3.115-fix-c++14.patch new file mode 100644 index 000000000000..3a05ea7d85ce --- /dev/null +++ b/sci-chemistry/sparky/files/3.115-fix-c++14.patch @@ -0,0 +1,32 @@ +Fix the custom new/new[] operators in order to account for changed +noexcept semantics in C++11. +See also: https://bugs.gentoo.org/show_bug.cgi?id=596012 + +Patch by Peter Levine + +--- a/c++/memalloc.cc ++++ b/c++/memalloc.cc +@@ -39,7 +39,10 @@ + + // ---------------------------------------------------------------------------- + // +-void *operator new(size_t size) throw(std::bad_alloc) ++void *operator new(size_t size) ++#if __cplusplus < 201103L ++throw(std::bad_alloc) ++#endif + { + void *value = allocate(size); + if (tracking_memory) +@@ -72,7 +75,10 @@ + + // ---------------------------------------------------------------------------- + // +-void *operator new[](size_t size) throw(std::bad_alloc) ++void *operator new[](size_t size) ++#if __cplusplus < 201103L ++throw(std::bad_alloc) ++#endif + { + void *value = allocate(size); + if (tracking_memory) diff --git a/sci-chemistry/sparky/files/3.115-ldflags.patch b/sci-chemistry/sparky/files/3.115-ldflags.patch new file mode 100644 index 000000000000..bd4020387682 --- /dev/null +++ b/sci-chemistry/sparky/files/3.115-ldflags.patch @@ -0,0 +1,61 @@ +diff --git a/c++/Makefile b/c++/Makefile +index aeb4daa..5cab356 100644 +--- a/c++/Makefile ++++ b/c++/Makefile +@@ -131,28 +131,28 @@ $(SPARKY_INSTALL)/python/sparky $(SPARKY_INSTALL)/python/lib-tk: + chmod 755 $@ + + sparky-no-python$(EXE_SUFFIX): main.o $(SPARKY_OBJS) +- $(CXX) -o $@ main.o $(SPARKY_OBJS) $(LDFLAGS) $(LDLIBS) ++ $(CXX) $(LDFLAGS) -o $@ main.o $(SPARKY_OBJS) $(LDLIBS) + + ucsfdata$(EXE_SUFFIX): ucsfdata.o $(NMR_OBJS) +- $(CXX) -o $@ ucsfdata.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) ++ $(CXX) $(LDFLAGS) -o $@ ucsfdata.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) + + pipe2ucsf$(EXE_SUFFIX): pipe2ucsf.o $(NMR_OBJS) +- $(CXX) -o $@ pipe2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) ++ $(CXX) $(LDFLAGS) -o $@ pipe2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) + + vnmr2ucsf$(EXE_SUFFIX): vnmr2ucsf.o $(NMR_OBJS) +- $(CXX) -o $@ vnmr2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) ++ $(CXX) $(LDFLAGS) -o $@ vnmr2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) + + bruk2ucsf$(EXE_SUFFIX): bruk2ucsf.o $(NMR_OBJS) +- $(CXX) -o $@ bruk2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) ++ $(CXX) $(LDFLAGS) -o $@ bruk2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) + + peaks2ucsf$(EXE_SUFFIX): peaks2ucsf.o $(NMR_OBJS) +- $(CXX) -o $@ peaks2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) ++ $(CXX) $(LDFLAGS) -o $@ peaks2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) + + matrix2ucsf$(EXE_SUFFIX): matrix2ucsf.o $(NMR_OBJS) +- $(CXX) -o $@ matrix2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS) ++ $(CXX) $(LDFLAGS) -o $@ matrix2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS) + + spy.so: python.o $(SPARKY_OBJS) +- $(CXX) $(LDSHARED) -o $@ python.o $(SPARKY_OBJS) $(LDFLAGS) $(LDLIBS) ++ $(CXX) $(LDSHARED) $(LDFLAGS) -o $@ python.o $(SPARKY_OBJS) $(LDLIBS) + + winsystem-$(PLATFORM).o: winsystem-$(PLATFORM).cc + $(CXX) $(CXXFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/winsystem-$(PLATFORM).cc +@@ -161,7 +161,7 @@ python.o: python.cc + $(CXX) $(CXXFLAGS) $(PYFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/python.cc + + _tkinter.so: _tkinter.o +- $(CXX) $(LDSHARED) -o $@ _tkinter.o $(LDFLAGS) $(TKLIBS) ++ $(CXX) $(LDSHARED) $(LDFLAGS) -o $@ _tkinter.o $(TKLIBS) + + _tkinter.o: _tkinter.c + $(CC) $(CFLAGS) $(TKFLAGS) $(PYFLAGS) -c $(SPARKY_SRC)/_tkinter.c +@@ -188,8 +188,8 @@ PYLDFLAGS = -L$(PYTHON_LIB)/config -lpython$(PYTHON_VERSION) + PYIFLAGS = -I$(PYTHON_INC) + + debug-sparky: main-debug.o python.o _tkinter.o $(SPARKY_OBJS) +- $(CXX) -o $@ main-debug.o python.o _tkinter.o $(SPARKY_OBJS) \ +- $(LDFLAGS) $(PYLDFLAGS) $(LDLIBS) ++ $(CXX) $(LDFLAGS) -o $@ main-debug.o python.o _tkinter.o $(SPARKY_OBJS) \ ++ $(PYLDFLAGS) $(LDLIBS) + + main-debug.o: main-debug.cc + $(CXX) $(CXXFLAGS) $(PYIFLAGS) -c $(SPARKY_SRC)/main-debug.cc diff --git a/sci-chemistry/sparky/files/3.115-makefile.patch b/sci-chemistry/sparky/files/3.115-makefile.patch new file mode 100644 index 000000000000..7c810dcbd8ae --- /dev/null +++ b/sci-chemistry/sparky/files/3.115-makefile.patch @@ -0,0 +1,17 @@ +diff --git a/Makefile b/Makefile +index bb27034..30979bd 100644 +--- a/Makefile ++++ b/Makefile +@@ -48,6 +48,12 @@ TKINTER_PYMOD = _tkinter$(PYMOD_SUFFIX) + all nopython $(SPY_PYMOD) $(TKINTER_PYMOD) $(EXECUTABLES) debug-sparky clean: force + cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $@ + ++libraries: ++ cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $(SPY_PYMOD) $(TKINTER_PYMOD) ++ ++binaries: ++ cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $(EXECUTABLES) debug-sparky ++ + Makefile.dep TAGS: force + cd $(SPARKY_SRC) && $(MAKE) -f Makefile -e $@ + diff --git a/sci-chemistry/sparky/files/3.115-paths.patch b/sci-chemistry/sparky/files/3.115-paths.patch new file mode 100644 index 000000000000..20d9a801ecd6 --- /dev/null +++ b/sci-chemistry/sparky/files/3.115-paths.patch @@ -0,0 +1,13 @@ +diff --git a/c++/paths.h b/c++/paths.h +index 2a21366..38aff52 100644 +--- a/c++/paths.h ++++ b/c++/paths.h +@@ -19,7 +19,7 @@ + // Installation subdirectories and files + // + #define SPARKY_MANUAL "manual" +-#define SPARKY_LIB "lib" ++#define SPARKY_LIB "." + #define SPARKY_PRINT "print-prolog.ps" // under lib directory + #define SPARKY_RESOURCE "Sparky" // under lib directory + #define SPARKY_SAMPLE_DATA "example" diff --git a/sci-chemistry/sparky/files/3.115-wrapper-r1.patch b/sci-chemistry/sparky/files/3.115-wrapper-r1.patch new file mode 100644 index 000000000000..d83b5b8510cc --- /dev/null +++ b/sci-chemistry/sparky/files/3.115-wrapper-r1.patch @@ -0,0 +1,41 @@ +diff --git a/bin/sparky b/bin/sparky +index 8b51212..270723a 100644 +--- a/bin/sparky ++++ b/bin/sparky +@@ -4,18 +4,6 @@ + # + + # ----------------------------------------------------------------------------- +-# Figure out Sparky installation directory from $0. +-# +-set sparky_exe = "$0" +-while (-l "$sparky_exe") +- set ls_sparky_exe = `ls -l "$sparky_exe"` +- set sparky_exe = `echo "$ls_sparky_exe" | sed 's/.* -> //'` +-end +-set sparky_bin = `dirname "$sparky_exe"` +-set sparky_bin = `cd "$sparky_bin"; pwd` +-set sparky_inst = `dirname "$sparky_bin"` +- +-# ----------------------------------------------------------------------------- + # Sparky uses the SPARKY_INSTALL environment variable to find its + # application resource file and print prolog file. + # +@@ -25,7 +13,7 @@ setenv SPARKY_INSTALL "$sparky_inst" + # If Python is available start Sparky as a Python extension. + # Otherwise the standalone version of Sparky is started. + # +-set PYTHON = "$SPARKY_INSTALL/python2.5/bin/python2.5" ++set PYTHON = GENTOO_PYTHON + if (! -e "$PYTHON") then + set PYTHON = python2.5 + endif +@@ -79,7 +67,7 @@ if ($status == 0) then + # --------------------------------------------------------------------------- + # Add the Sparky package and Tkinter to the Python path + # +- set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/lib-tk" ++ set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/sparky" + if ($?PYTHONPATH) then + setenv PYTHONPATH "${SPARKY_PYTHONPATH}:$PYTHONPATH" + else diff --git a/sci-chemistry/sparky/metadata.xml b/sci-chemistry/sparky/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/sparky/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/sparky/sparky-3.115-r2.ebuild b/sci-chemistry/sparky/sparky-3.115-r2.ebuild new file mode 100644 index 000000000000..e664747fea13 --- /dev/null +++ b/sci-chemistry/sparky/sparky-3.115-r2.ebuild @@ -0,0 +1,117 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="tk" + +inherit flag-o-matic prefix python-single-r1 toolchain-funcs + +DESCRIPTION="Graphical NMR assignment and integration program for large polymers" +HOMEPAGE="http://www.cgl.ucsf.edu/home/sparky/" +SRC_URI="http://www.cgl.ucsf.edu/home/sparky/distrib-${PV}/${PN}-source-${PV}.tar.gz" + +LICENSE="sparky" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + app-shells/tcsh + dev-lang/tcl:0= + dev-lang/tk:0=" +DEPEND="${RDEPEND}" + +RESTRICT="mirror" + +S="${WORKDIR}/${PN}" + +PATCHES=( + "${FILESDIR}"/${PV}-ldflags.patch + "${FILESDIR}"/${PV}-wrapper-r1.patch + "${FILESDIR}"/${PV}-paths.patch + "${FILESDIR}"/${PV}-makefile.patch + "${FILESDIR}"/${PV}-fix-c++14.patch +) + +pkg_setup() { + python-single-r1_pkg_setup + TKVER=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2) + PYVER=${EPYTHON#python} +} + +src_prepare() { + default + + sed -i \ + -e "s:^\(set PYTHON =\).*:\1 ${PYTHON}:g" \ + -e "s:^\(setenv SPARKY_INSTALL[[:space:]]*\).*:\1 ${EPREFIX}/usr/$(get_libdir)/${PN}:g" \ + -e "s:tcl8.4:tcl${TKVER}:g" \ + -e "s:tk8.4:tk${TKVER}:g" \ + -e "s:^\(setenv TCLTK_LIB[[:space:]]*\).*:\1 ${EPREFIX}/usr/$(get_libdir):g" \ + "${S}"/bin/sparky || die + eprefixify "${S}"/bin/sparky +} + +src_compile() { + emake \ + SPARKY="${S}" \ + PYTHON_VERSION="${PYVER}" \ + PYTHON_PREFIX="${EPREFIX}/usr" \ + PYTHON_LIB="${EPREFIX}/usr/$(get_libdir)" \ + PYTHON_INC="$(python_get_includedir)" \ + TK_PREFIX="${EPREFIX}/usr" \ + TCLTK_VERSION="${TKVER}" \ + TKLIBS="-L${EPREFIX}/usr/$(get_libdir)/ -ltk -ltcl -lX11" \ + CXX="$(tc-getCXX)" \ + CC="$(tc-getCC)" \ + LDSHARED="-shared" \ + binaries + + rm c++/*.o || die + + emake \ + SPARKY="${S}" \ + PYTHON_VERSION="${PYVER}" \ + PYTHON_PREFIX="${EPREFIX}/usr" \ + PYTHON_LIB="${EPREFIX}/usr/$(get_libdir)" \ + PYTHON_INC="$(python_get_includedir)" \ + TK_PREFIX="${EPREFIX}/usr" \ + TCLTK_VERSION="${TKVER}" \ + TKLIBS="-L${EPREFIX}/usr/$(get_libdir)/ -ltk -ltcl -lX11" \ + CXX="$(tc-getCXX)" \ + CC="$(tc-getCC)" \ + CXXFLAGS="${CXXFLAGS} -fPIC" \ + CFLAGS="${CFLAGS} -fPIC" \ + LDSHARED="-shared -fPIC" \ + libraries +} + +src_install() { + # The symlinks are needed to avoid hacking the complete code to fix the locations + dobin c++/{{bruk,matrix,peaks,pipe,vnmr}2ucsf,ucsfdata,sparky-no-python} bin/${PN} + + insinto /usr/share/${PN}/ + doins lib/{print-prolog.ps,Sparky} + dosym ../../share/${PN}/print-prolog.ps /usr/$(get_libdir)/${PN}/print-prolog.ps + dosym ../../share/${PN}/Sparky /usr/$(get_libdir)/${PN}/Sparky + + python_moduleinto ${PN} + python_domodule python/*.py c++/{spy.so,_tkinter.so} + dosym ../${EPYTHON}/site-packages /usr/$(get_libdir)/${PN}/python + + rm manual/{pkzip.cfg,Makefile} || die + mv {manual/,}manual.ps || die + local DOCS=( README manual.ps ) + local HTML_DOCS=( manual/. ) + einstalldocs + newdoc python/README README.python + dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/${PN}/manual + + if use examples; then + dodoc -r example + dosym ../../share/doc/${PF}/example /usr/$(get_libdir)/${PN}/example + fi +} diff --git a/sci-chemistry/suitename/Manifest b/sci-chemistry/suitename/Manifest new file mode 100644 index 000000000000..c7cde63b8319 --- /dev/null +++ b/sci-chemistry/suitename/Manifest @@ -0,0 +1,5 @@ +DIST suitename.0.3.070628.src.tgz 29914 SHA256 5c2a709aa2d815b259475344aa2b982c157868eb9a7e5d6407b8f525f7e28c4c SHA512 27811e2511da760c3c35d0a44aa798a35610a0e80a72d8aa58b78cb780156508f96e1890f558b1aa43bc3469d433352b29e53dca79f3a876ae2b7073f8e73088 WHIRLPOOL f4d84180df12062ebfe402231276808bd28280c44c83559330071225aaa8f29c70cd7edf24c7657bdc53d6359df6dc61b7a601f01cb5e164eca3b017d386c6ec +EBUILD suitename-0.3.070628.ebuild 760 SHA256 a1f12feff7ff7c7ebb917ea21b856df816f28ba28c0f797eb5aaff98c2667cf4 SHA512 59764e2a91931807a5a0f3f18de7b21064f6bb31311350d921a59d2d602b5433fc849ff16117504ababefc70ca007b302a67fb68f80ea38d01cd695fdf48cd4c WHIRLPOOL d313ff5518d51eafe443dcd936ca19c1d6934fdf061b6a15efd777cb40627053c6157dc62c43a3df483e214ae21f102f4d870253218f49cbc59e8c90299d7a84 +MISC ChangeLog 2588 SHA256 87357a9964e9bd5d610f025969e30094aafd92be7faf707bf23d00ed691480a1 SHA512 f5895f54c9aa599e1a4fcd033daf38f216abfab251aa765ffd73c33eedf2261268cd177d3f052c23eba25bcafdc3ab67f5538c6132a66d8c2f0d14cb83334075 WHIRLPOOL b3e60a9b813b480cef2ca501419b443454a98d18ae76b02aa68ac03ce9813989b0694188f5002a79e5992e34ee35fcf49bcdabbfacef061bddcc0b653512bd0c +MISC ChangeLog-2015 590 SHA256 5f56515891621af4b9dc205d63d2a437cfc9300cff98878987b77319c7a1ad96 SHA512 3013e606c72fcc3d8ab509b4a7d6fed23bb39eabd341e070812333a9062e31630c000dd028be4c8e5cdc5edda2e19c482236644e6e83527b39008c547a8ae91f WHIRLPOOL 9a6ac47068b28aec29643a192717aad45c94208822bc6d483119ff7a12f6de4fb0d68864ce9bf5eeeb0adeb94dcbe0abdbf4e42f2757ac44de20e54503cc5e3e +MISC metadata.xml 1118 SHA256 3d02c415cd222447e1b17c54fef4be2dc5b1ac727c4ccb795955e6e50183d9f6 SHA512 7b2b6baa9bbc3e4ff3e2b2c0ba15dce0af04b06133c96872bbbb3626566a025d1b7d5472fc159e879e7be0cf50b5c27ebbcbd8def5cb182fc3654b893d88f2f2 WHIRLPOOL a5faa66f566ce3eada72ec1264d9ae21c56e0d599152b089d4a4ec27c6c0b82d101b7e53f6a1aee3accdd94d6e6585a578a3f66e516221885248bce3f460b740 diff --git a/sci-chemistry/suitename/metadata.xml b/sci-chemistry/suitename/metadata.xml new file mode 100644 index 000000000000..e816416cfd5d --- /dev/null +++ b/sci-chemistry/suitename/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +Suitename is a new C program that supports the ROC RNA Ontology Consortium +consensus RNA backbone nomenclature and conformer-list development (see our RNA +backbone rotamer section. +From dihedral-angle input for a specific RNA structure (usually from Dangle), +Suitename categorizes the RNA backbone geometry of each suite (the +sugar-to-sugar version of a residue) either as an outlier ("!!") or as belonging +to one of the 53 defined conformer bins. The output is either a +one-line-per-suite report, or a linear conformer string (as shown below the +image here) in one of several variant formats. Suitename is built into +MolProbity, producing entries in the multi-criterion chart for an RNA model and +also a suitestring file. The Suitename code is made available here for bulk or +individual command-line use. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/suitename/suitename-0.3.070628.ebuild b/sci-chemistry/suitename/suitename-0.3.070628.ebuild new file mode 100644 index 000000000000..e0306fac8f29 --- /dev/null +++ b/sci-chemistry/suitename/suitename-0.3.070628.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit toolchain-funcs + +MY_P="${PN}.${PV}" + +DESCRIPTION="The ROC RNA Ontology Consortium consensus RNA backbone nomenclature and conformer-list development" +HOMEPAGE="http://kinemage.biochem.duke.edu/software/suitename.php" +SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${MY_P}.src.tgz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="richardson" +IUSE="" + +S="${WORKDIR}"/${MY_P} + +src_prepare() { + tc-export CC + cp Makefile.linux Makefile || die + sed \ + -e 's:cc:${CC}:g' \ + -e "s:-o:${LDFLAGS} -o:g" \ + -i Makefile || die +} + +src_compile() { + emake CFLAGS="${CFLAGS}" +} + +src_install() { + dobin ${PN} +} diff --git a/sci-chemistry/surf/Manifest b/sci-chemistry/surf/Manifest new file mode 100644 index 000000000000..de36ce2287c2 --- /dev/null +++ b/sci-chemistry/surf/Manifest @@ -0,0 +1,5 @@ +DIST surf-1.0.tar.Z 74347 SHA256 6d032e4b749e5e1971b5d97b0fcf552029068a87bcaebd6ce92db27179f7cb0a SHA512 55b0e771f880931e43d677498ef4cdd92e5f57980d90b686b13c7ae612c8d695353a6f3b5ad0dab184d44e67d8cc5244e7b3f45b4f067c4174ed4399c184d435 WHIRLPOOL 961e117b1e9fd5357224db76520fba7339da9e9f4a8aac73cd5b2f13e89b4e6f8ad731c092d1a5c52754b1f07a875bce253ba991b673e7bfa1f647b0d30226ef +EBUILD surf-1.0.ebuild 822 SHA256 429c0d6e36ec40bb8ace7470c78aa6d253cbe4da0aae78d67dbe6985ec2fc58c SHA512 94b7de7a59085f10b60c3aa8ab5280a441239cb63ea3723d15dac949295a07d401c820c5b24e7ff1d03571086c6a1ead3a43d2688a17d6ab4928c9728270f706 WHIRLPOOL 95f4195361af92601c2a000a9613cf90050a31f9511edfd8aa93644646c0da1bd255e0e21aad1b762097d89437bad75766e6c959af628c74a530d9bf556f7301 +MISC ChangeLog 2419 SHA256 957f8d72b917e14204a2e0976cf7c74adc5fdf81f89e6f5eef08eab097e8be6e SHA512 1f84abfe31398b7713009929c2e3fd01deadbbdbec60d3eb40df76c0c6bffa18f083182b12b399cfdad0ab906e0df9a7b726f1e56b0f54b32e772808343ef60e WHIRLPOOL 50241b796fce8fc9e286039e29fb15c7987e85706c1317565cb5fddf8e3513a1c2b8bc3f8661cc8d700ef664215acec6965730f4322370a117a4790de831fb61 +MISC ChangeLog-2015 1005 SHA256 1f596bedd0ae1480dc6c961fd3c96f8961e80181d594e416a8eb9bb58815515b SHA512 e8cd17d51304f4e8ce58981322abc078dd989f02b63ffafd46a0322735de42f0b994c5ba08b591c253a8b25b73de38044b65e51b13cf906fa30b83137ea49be3 WHIRLPOOL 12d556624805f11cb95ef5238568caa720b71495485039971105de245c52efaec91bf3340de2694b73c65bbaae136cc5912e65f26566bc5172e8946192d98745 +MISC metadata.xml 261 SHA256 f53f2259ad8695c56f1457bcbd63ad8f51108ec471d728cd2fe6f523b36b09d8 SHA512 72682d17ec2b918131b551bd1ff41004965d3cf0c00d24222b34741d2eabf601cf36d4266be70ba7fb7bd0ab55d9dcb5b8e4ca41125bc31f176516797459c8c7 WHIRLPOOL 8ae9531cec25662e7d2a9df3c46039a66da22cb0becfc5cb2eacbb0ea5cfedf0491bd7110465ae37c4e8263b5a962f4973eed3dc569db0d524506943014444a2 diff --git a/sci-chemistry/surf/metadata.xml b/sci-chemistry/surf/metadata.xml new file mode 100644 index 000000000000..4ac68c154bb0 --- /dev/null +++ b/sci-chemistry/surf/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> +</maintainer> +</pkgmetadata> diff --git a/sci-chemistry/surf/surf-1.0.ebuild b/sci-chemistry/surf/surf-1.0.ebuild new file mode 100644 index 000000000000..138830fe777c --- /dev/null +++ b/sci-chemistry/surf/surf-1.0.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="4" + +inherit toolchain-funcs + +DESCRIPTION="Solvent accesible Surface calculator" +HOMEPAGE="http://www.ks.uiuc.edu/" +SRC_URI="http://www.ks.uiuc.edu/Research/vmd/extsrcs/surf.tar.Z -> ${P}.tar.Z" + +LICENSE="SURF" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" +IUSE="" + +DEPEND=" + !www-client/surf + sys-apps/ed + x11-misc/makedepend" +RDEPEND="" + +S=${WORKDIR} + +src_prepare() { + sed \ + -e 's:$(CC) $(CFLAGS) $(OBJS):$(CC) $(CFLAGS) $(LDFLAGS) $(OBJS):g' \ + -i Makefile || die +} + +src_compile() { + emake depend \ + && emake \ + CC="$(tc-getCC)" \ + OPT_CFLAGS="${CFLAGS} \$(INCLUDE)" \ + CFLAGS="${CFLAGS} \$(INCLUDE)" \ + || die +} + +src_install() { + dobin ${PN} || die + dodoc README || die +} diff --git a/sci-chemistry/theseus/Manifest b/sci-chemistry/theseus/Manifest new file mode 100644 index 000000000000..d3a37f389528 --- /dev/null +++ b/sci-chemistry/theseus/Manifest @@ -0,0 +1,9 @@ +DIST theseus_2.0.6.tar.gz 1257560 SHA256 f63f4d5fd9ce9d30048312e31807a1a413b433e2bbcfd0cefb3703f455551c23 SHA512 70604c468eb841b92e77a3e91cd57120b96c171512fb1cc31a407b7c4816150dfa31ec123fb9568a842e623f3252c60df0dc53d40fa2a4aece6e3c77039f4696 WHIRLPOOL 01c73e5bec0f4e9a98cd926a15f3213f30d20db10a500e88cfa54e31b92324d3fb741899c30c5c45e8d5a2d31eb68e742113b29a077f70430cf7acda9c02bc54 +DIST theseus_3.0.0.tar.gz 1213574 SHA256 4e474efabf1cfc9a48e96e86ac9e5b0f8035b57677017542e66478759bdc7866 SHA512 251e6273624126406609691e1205d9693c18dcbc8c81e10c77101ac4a1b6bdffcb56a47fd5fdc7ed6ed4fa107c2ed26b03a1780f951f9cc69a25c0722996e7b2 WHIRLPOOL 5a15c0f5270411114ebbca4fc9cad1e4db0449d1e6d8d1693f1e58d6a54f61b401cc6a2df2539d2ca34dd4dc52a09e1c45c0af8b80eb5c8916d8f168bf536ad3 +DIST theseus_3.3.0.tar.gz 22548124 SHA256 3cfd4f906717f9cb8e77f689fc97059b32df355c0696077034ea99a485e3f2fe SHA512 1fba3e8019a40214defdae13d4721d170ee698337d8efd4e872af22f8ab3cb1fdd52fa9f19a858ee51bc98150692af0c6016033feb0d76f29acaf7fffbb430e2 WHIRLPOOL c1baf4daea1e2a0c78b73d8d91ff735aa9bb82bd6edf533aab0f9d20a9e82b7f61fdf8c4b09c92b58447f686e954b6eaf7f02d7c9e5304c8d52b4c09b6d323af +EBUILD theseus-2.0.6.ebuild 1449 SHA256 6a73f8b5cb38a26472f5b4588c9c3c507d13d86ec879b7db7c37c1be503d3f98 SHA512 35fce318510a70da251151061013e52dc0c16b0bdb8aed4ecd1dca2deb53a662290d4700a5df3bfa755c785e8b481cdd7f83a2263a3823823261044079e69a26 WHIRLPOOL 544a8d7f6b18d8da80f57c04a20d24a8734a45b9916e8f5fb330a5263416f79dd56413be851c12e584ebb14fed546c48cbda06016efbc593f59c96c2b67871cc +EBUILD theseus-3.0.0.ebuild 1503 SHA256 aeacc8a235a96451545179aa398d6501cfd03a5c60800b2f5cce4a46e9a4dc88 SHA512 cb2824c8e5fff646ffd6523cb47385143e366ad19e92685b411d4f3ac8827d16260da048e29666ce3aa7a328d3ee136ef309e5443e252dac1862f987bac74bda WHIRLPOOL 141f3375a419c25fe84c1200c78f9a10d7cefca0fccc78bc7e575d514802f6569315826cec3d028b9a3c0cf14712272b05ad05c53e228f554a2683c04f4ebe6f +EBUILD theseus-3.3.0.ebuild 1503 SHA256 aeacc8a235a96451545179aa398d6501cfd03a5c60800b2f5cce4a46e9a4dc88 SHA512 cb2824c8e5fff646ffd6523cb47385143e366ad19e92685b411d4f3ac8827d16260da048e29666ce3aa7a328d3ee136ef309e5443e252dac1862f987bac74bda WHIRLPOOL 141f3375a419c25fe84c1200c78f9a10d7cefca0fccc78bc7e575d514802f6569315826cec3d028b9a3c0cf14712272b05ad05c53e228f554a2683c04f4ebe6f +MISC ChangeLog 2676 SHA256 5de717cb694416f8de834b556fbf92c448a8f206a3ad1a04f879e3f696392efd SHA512 829d5fd143fd890f84cdc76477e5751b439f882cee5f777405d5c48cac44db1a2bbf0b244a68dc510ba55522a3a4de2794bf926b930c545c759ae6423735e580 WHIRLPOOL e0af631987b9e06bf56648f09348d5c8f7164a453858f34f0215b4e85509d2f2dd631f913def416358bfabb67eac6c70fe6ea0637756374bd409938ebaedd3d2 +MISC ChangeLog-2015 1688 SHA256 37b31fd290437d848279ffd703a98710a93c0f5e2df6d8821e619542cfcf93bd SHA512 776e93efc0052180316f4c234a13f29b498c83797c3c1ae5040861c3990494baa04be52881a952b2a8514068a9ccb9b993951074a6b0a2e11c9283b301d54a62 WHIRLPOOL 6ada67fe0de5ff0cb7cb8eb86fa01ab7ddc84cbd44212a39199191f459b7b7f596a6885acdfc0d55fdc8412b6b5175bfc9bc2cd607a32248e72482950b0501ed +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/theseus/metadata.xml b/sci-chemistry/theseus/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/theseus/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/theseus/theseus-2.0.6.ebuild b/sci-chemistry/theseus/theseus-2.0.6.ebuild new file mode 100644 index 000000000000..7c3f3783602c --- /dev/null +++ b/sci-chemistry/theseus/theseus-2.0.6.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit multilib toolchain-funcs + +DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures" +HOMEPAGE="http://www.theseus3d.org/" +SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RDEPEND=" + sci-libs/gsl + || ( + sci-biology/muscle + sci-biology/probcons + sci-biology/mafft + sci-biology/t-coffee + sci-biology/kalign + sci-biology/clustalw:2 + )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}"/${PN}_src/ + +src_prepare() { + cat >> make.inc <<- EOF + ARCH = $(tc-getAR) + ARCHFLAGS = -rvs + RANLIB = $(tc-getRANLIB) + LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir) + SYSLIBS = $(pkg-config --libs gsl) -lpthread + LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus + LIBDIR = -L./lib + INSTALLDIR = "${ED}"/usr/bin + OPT = + WARN = + CFLAGS = ${CFLAGS} \$(WARN) + CC = $(tc-getCC) + EOF + + sed \ + -e 's|theseus:|theseus: libs|g' \ + -e '/-o theseus/s:$(CC):$(CC) ${LDFLAGS}:g' \ + -i Makefile || die + + sed \ + -e 's:/usr/bin/sed:sed:g' \ + -e "s:/usr/local/bin/:/usr/bin/:g" \ + -e "s:/usr/bin/:${EPREFIX}/usr/bin/:g" \ + -i theseus_align || die +} + +src_install() { + dobin theseus theseus_align + dodoc theseus_man.pdf README AUTHORS + use examples && insinto /usr/share/${PN} && doins -r examples +} diff --git a/sci-chemistry/theseus/theseus-3.0.0.ebuild b/sci-chemistry/theseus/theseus-3.0.0.ebuild new file mode 100644 index 000000000000..9eebccc8bc96 --- /dev/null +++ b/sci-chemistry/theseus/theseus-3.0.0.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit multilib toolchain-funcs + +DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures" +HOMEPAGE="http://www.theseus3d.org/" +SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RDEPEND=" + sci-libs/gsl + || ( + sci-biology/muscle + sci-biology/probcons + sci-biology/mafft + sci-biology/t-coffee + sci-biology/kalign + sci-biology/clustalw:2 + )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}"/${PN}_src/ + +src_prepare() { + cat >> make.inc <<- EOF + ARCH = $(tc-getAR) + ARCHFLAGS = -rvs + RANLIB = $(tc-getRANLIB) + LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir) + SYSLIBS = $(pkg-config --libs gsl) -lpthread + LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus + LIBDIR = -L./lib + INSTALLDIR = "${ED}"/usr/bin + OPT = + WARN = + CFLAGS = ${CFLAGS} -std=c11 \$(WARN) + CC = $(tc-getCC) + EOF + + sed \ + -e 's|theseus:|theseus: libs|g' \ + -e '/-o theseus/s:$(CC):$(CC) ${LDFLAGS}:g' \ + -i Makefile || die + + sed \ + -e 's:/usr/bin/sed:sed:g' \ + -e "s:/usr/local/bin/:/usr/bin/:g" \ + -e "s:/usr/bin/:${EPREFIX}/usr/bin/:g" \ + -i theseus_align || die +} + +src_compile () { + emake ltheseus + default +} + +src_install() { + dobin theseus theseus_align + dodoc theseus_man.pdf README AUTHORS + use examples && insinto /usr/share/${PN} && doins -r examples +} diff --git a/sci-chemistry/theseus/theseus-3.3.0.ebuild b/sci-chemistry/theseus/theseus-3.3.0.ebuild new file mode 100644 index 000000000000..9eebccc8bc96 --- /dev/null +++ b/sci-chemistry/theseus/theseus-3.3.0.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit multilib toolchain-funcs + +DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures" +HOMEPAGE="http://www.theseus3d.org/" +SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RDEPEND=" + sci-libs/gsl + || ( + sci-biology/muscle + sci-biology/probcons + sci-biology/mafft + sci-biology/t-coffee + sci-biology/kalign + sci-biology/clustalw:2 + )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}"/${PN}_src/ + +src_prepare() { + cat >> make.inc <<- EOF + ARCH = $(tc-getAR) + ARCHFLAGS = -rvs + RANLIB = $(tc-getRANLIB) + LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir) + SYSLIBS = $(pkg-config --libs gsl) -lpthread + LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus + LIBDIR = -L./lib + INSTALLDIR = "${ED}"/usr/bin + OPT = + WARN = + CFLAGS = ${CFLAGS} -std=c11 \$(WARN) + CC = $(tc-getCC) + EOF + + sed \ + -e 's|theseus:|theseus: libs|g' \ + -e '/-o theseus/s:$(CC):$(CC) ${LDFLAGS}:g' \ + -i Makefile || die + + sed \ + -e 's:/usr/bin/sed:sed:g' \ + -e "s:/usr/local/bin/:/usr/bin/:g" \ + -e "s:/usr/bin/:${EPREFIX}/usr/bin/:g" \ + -i theseus_align || die +} + +src_compile () { + emake ltheseus + default +} + +src_install() { + dobin theseus theseus_align + dodoc theseus_man.pdf README AUTHORS + use examples && insinto /usr/share/${PN} && doins -r examples +} diff --git a/sci-chemistry/threeV/Manifest b/sci-chemistry/threeV/Manifest new file mode 100644 index 000000000000..57d0dc6f4d60 --- /dev/null +++ b/sci-chemistry/threeV/Manifest @@ -0,0 +1,7 @@ +AUX threeV-1.2-format-security.patch 7116 SHA256 601a566412b8204048e3846c3c4d7741382b816b25e46b05320040d4e9f515ba SHA512 9ed991640b297090a4b35a8d04f67da4eba21c0cf828a06120fd31a55ca809a3485da8e85db759311c1b136b37ae3214c5c1000cc8fb54491f59f454b22f87d3 WHIRLPOOL 79b7a560885499370010f68f9adf4c1821a81e2fb8ef1c1e489da7e3a97951006964bdb65e73c73b9d40dbcecb3a97d0e7a6277bea68a665bc10165cc09f11bb +AUX threeV-1.2-gentoo.patch 3085 SHA256 e88ad3a84709b6c948f27cf4e81c0850ba7417cda5c2d7cbc9ff86db6f184db8 SHA512 493fc39b2d3cf1325ea00ad572e8c4c62ae48f55a82fd5eb6a1f7e91900ecfdf6cb174ec43b2fb748d6708099ddb395af34045a4439f1dbc0c574169539344a0 WHIRLPOOL d51af86ea1288fcb1ce07b6f4e282498e1f0a34c02c46677a3a4bb010baa1432aea96823938feaf3643ac383988f0296cac371d587118ca0dcf1d5b1f6d4bc77 +DIST 3v-1.2.tgz 599194 SHA256 ae11ce61e6b7cac6aa07d91914b59507a04a1dbfbe624ed8356154cbabc6e8af SHA512 063747e46be1ab8af585909185b735edbbb760945f9d4d345d478a264e3d90c551d72f578239e7eff7768482d18b34d2b00831f87e109ec87cb36b0fd4e6a757 WHIRLPOOL ca497066f3f48df53432ad6cc358a238e5ed360f40446d977361fd8615ba14562a249c098e6c241924de819b3b27e44c4d69bbdb8abfebc46496cb0f7d3d36a9 +EBUILD threeV-1.2-r1.ebuild 745 SHA256 80e3cb30ea99a5b813e57a4e14c60f6ecf31f741155be5ae3cdd1df4f87f654f SHA512 eec0425c83705264670ccba3d8b839717bf1135114fe7baa637d638fe3214c6bc2ec9e7331b9bfc11e6e1bf530ed6ea73164c400c4344d9ca65b0b244338ee02 WHIRLPOOL dff6a9db7b52a478fe2457718da063be52033ec6caf5627d23a0c028b1df03cfa6b3b35faa94bb0fb24db3246d64174103537eb4abb80aa11a129f9b7854c12c +MISC ChangeLog 2590 SHA256 08eb2a41838f96a8b65db863d647856de5bf4a861986d95257fd4305ac6b0bf4 SHA512 0a529c12e18e8bf0a26243de29f6a570d2c2c67839b7d59bdfa0ca07f78fbb4b38fa5eee22471221c861dd067fc9d39c2baa84fbb46fe7e02e89f12014c0af83 WHIRLPOOL 4cabaaa4adecc16b0838e93c6c90f17452f5810d9ca5c7fea546b8b05af61404c97aba9cc651fe91131e6cdd28ababdfa55065305f11c7472d6361c28efec658 +MISC ChangeLog-2015 461 SHA256 e8749e891c116adbd3fe69cc7afc4ec906605880b446b2407e0c803606c13cb7 SHA512 7328092b693879e324b62ffc0412275efdcd7ecbff1fdc81d7d9590697261ce56e3e4034ae73e108c8f0de76e905f8a1f46c92ca1162679632a72d651ef8290c WHIRLPOOL 3a2097b716be35f1b7a96336a47357c1d6d8196a25904b8bb4a93f85e55b1c1a5909d6c4307ca4adecba0c9a5dc641b65fce55fecc7af5fd801516d87396f966 +MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d diff --git a/sci-chemistry/threeV/files/threeV-1.2-format-security.patch b/sci-chemistry/threeV/files/threeV-1.2-format-security.patch new file mode 100644 index 000000000000..b693559900ad --- /dev/null +++ b/sci-chemistry/threeV/files/threeV-1.2-format-security.patch @@ -0,0 +1,198 @@ + cavities.cpp | 8 ++++---- + channel.cpp | 10 +++++----- + fsv_calc.cpp | 8 ++++---- + solvent.cpp | 8 ++++---- + tunnel.cpp | 8 ++++---- + vdw.cpp | 8 ++++---- + volume.cpp | 8 ++++---- + 7 files changed, 29 insertions(+), 29 deletions(-) + +diff --git a/cavities.cpp b/cavities.cpp +index 418a1a7..96b6a15 100644 +--- a/cavities.cpp ++++ b/cavities.cpp +@@ -35,7 +35,7 @@ int main(int argc, char *argv[]) { + + while(argc > 1 && argv[1][0] == '-') { + if(argv[1][1] == 'i') { +- sprintf(file,&argv[2][0]); ++ sprintf(file,"%s",&argv[2][0]); + } else if(argv[1][1] == 'g') { + GRID = atof(&argv[2][0]); + } else if(argv[1][1] == 's') { +@@ -45,11 +45,11 @@ int main(int argc, char *argv[]) { + } else if(argv[1][1] == 't') { + trim_rad = atof(&argv[2][0]); + } else if(argv[1][1] == 'e') { +- sprintf(ezdfile,&argv[2][0]); ++ sprintf(ezdfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'm') { +- sprintf(mrcfile,&argv[2][0]); ++ sprintf(mrcfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'o') { +- sprintf(pdbfile,&argv[2][0]); ++ sprintf(pdbfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'h') { + cerr << "./Cavities.exe -i <file> -g <grid spacing> -s <shell radius> " << endl + << "\t-p <probe radius> -t <trim_probe_rad> " << endl +diff --git a/channel.cpp b/channel.cpp +index c5acd20..9040631 100644 +--- a/channel.cpp ++++ b/channel.cpp +@@ -35,7 +35,7 @@ int main(int argc, char *argv[]) { + + while(argc > 1 && argv[1][0] == '-') { + if(argv[1][1] == 'i') { +- sprintf(file,&argv[2][0]); ++ sprintf(file,"%s",&argv[2][0]); + } else if(argv[1][1] == 'b') { + BIGPROBE = atof(&argv[2][0]); + } else if(argv[1][1] == 's') { +@@ -49,13 +49,13 @@ int main(int argc, char *argv[]) { + } else if(argv[1][1] == 'z') { + z = atof(&argv[2][0]); + } else if(argv[1][1] == 'i') { +- sprintf(file,&argv[2][0]); ++ sprintf(file,"%s",&argv[2][0]); + } else if(argv[1][1] == 'o') { +- sprintf(pdbfile,&argv[2][0]); ++ sprintf(pdbfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'e') { +- sprintf(ezdfile,&argv[2][0]); ++ sprintf(ezdfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'm') { +- sprintf(mrcfile,&argv[2][0]); ++ sprintf(mrcfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'g') { + GRID = atof(&argv[2][0]); + } else if(argv[1][1] == 'h') { +diff --git a/fsv_calc.cpp b/fsv_calc.cpp +index 9f81347..ef765b8 100644 +--- a/fsv_calc.cpp ++++ b/fsv_calc.cpp +@@ -34,7 +34,7 @@ int main(int argc, char *argv[]) { + + while(argc > 1 && argv[1][0] == '-') { + if(argv[1][1] == 'i') { +- sprintf(file,&argv[2][0]); ++ sprintf(file,"%s",&argv[2][0]); + } else if(argv[1][1] == 's') { + SMPROBE = atof(&argv[2][0]); + } else if(argv[1][1] == 'b') { +@@ -44,11 +44,11 @@ int main(int argc, char *argv[]) { + } else if(argv[1][1] == 'g') { + GRID = atof(&argv[2][0]); + } else if(argv[1][1] == 'o') { +- sprintf(pdbfile,&argv[2][0]); ++ sprintf(pdbfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'e') { +- sprintf(ezdfile,&argv[2][0]); ++ sprintf(ezdfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'm') { +- sprintf(mrcfile,&argv[2][0]); ++ sprintf(mrcfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'h') { + cerr << "./FsvCalc.exe -i <file> -b <big_probe> -s <small_probe> " << endl + << "\t-t <trim probe> -g <gridspace> " << endl +diff --git a/solvent.cpp b/solvent.cpp +index d857696..bc9d67f 100644 +--- a/solvent.cpp ++++ b/solvent.cpp +@@ -34,7 +34,7 @@ int main(int argc, char *argv[]) { + + while(argc > 1 && argv[1][0] == '-') { + if(argv[1][1] == 'i') { +- sprintf(file,&argv[2][0]); ++ sprintf(file,"%s",&argv[2][0]); + } else if(argv[1][1] == 's') { + SMPROBE = atof(&argv[2][0]); + } else if(argv[1][1] == 'b') { +@@ -42,11 +42,11 @@ int main(int argc, char *argv[]) { + } else if(argv[1][1] == 't') { + TRIMPROBE = atof(&argv[2][0]); + } else if(argv[1][1] == 'e') { +- sprintf(ezdfile,&argv[2][0]); ++ sprintf(ezdfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'm') { +- sprintf(mrcfile,&argv[2][0]); ++ sprintf(mrcfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'o') { +- sprintf(pdbfile,&argv[2][0]); ++ sprintf(pdbfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'g') { + GRID = atof(&argv[2][0]); + } else if(argv[1][1] == 'h') { +diff --git a/tunnel.cpp b/tunnel.cpp +index 0094d05..7472aaa 100644 +--- a/tunnel.cpp ++++ b/tunnel.cpp +@@ -40,7 +40,7 @@ int main(int argc, char *argv[]) { + + while(argc > 1 && argv[1][0] == '-') { + if(argv[1][1] == 'i') { +- sprintf(file,&argv[2][0]); ++ sprintf(file,"%s",&argv[2][0]); + } else if(argv[1][1] == 'g') { + GRID = atof(&argv[2][0]); + } else if(argv[1][1] == 's') { +@@ -50,11 +50,11 @@ int main(int argc, char *argv[]) { + } else if(argv[1][1] == 't') { + trim_prb = atof(&argv[2][0]); + } else if(argv[1][1] == 'e') { +- sprintf(ezdfile,&argv[2][0]); ++ sprintf(ezdfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'm') { +- sprintf(mrcfile,&argv[2][0]); ++ sprintf(mrcfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'o') { +- sprintf(pdbfile,&argv[2][0]); ++ sprintf(pdbfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'h') { + cerr << "./Tunnel.exe -i <file> -g <grid spacing> -p <tunnel probe radius>" << endl + << "\t-e <EZD outfile> -o <PDB outfile> -m <MRC outfile>" << endl +diff --git a/vdw.cpp b/vdw.cpp +index 4df73f5..0e26edc 100644 +--- a/vdw.cpp ++++ b/vdw.cpp +@@ -32,13 +32,13 @@ int main(int argc, char *argv[]) { + + while(argc > 1 && argv[1][0] == '-') { + if(argv[1][1] == 'i') { +- sprintf(file,&argv[2][0]); ++ sprintf(file,"%s",&argv[2][0]); + } else if(argv[1][1] == 'o') { +- sprintf(pdbfile,&argv[2][0]); ++ sprintf(pdbfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'e') { +- sprintf(ezdfile,&argv[2][0]); ++ sprintf(ezdfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'm') { +- sprintf(mrcfile,&argv[2][0]); ++ sprintf(mrcfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'g') { + GRID = atof(&argv[2][0]); + } else if(argv[1][1] == 'h') { +diff --git a/volume.cpp b/volume.cpp +index a2ca9ad..c304b94 100644 +--- a/volume.cpp ++++ b/volume.cpp +@@ -32,15 +32,15 @@ int main(int argc, char *argv[]) { + + while(argc > 1 && argv[1][0] == '-') { + if(argv[1][1] == 'i') { +- sprintf(file,&argv[2][0]); ++ sprintf(file,"%s",&argv[2][0]); + } else if(argv[1][1] == 'p') { + PROBE = atof(&argv[2][0]); + } else if(argv[1][1] == 'o') { +- sprintf(pdbfile,&argv[2][0]); ++ sprintf(pdbfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'e') { +- sprintf(ezdfile,&argv[2][0]); ++ sprintf(ezdfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'm') { +- sprintf(mrcfile,&argv[2][0]); ++ sprintf(mrcfile,"%s",&argv[2][0]); + } else if(argv[1][1] == 'g') { + GRID = atof(&argv[2][0]); + } else if(argv[1][1] == 'h') { diff --git a/sci-chemistry/threeV/files/threeV-1.2-gentoo.patch b/sci-chemistry/threeV/files/threeV-1.2-gentoo.patch new file mode 100644 index 000000000000..556e928d5818 --- /dev/null +++ b/sci-chemistry/threeV/files/threeV-1.2-gentoo.patch @@ -0,0 +1,107 @@ +diff --git a/Makefile b/Makefile +index a58462c..616f51a 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,7 +1,7 @@ +-CC = g++ +-EXT=$(shell ./cpuflags.pl --opt ) +-FLAGS = -Wall $(EXT) +-#FLAGS = -O3 -Wall -ffast-math ++CXX ?= g++ ++#EXT=$(shell ./cpuCXXFLAGS.pl --opt ) ++#CXXFLAGS = -Wall $(EXT) ++#CXXFLAGS = -O3 -Wall -ffast-math + OBJS = utils-main.o utils-output.o utils-mrc.o + + all: cav chan fsv sol tun vdw vol +@@ -17,54 +17,65 @@ volume: vol + objects: utils-main.o utils-output.o utils-mrc.o + + cav: objects cavities.cpp +- $(CC) $(FLAGS) -o Cavities.exe $(OBJS) cavities.cpp +- chmod 777 Cavities.exe +- mv Cavities.exe ../bin ++ $(CXX) $(CXXFLAGS) -c -o cavities.o cavities.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o Cavities $(OBJS) cavities.o ++ chmod 755 Cavities ++ mv Cavities ../bin + + chan: objects channel.cpp +- $(CC) $(FLAGS) -o Channel.exe $(OBJS) channel.cpp +- chmod 777 Channel.exe +- mv Channel.exe ../bin ++ $(CXX) $(CXXFLAGS) -c -o channel.o channel.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o Channel $(OBJS) channel.o ++ chmod 755 Channel ++ mv Channel ../bin + + fsv: objects fsv_calc.cpp +- $(CC) $(FLAGS) -o FsvCalc.exe $(OBJS) fsv_calc.cpp +- chmod 777 FsvCalc.exe +- mv FsvCalc.exe ../bin ++ $(CXX) $(CXXFLAGS) -c -o fsv_calc.o fsv_calc.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o FsvCalc $(OBJS) fsv_calc.o ++ chmod 755 FsvCalc ++ mv FsvCalc ../bin + + sol: objects solvent.cpp +- $(CC) $(FLAGS) -o Solvent.exe $(OBJS) solvent.cpp +- chmod 777 Solvent.exe +- mv Solvent.exe ../bin ++ $(CXX) $(CXXFLAGS) -c -o solvent.o solvent.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o Solvent $(OBJS) solvent.o ++ chmod 755 Solvent ++ mv Solvent ../bin + + tun: objects tunnel.cpp +- $(CC) $(FLAGS) -o Tunnel.exe $(OBJS) tunnel.cpp +- chmod 777 Tunnel.exe +- mv Tunnel.exe ../bin ++ $(CXX) $(CXXFLAGS) -c -o tunnel.o tunnel.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o Tunnel $(OBJS) tunnel.o ++ chmod 755 Tunnel ++ mv Tunnel ../bin + + vdw: objects vdw.cpp +- $(CC) $(FLAGS) -o VDW.exe $(OBJS) vdw.cpp +- chmod 777 VDW.exe +- mv VDW.exe ../bin ++ $(CXX) $(CXXFLAGS) -c -o vdw.o vdw.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o VDW $(OBJS) vdw.o ++ chmod 755 VDW ++ mv VDW ../bin + + vol: objects volume.cpp +- $(CC) $(FLAGS) -o Volume.exe $(OBJS) volume.cpp +- chmod 777 Volume.exe +- mv Volume.exe ../bin ++ $(CXX) $(CXXFLAGS) -c -o volume.o volume.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o Volume $(OBJS) volume.o ++ chmod 755 Volume ++ mv Volume ../bin + + utils-main.o: utils-main.cpp +- $(CC) $(FLAGS) -c -o utils-main.o utils-main.cpp ++ $(CXX) $(CXXFLAGS) -c -o utils-main.o utils-main.cpp + + utils-output.o: utils-main.o utils-output.cpp +- $(CC) $(FLAGS) -c -o utils-output.o utils-output.cpp ++ $(CXX) $(CXXFLAGS) -c -o utils-output.o utils-output.cpp + + utils-mrc.o: utils-mrc.cpp +- $(CC) $(FLAGS) -c -o utils-mrc.o utils-mrc.cpp ++ $(CXX) $(CXXFLAGS) -c -o utils-mrc.o utils-mrc.cpp ++ ++install: ++ install -d $(DESTDIR)/usr/bin ++ install ../bin/* $(DESTDIR)/usr/bin/ + + clean: + rm -fv *.o *~ + + distclean: +- rm -fv *.o ../bin/*.exe *~ ++ rm -fv *.o ../bin/* *~ + + none: + echo "Please type make xxx, where xxx = cav, cha, fsv, sol, tun, vdw, or vol" diff --git a/sci-chemistry/threeV/metadata.xml b/sci-chemistry/threeV/metadata.xml new file mode 100644 index 000000000000..da36ecbfcd6a --- /dev/null +++ b/sci-chemistry/threeV/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/threeV/threeV-1.2-r1.ebuild b/sci-chemistry/threeV/threeV-1.2-r1.ebuild new file mode 100644 index 000000000000..1d4a1e1f3466 --- /dev/null +++ b/sci-chemistry/threeV/threeV-1.2-r1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="3V: Voss Volume Voxelator" +HOMEPAGE="http://geometry.molmovdb.org/3v/" +SRC_URI="http://geometry.molmovdb.org/3v/3v-${PV}.tgz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +PDEPEND="sci-chemistry/msms-bin" +# sci-chemistry/usf-rave" + +S="${WORKDIR}/3v-${PV}/src" + +PATCHES=( + "${FILESDIR}"/${P}-gentoo.patch + "${FILESDIR}"/${P}-format-security.patch +) + +src_prepare() { + default + tc-export CXX + emake distclean + + export MAKEOPTS+=" V=1" +} + +src_install() { + emake DESTDIR="${ED}" install + + cd .. || die + dodoc AUTHORS ChangeLog QUICKSTART README TODO VERSION +} diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest new file mode 100644 index 000000000000..a6f2060da5e8 --- /dev/null +++ b/sci-chemistry/tinker/Manifest @@ -0,0 +1,7 @@ +AUX 7.1.2-openmp.patch 400 SHA256 67cf53b3801814ab39b4bdbb40db9f500cbc4740e2b7db94a945829ef1961cec SHA512 1af405acc753d602501589725374e88964a55e5954cb77eb1f3c0156fa73936552be9ce5fc4f36c855dfbd4043f12749dfc95aa9b946d80d0e5e6e8100e84ad4 WHIRLPOOL 6f20e980f63f79d3443f46d5608ad241723b73026cc3ec85437cb741a1c2b7b3fe74de428097583f3f34ac05d85e14edfe0490a04d48cccfd64d4ded2850dfb2 +AUX tinker-7.1.2-build.patch 360 SHA256 26fba46b9a72407cfd194cf74d5044b06b41164ae039b0b97f29b1840be4f765 SHA512 b20a4d8e75a781cd9c769dd0b5ae4e1039ea54d7ac61fc3605543b796afa2f4f3957be439f338fd47090a17e9153a466c2f76b364f4d9b7a2705b746f6cefbd3 WHIRLPOOL e102e8fafacc51160e191535355ae6fc7216c76b21234f6878c252eeebcb306bac8678413da26b44ff20a32b7652eda189eb66eb44efd577eb007e8685f8222f +DIST tinker-7.1.2.tar.gz 28468683 SHA256 fdee18915cff9044fd083bb2271083c221db6d05de2cb98fc111b136e23e6899 SHA512 4524259754b0f11d7e2e8997ebd85eae7d28f8dbb1edb2d9818aa0a96640de0049aa4937236694f1a11743dee187d612f775b233a73cc96c2708d620457a7dc2 WHIRLPOOL f3e29eaf67d25ae6d4f3c4e3546798e66bd626929fddd45b9d1ff9f2143cd57dcc5079226f3ceaa142f4c6a168c4a150a51be1336a5ca13384338795ef3a6d46 +EBUILD tinker-7.1.2.ebuild 2275 SHA256 ddb245287de264e81e8c1ea7b0ef3749aaf9d218f49b6d165d3b1ecc41437c22 SHA512 d617f08cf03f35e78f0561214dcc0c7c4af0fedce69214a302ca8dee2c2a3577ba002671f4cce8a86cb3ca76084ce99eff6a2e90ecfc940c7aa56fd588edda2c WHIRLPOOL 6875ec865fd927d27c9fd5644da5b6a739f45e275f7e1a424a470e8610d5aa45e28ef03b5c200c6419e694928fc5841980c62c770cfe10c366a95d4ac9b1cf85 +MISC ChangeLog 2546 SHA256 40f1e60e2f001e8fc7c6cdb4c5effb89840a850c45347fe6e9e9fd74905ccd61 SHA512 fc9b14a4abb63367ae77af1c6eb7f49ac4169cb6df6250d5daa7b34559361860a6fda404976eacec50d0149c4b4d48eb59c45addf58e5133bcf9fb9be87e1588 WHIRLPOOL 107d50ddc5826ce1e19e9c9d47a1a7356b9aed04bcce26e95d73437215e5074a914320af789333ec4f1cfa6415277519d9191822b210265d353021e4bec125b7 +MISC ChangeLog-2015 5325 SHA256 628dfafc7626fc1bb8e814c00f4f80e559a5c14a539709499e196e848182c4cd SHA512 a8f802aca8a0e694569ddf5174d7a60c840435d11f745e705d9e381d93ebfdf636c6b790b9f02638b51101e28e688532f09566a6384ec83f7cc5d3af6bf34c86 WHIRLPOOL 81e4ec3bd16032f86598883c50e4a8e93123ef8f8394f8665d2268afbe154fd8b10178eb733188d11078d8f630662db048be7e105e953cd4b30ae90d59be9d38 +MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d diff --git a/sci-chemistry/tinker/files/7.1.2-openmp.patch b/sci-chemistry/tinker/files/7.1.2-openmp.patch new file mode 100644 index 000000000000..f3e8e2932b4a --- /dev/null +++ b/sci-chemistry/tinker/files/7.1.2-openmp.patch @@ -0,0 +1,15 @@ +diff --git a/source/initial.f b/source/initial.f +index 835f228..4099c74 100644 +--- a/source/initial.f ++++ b/source/initial.f +@@ -73,8 +73,8 @@ c + c + c Intel compiler extensions to OpenMP standard + c +-!$ call kmp_set_stacksize_s (2**28) +-!$ call kmp_set_blocktime (0) ++! call kmp_set_stacksize_s (2**28) ++! call kmp_set_blocktime (0) + c + c values of machine precision constants + c diff --git a/sci-chemistry/tinker/files/tinker-7.1.2-build.patch b/sci-chemistry/tinker/files/tinker-7.1.2-build.patch new file mode 100644 index 000000000000..d6ef484b19a4 --- /dev/null +++ b/sci-chemistry/tinker/files/tinker-7.1.2-build.patch @@ -0,0 +1,17 @@ + make/Makefile | 3 +-- + 1 file changed, 1 insertion(+), 2 deletions(-) + +diff --git a/make/Makefile b/make/Makefile +index 61d5037..9be384a 100644 +--- a/make/Makefile ++++ b/make/Makefile +@@ -719,8 +719,7 @@ EXEFILES = alchemy.x \ + %.x: %.o libtinker.a + ${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@ + +-all: +- ${EXEFILES} ++all: ${EXEFILES} + + install: + rename diff --git a/sci-chemistry/tinker/metadata.xml b/sci-chemistry/tinker/metadata.xml new file mode 100644 index 000000000000..da36ecbfcd6a --- /dev/null +++ b/sci-chemistry/tinker/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/tinker/tinker-7.1.2.ebuild b/sci-chemistry/tinker/tinker-7.1.2.ebuild new file mode 100644 index 000000000000..46a8d2feb0f2 --- /dev/null +++ b/sci-chemistry/tinker/tinker-7.1.2.ebuild @@ -0,0 +1,105 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic fortran-2 java-pkg-opt-2 toolchain-funcs + +DESCRIPTION="Molecular modeling package that includes force fields, such as AMBER and CHARMM" +HOMEPAGE="http://dasher.wustl.edu/tinker/" +SRC_URI="http://dasher.wustl.edu/${PN}/downloads/${P}.tar.gz" + +SLOT="0" +LICENSE="Tinker" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +DEPEND=" + >=virtual/jdk-1.6" + +RDEPEND=" + >=sci-libs/fftw-3.2.2-r1[fortran,threads] + dev-libs/maloc + !sys-apps/bar + !dev-util/diffuse + >=virtual/jre-1.6" + +RESTRICT="mirror" + +S="${WORKDIR}"/${PN}/source + +pkg_setup() { + fortran-2_pkg_setup + java-pkg-opt-2_pkg_setup + tc-has-openmp || die "Please use an openmp capable compiler like gcc[openmp]" +} + +src_prepare() { + sed 's:strip:true:g' -i ../make/Makefile + [[ $(tc-getFC) =~ "ifort" ]] || epatch "${FILESDIR}"/${PV}-openmp.patch + cd .. && epatch "${FILESDIR}"/${P}-build.patch +} + +src_compile() { + local javalib= + for i in $(java-config -g LDPATH | sed 's|:| |g'); do + [[ -f ${i}/libjvm.so ]] && javalib=${i} + done + + # use dummy routines in pmpb.f instead of apbs calls + rm pmpb.c || die + + if [[ $(tc-getFC) =~ "gfortran" ]]; then + append-flags -fopenmp + _omplib="-lgomp" + else + append-flags -openmp + _omplib="-liomp5" + fi + + _fftwlib="$($(tc-getPKG_CONFIG) --libs fftw3 fftw3_threads)" + + emake \ + -f ../make/Makefile \ + F77="$(tc-getFC)" \ + CC="$(tc-getCC) -c" \ + F77FLAGS=-c \ + OPTFLAGS="${FFLAGS}" \ + LINKFLAGS="${LDFLAGS} -Wl,-rpath ${javalib}" \ + INCLUDEDIR="$(java-pkg_get-jni-cflags) -I${EPREFIX}/usr/include" \ + LIBS="-lmaloc -L${javalib} -ljvm ${_omplib} ${_fftwlib}" \ + all + + mkdir "${S}"/../bin || die + + emake \ + -f ../make/Makefile \ + BINDIR="${S}"/../bin \ + rename +} + +src_test() { + cd "${WORKDIR}"/${PN}/test/ + for test in *.run; do + einfo "Testing ${test} ..." + bash ${test} || die + done +} + +src_install() { + dobin "${WORKDIR}"/${PN}/perl/mdavg "${WORKDIR}"/${PN}/bin/* + + insinto /usr/share/${PN}/ + doins -r "${WORKDIR}"/${PN}/params + + dodoc \ + "${WORKDIR}"/${PN}/doc/{*.txt,*.pdf,0README} + + if use examples; then + insinto /usr/share/${P} + doins -r "${WORKDIR}"/${PN}/example + + doins -r "${WORKDIR}"/${PN}/test + fi + +} diff --git a/sci-chemistry/tm-align/Manifest b/sci-chemistry/tm-align/Manifest new file mode 100644 index 000000000000..3391dc09b19d --- /dev/null +++ b/sci-chemistry/tm-align/Manifest @@ -0,0 +1,8 @@ +AUX CMakeLists.txt 182 SHA256 e6543e2fba46dc09d1892106b1d9c154485ee269d2b88c16a1973605fae44b53 SHA512 1e77edbfb2184e11c09fc2133eb40bd9d4b2fb04a30139134939482f4e817ebfa5c316e8d75a6fd5aa866ef1f6f56d65df924dc41cfb698330943e0bc433948d WHIRLPOOL 370a6b0e2ba20b7c7316aaba34b6dd6962673014fa7d2aee8ae04630b98abb24f5302eca80ea4c92d84fea149c98003d4b5c1ac44266a488cc937f06f51f6192 +DIST TMtools20140601.tar.gz 934391 SHA256 5032f7ab1824c8b2191b4a3667e1405feb6ccf7c900f57632aa506fff8ec1bf5 SHA512 99b90425ff051c836e19225601ddfb1576bec9c8f233aafeba96075f924a3c0892b5b1cfef36254ff5ef468a6dbf64f7fcc9a3ce24a0d869b3c1eb87c0149765 WHIRLPOOL 5ba7d9cb71e3055dff62851c68e127314b9ca70c4bbc39aeba35e5a4b02dc0cffeacb52c6369c90875d8062603c830acf604cfc339bdecfeb3dd6c10015e20de +DIST TMtools20150914.tar.gz 982948 SHA256 de318e77ac5d7b9bf095bdc1c0d03d5536d6d7099ec2b6a2c201136da9274da4 SHA512 5fda29f6437ac9b0216a037496a01502de07e5a36736815833cb09217158a959370e750b75c55a54a49c733e4bd28be53b2dcbb25d71e2897273a4280ed3b530 WHIRLPOOL d366aa0d62d11b4af6137f87168c6156257c9e91c76c165ad256115016e571c94dce4235f015b5c0adecc4a8104ea432f53de2bd135332596235c56b9830b19f +EBUILD tm-align-20140601.ebuild 694 SHA256 0f5e5633cba4661a3d5a8c69530431e9733e9d014fb2ec3531c431c50dade863 SHA512 4eb692a19807887695a24df808954cce7a22b814e20f1a9b2f613ca1a3f1dbcbfe6985b14199d7bd79336e106c3080c2a0b78a09ee98b054775497f582fb1742 WHIRLPOOL d74b1bceb95630d514c1a26f6f80917e08362c585f947c7bf4bc116bb97bbee9c1759d29cb4673048ae85b90b6d2b7ac04ac21e2ea450e3211079ef5ff3a3b7b +EBUILD tm-align-20150914.ebuild 698 SHA256 b6279a5af8cf62d806a94efe8e2e61536046bb79a32a4dcf45500d7cd1437b41 SHA512 df375fa14b80cee3bb2ad5c6228463a1913fc0e3996f8bbf0e06ebfdbb132d7b2cf7f07a0a5549a31b1d140cbc6602f9cd16a621dc941076596cd96e4dce9b62 WHIRLPOOL 15f6c5f2572deced977ee97a3059520f622e54ccdb90fd4045d20223eab36382ff519b4dbf34bf287f0e32b6fb05de995a25aac7baaeba0a50b2629867d89cab +MISC ChangeLog 2812 SHA256 43e90762228184b9221b087a4f7d4670b45103a99f3db780556d8c0702d28ef8 SHA512 1130102744919d132129fbc2ff703b5c48c97b260408a87e9b66eb73bbbe8c755d8cdae44fb38184c2c441ca5e78ebcd20bed351da7863c89c63a1e2bc7e1415 WHIRLPOOL 538efd41ed348454ad12f0d7ca96afe60a8248257957bb9247346edceb20b7c52a0c431df2ad78e303b8287d365d63725d4f0e39c2a797d4d19488c20aca4f9b +MISC ChangeLog-2015 2389 SHA256 f157cdec36f5cba4376118b523b8e33fda88ccaa37996d28bc16575d03dd556d SHA512 05b4f47350faa98113ab210b56cd95d18c0f4bc08f64b1c3536f48e992687a0e44f36532be1c1d8e2d16185c13b6785a6728e7976b81fd623ac46a6503e39a57 WHIRLPOOL e0d90cf549cfecd1fb4c9af270ad5b4a73b95d10086044414b58114fca3bcee5676925eaa8b911158e539522dd157517e3d17374a9ebafaff40affc4543f206f +MISC metadata.xml 1294 SHA256 417eefaac27cd5cc6361380ab3f6c337c73183a640350bcff551f4a9d0a32a5d SHA512 e1b90b61682c3c1099c3b2d5d5fad166e408b14aca67e49521f470b2df1c746aa4c1eeae06f4f67fe6ccf8ded94c5fbe7a194a441fae8fab450f69acdcb49663 WHIRLPOOL 93ae5b38da45b883b46209cfc5f9be7103c3517c1ef76920856d72f312028c40ba503bed3c60a1c34a90809eb91467adfe5968428aa59cffe85f88f32959b6cb diff --git a/sci-chemistry/tm-align/files/CMakeLists.txt b/sci-chemistry/tm-align/files/CMakeLists.txt new file mode 100644 index 000000000000..506ef136309e --- /dev/null +++ b/sci-chemistry/tm-align/files/CMakeLists.txt @@ -0,0 +1,6 @@ +cmake_minimum_required (VERSION 2.6) +project (TMTools Fortran) +add_executable(TMalign TMalign.f) +add_executable(TMscore TMscore.f) + +install (TARGETS TMalign TMscore DESTINATION bin) diff --git a/sci-chemistry/tm-align/metadata.xml b/sci-chemistry/tm-align/metadata.xml new file mode 100644 index 000000000000..f53ebfe8d765 --- /dev/null +++ b/sci-chemistry/tm-align/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +TM-align is a computer algorithm for protein structure alignment using dynamic +programming and TM-score rotation matrix. An optimal alignment between two +proteins, as well as the TM-score, will be reported for each comparison. The +value of TM-score lies in (0,1]. In general, a comparison of TM-score smaller +0.2 indicates that there is no similarity between two structures; a TM-score +greater 0.5 means the structures share the same fold. + +What is the difference between TM-score and TM-align? The TM-score program +is to compare two models based on their given and known residue equivalency. +It is usually NOT applied to compare two proteins of different sequences. The +TM-align is a structural alignment program for comparing two proteins whose +sequences can be different. The TM-align will first find the best equivalent +residues of two proteins based on the structure similarity and then output a +TM-score. The TM-score values in both programs have the same definition. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/tm-align/tm-align-20140601.ebuild b/sci-chemistry/tm-align/tm-align-20140601.ebuild new file mode 100644 index 000000000000..9159714e0193 --- /dev/null +++ b/sci-chemistry/tm-align/tm-align-20140601.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils flag-o-matic fortran-2 + +DESCRIPTION="Quick & Accurate Structural Alignment" +HOMEPAGE="http://zhanglab.ccmb.med.umich.edu/TM-align/" +SRC_URI="http://zhanglab.ccmb.med.umich.edu/TM-align/TMtools${PV}.tar.gz" + +LICENSE="tm-align" +SLOT="0" +KEYWORDS="amd64 ppc ppc64 x86 ~amd64-linux ~x86-linux" +IUSE="static custom-cflags" + +S="${WORKDIR}" + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + use static && append-fflags -static && append-ldflags -static + # recommended by upstream + use custom-cflags || replace-flags -O* -O3 && append-fflags -ffast-math +} diff --git a/sci-chemistry/tm-align/tm-align-20150914.ebuild b/sci-chemistry/tm-align/tm-align-20150914.ebuild new file mode 100644 index 000000000000..4d36b45a8cad --- /dev/null +++ b/sci-chemistry/tm-align/tm-align-20150914.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils flag-o-matic fortran-2 + +DESCRIPTION="Quick & Accurate Structural Alignment" +HOMEPAGE="http://zhanglab.ccmb.med.umich.edu/TM-align/" +SRC_URI="http://zhanglab.ccmb.med.umich.edu/TM-align/TMtools${PV}.tar.gz" + +LICENSE="tm-align" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="static custom-cflags" + +S="${WORKDIR}" + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt . || die + use static && append-fflags -static && append-ldflags -static + # recommended by upstream + use custom-cflags || replace-flags -O* -O3 && append-fflags -ffast-math +} diff --git a/sci-chemistry/viewmol/Manifest b/sci-chemistry/viewmol/Manifest new file mode 100644 index 000000000000..732b77c48906 --- /dev/null +++ b/sci-chemistry/viewmol/Manifest @@ -0,0 +1,7 @@ +AUX 2.4.1-change-default-paths.patch 2745 SHA256 a351262fc6c90eb50dd603ee8447eae756e4014b184d3603d540e09bb77cc2ac SHA512 9dda6e39f43706f9868eb02402137573d58e90b14940ad5d10ede6088e49d2ebd8a114ffda3cf4a69bee5874cc0a16b83bb4ea86281203765c5d861cb8dac6dd WHIRLPOOL d500116a4e8e0880470f35097e604f957e4ba918f7279bb4078d5054d338db00f52bedac4cee1cd369d6b446ceefdbc49c399416bf34560eaec0ed36a1c98783 +AUX 2.4.1-remove-icc-check.patch 1020 SHA256 123063ddb68f905580e37a0a83060150cc359499d5b17418bf9b6e5a53d95ea1 SHA512 ea2a1a58730561fcf2bc05a0f23dc2108cf2fd97d228a7a6305d3323abda5ce3510793dbebf2253cef9e6d60326889079bc6a9639228b1b2bfd9d9a3b8c03ebb WHIRLPOOL 9c360865c816bbb61b581729ead42d0c90e31428412f2911c8f87e3ee1af43cab70b5e21f44a519f2c791c909c6d4550d07c17110dc4118629947b6b33612e71 +DIST viewmol-2.4.1.src.tgz 2229379 SHA256 dfed3eed6441d89c4bf2be1c13cbe263341c8880edf1742d446fc0f8f4a99e19 SHA512 42701d570d97e77b84597950a9068dfdf48faf4e551957383c8eea38f082c1ad136c17b7cbd3903673478506116d6fc08d1288842e74d6a9776526c685083584 WHIRLPOOL 0e8703cb763d15543de54b626a3be072d3ca36da04b3728e2d19d11436282ed4f7947017bf03016da3ba3ce3cacbdb7cfa2bcf68dbdfea81040403e8dde90d93 +EBUILD viewmol-2.4.1-r3.ebuild 2244 SHA256 22241c85ce536357c956c5981072098f526dcfad9d5ac3018e82cfed44e24566 SHA512 883277f1919a18c6ef5c0086a7d6e71f2555e8fce2b51c38133ad654e693fa73c0507a81dbb5487f7c921196638da7f9a677fd401ed74c2495aa85f2475c603f WHIRLPOOL 6c4683bdb08397ed22711a8caa1716cade92e0295ab1e9e675d608a90c25380e67002a0be52466c048a7db9ab858ffce6081400c09c0b3094f874b73dcb7c751 +MISC ChangeLog 2670 SHA256 31a74d4c3ebc9da90788bbafece6e83649aabd25abb049abce2a33f3a70c1371 SHA512 9f84f35b254e5d9786c347799f508724a28272161e9c07bca830ce5892e3b10b070e07c61194cb62c72de857e0659075aa9ef93e053a32bdeadfea5f684d80eb WHIRLPOOL 739eb2e5734097b128fe41e626f7cd30bb4906def8dfbef45c54d25b6db696769ccdfe498a9902b53f85d4bc6fc1a024a2aa29cc89979912c5d16adea27339b1 +MISC ChangeLog-2015 2592 SHA256 4453862c6e856a1d30a3ac1e6d7680f2e22c88f7c6fa72558fe84418834efc90 SHA512 9ccfd4c565cc9065ad20a9b6c128745acc05da6bbc6cfdfdd321b6e7b74d9a175967923ea186bbe186f14e7e266201889dbcf7b04d7710c221363bca3a9f5117 WHIRLPOOL 76b9d75e25058fff7ed9a67552a38f89b8850017d02312c98e9d7f9d3ecc7af72dcbb29d1345a06d6da938e962205b4fa73fbb01cf6e11de6a6170c8e392da43 +MISC metadata.xml 342 SHA256 a1ab56cabcebc0343826a7c079fe48f75af51a6b6b7231a0e085a8fc72a9a2b0 SHA512 f77c63597bc5df26ba6dd136ee943f78562c5d99fefc1b435633c602a6eb3433600976884085ea8aa8f87f2f79fd495e9b51f918290bc1751e66d7515fe4e039 WHIRLPOOL ff49efd1ab9dced97e3fa4d3152811ef9d83407d41c34141b03f29ab0757a35e0492744ce63fa1f2d8fa51e2ca1fa4b24da9de362174df87ad24f54d94761cec diff --git a/sci-chemistry/viewmol/files/2.4.1-change-default-paths.patch b/sci-chemistry/viewmol/files/2.4.1-change-default-paths.patch new file mode 100644 index 000000000000..4b1edef7ef8b --- /dev/null +++ b/sci-chemistry/viewmol/files/2.4.1-change-default-paths.patch @@ -0,0 +1,68 @@ +diff --git a/source/getrc.c b/source/getrc.c +index a39b436..c130096 100644 +--- a/getrc.c ++++ b/getrc.c +@@ -87,7 +87,7 @@ extern XtAppContext app; + + static char viewmolpath[MAXLENLINE]; + +-#define DEFAULTPATH "/usr/local/lib/viewmol" ++#define DEFAULTPATH "@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR/viewmol" + + int getrc(void) + { +diff --git a/source/install b/source/install +index 580865b..f136af3 100755 +--- a/install ++++ b/install +@@ -54,24 +54,27 @@ fi + cp $dirorig/viewmol $ROOT/bin + chmod 711 $ROOT/bin/viewmol + +-# install other files needed in $ROOT/lib/viewmol +-if [ ! -d $ROOT/lib/viewmol/$dir ] ++# install other files needed in $ROOT/GENTOOLIBDIR/viewmol ++if [ ! -d $ROOT/GENTOOLIBDIR/viewmol/$dir ] + then +- mkdir -p $ROOT/lib/viewmol/$dir +- chmod 755 $ROOT/lib/viewmol/$dir ++ mkdir -p $ROOT/GENTOOLIBDIR/viewmol/$dir ++ chmod 755 $ROOT/GENTOOLIBDIR/viewmol/$dir + fi + cd $dirorig +-cp tm bio readgamess readgauss readmopac readpdb $ROOT/lib/viewmol/$dir +-chmod 711 $ROOT/lib/viewmol/$dir/* ++cp tm bio readgamess readgauss readmopac readpdb $ROOT/GENTOOLIBDIR/viewmol/$dir ++chmod 711 $ROOT/GENTOOLIBDIR/viewmol/$dir/* + cd ../.. +-cp readdmol readdmol.awk readgulp readpqs writecar writegauss.py writemol writetm $ROOT/lib/viewmol +-chmod 755 $ROOT/lib/viewmol/* +-cp -r doc examples locale scripts tests $ROOT/lib/viewmol +-find $ROOT/lib/viewmol -type f -exec chmod a+r {} \; +-find $ROOT/lib/viewmol -type d -exec chmod a+rx {} \; +-sed 's/\/source//g' viewmolrc > $ROOT/lib/viewmol/viewmolrc +-chmod -R 644 $ROOT/lib/viewmol/viewmolrc +-if [ -d /usr/X11R6/lib/X11/app-defaults ] ++cp readdmol readdmol.awk readgulp readpqs writecar writegauss.py writemol writetm $ROOT/GENTOOLIBDIR/viewmol ++chmod 755 $ROOT/GENTOOLIBDIR/viewmol/* ++mkdir -p $ROOT/usr/share/viewmol $ROOT/usr/share/doc/GENTOODOCDIR/ $ROOT/GENTOOLIBDIR/viewmol/ ++cp -r examples scripts tests $ROOT/usr/share/viewmol ++cp -r locale $ROOT/GENTOOLIBDIR/viewmol/ ++cp -r doc/* examples scripts tests $ROOT/usr/share/doc/GENTOODOCDIR/ ++find $ROOT/GENTOOLIBDIR/viewmol -type f -exec chmod a+r {} \; ++find $ROOT/GENTOOLIBDIR/viewmol -type d -exec chmod a+rx {} \; ++sed 's/\/source//g' viewmolrc > $ROOT/GENTOOLIBDIR/viewmol/viewmolrc ++chmod -R 644 $ROOT/GENTOOLIBDIR/viewmol/viewmolrc ++if [ -d $ROOT/X11R6/GENTOOLIBDIR/X11/app-defaults ] + then + locale=`echo $LANG | cut -c1-2` + if [ "$locale" = "en" ] +@@ -82,6 +85,6 @@ then + # The C locale is defined by default for rpm builds, overwrite it + locale="en_US" + fi +- cp locale/${locale}/Viewmol /usr/X11R6/lib/X11/app-defaults +- chmod a+r /usr/X11R6/lib/X11/app-defaults/Viewmol ++ cp locale/${locale}/Viewmol ${ROOT}/X11R6/GENTOOLIBDIR/X11/app-defaults ++ chmod a+r ${ROOT}/X11R6/GENTOOLIBDIR/X11/app-defaults/Viewmol + fi diff --git a/sci-chemistry/viewmol/files/2.4.1-remove-icc-check.patch b/sci-chemistry/viewmol/files/2.4.1-remove-icc-check.patch new file mode 100644 index 000000000000..fd91e0a5a434 --- /dev/null +++ b/sci-chemistry/viewmol/files/2.4.1-remove-icc-check.patch @@ -0,0 +1,22 @@ +--- a/getmachine ++++ b/getmachine +@@ -269,19 +269,11 @@ + makedir + cat ../.config.$os > makefile + use_icc=`type icc 2> /dev/null` +- if [ "$use_icc" = "" ] +- then + findProcessor + echo 'COMPILER=gcc' >> makefile + echo "OPT=-O6 -mcpu=$processor -fomit-frame-pointer -ffast-math -malign-double" >> makefile + echo 'CFLAGS=-Wall -I/usr/X11R6/include -DLINUX -Wno-strict-aliasing' >> makefile + echo "LDFLAGS=$LINKFORSHARED" >> makefile +- else +- echo 'COMPILER=icc' >> makefile +- echo 'OPT=-O2 -ipo' >> makefile +- echo 'CFLAGS=-I/opt/intel/compiler50/ia32/include -I/usr/X11R6/include -DLINUX' >> makefile +- echo "LDFLAGS=$LINKFORSHARED -ipo" >> makefile +- fi + echo 'SCANDIR=' >> makefile + echo 'INCLUDE=$(TIFFINCLUDE) -I$(PNGINCLUDE) -I$(PYTHONINCLUDE)' >> makefile + echo 'LIBRARY=$(LIBTIFF) $(LIBPNG) -L$(LIBPYTHON)' >> makefile diff --git a/sci-chemistry/viewmol/metadata.xml b/sci-chemistry/viewmol/metadata.xml new file mode 100644 index 000000000000..335c7edd503b --- /dev/null +++ b/sci-chemistry/viewmol/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">viewmol</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/viewmol/viewmol-2.4.1-r3.ebuild b/sci-chemistry/viewmol/viewmol-2.4.1-r3.ebuild new file mode 100644 index 000000000000..7881b3a708c3 --- /dev/null +++ b/sci-chemistry/viewmol/viewmol-2.4.1-r3.ebuild @@ -0,0 +1,90 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="tk(-)" + +inherit prefix python-single-r1 toolchain-funcs + +DESCRIPTION="Open-source graphical front end for computational chemistry programs" +HOMEPAGE="http://viewmol.sourceforge.net/" +SRC_URI="mirror://sourceforge/viewmol/${P}.src.tgz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + media-libs/libpng:0= + media-libs/tiff:0 + virtual/glu + virtual/opengl + x11-libs/libX11 + x11-libs/libXi + x11-libs/libXmu + x11-libs/libXt + x11-libs/motif:0 + ${PYTHON_DEPS}" +DEPEND="${RDEPEND} + x11-proto/inputproto + x11-proto/xproto" + +S="${WORKDIR}/${P}/source" + +PATCHES=( + "${FILESDIR}"/${PV}-remove-icc-check.patch + "${FILESDIR}"/${PV}-change-default-paths.patch +) + +src_prepare() { + default + + eprefixify getrc.c + sed "s:GENTOOLIBDIR:$(get_libdir):g" -i install getrc.c || die + sed "s:GENTOODOCDIR:${PF}:g" -i install || die + + mkdir "$(uname -s)" || die + cd "$(uname -s)" || die + + cat >> ".config.$(uname -s)" <<- EOF || die + LIBTIFF = -L"${EPREFIX}/usr/$(get_libdir)" + TIFFINCLUDE = "${EPREFIX}/usr/include" + + LIBPNG = -L"${EPREFIX}/usr/$(get_libdir)" + PNGINCLUDE = "${EPREFIX}/usr/include" + + PYTHONVERSION = ${EPYTHON} + PYTHONINCLUDE = $(python_get_CFLAGS) + PYTHONLIB = $(python_get_LIBS) + + COMPILER = $(tc-getCC) + CFLAGS = ${CFLAGS} -DLINUX + LDFLAGS = ${LDFLAGS} + SCANDIR= + INCLUDE=\$(TIFFINCLUDE) -I\$(PNGINCLUDE) \$(PYTHONINCLUDE) + LIBRARY=\$(LIBTIFF) \$(LIBPNG) \$(PYTHONLIB) + LIBS=-L"${EPREFIX}/usr/$(get_libdir)" -ltiff -lpng -lz -lGLU -lGL -L"${EPREFIX}/usr/X11R6/lib" -lXm -lXmu -lXp -lXi -lXext -lXt -lX11 -lpthread -lutil -ldl -lm + EOF + + cp .config.$(uname -s) makefile || die + cat ../Makefile >> makefile || die +} + +src_compile() { + emake -C "$(uname -s)" viewmol_ tm_ bio_ readgamess_ readgauss_ readmopac_ readpdb_ + "${EPREFIX}"/bin/bash makeTranslations || die +} + +src_install() { + ./install "${ED%/}"/usr || die + + # fix broken layout + mv "${ED%/}"/usr/{usr/share,} || die + rm -rf "${ED%/}"/usr/usr || die + mv "${ED%/}"/usr/{$(get_libdir)/${PN}/locale,share} || die + mv "${ED%/}"/usr/{$(get_libdir),libexec} || die +} diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest new file mode 100644 index 000000000000..aa1283c7ab08 --- /dev/null +++ b/sci-chemistry/vmd/Manifest @@ -0,0 +1,8 @@ +AUX vmd-1.9.1-cuda-device_ptr.patch 934 SHA256 8d32ebe81adb4ec0186ceba08743c0b6a25c76b3c58edaefa85df38328aaa87e SHA512 274756fe17fdcc39ce471c3187f3076407d34b64e49b0006ee30525a952277b2b5c713fffa8786162dc542eef2b021f2bf7339736cf9e81b673d5146114829ed WHIRLPOOL 400959a0b52ce0026308bf2c251de9e0c87ee65c8c10844a7cd2f21b319623868316970247984a22b19dcd17a15e8cdf6959b60c5575a05f3709191a55eb4fb2 +AUX vmd-1.9.2-format-security.patch 550 SHA256 4e3fa85105117ab4c259ae6e58fb38fee668fc3000b981369841f98740c0ba61 SHA512 81a71ee4c4c438d18f3a393ebad5c9a08f1a7bb95fa58b78a8798955a34ae2494f80fa074b973a1b595862080e9103d21e509443742cfe2bc3cf77f10c0e3c9d WHIRLPOOL 8a2b64514ba9876bdbc2c4afa9ae48b4742099c1cb39b3835f4e340e0b4330cf06f28f92320c15481d4d6ed27c8491dc899572c091a952fa17eb1b0356b01aed +DIST vmd-1.9.2-gentoo-patches.tar.xz 14896 SHA256 91508b384cb0a8aab8d8cfc31c1e7e0bc4225dbd7cdb36fbaefcfe8baca9442c SHA512 0516b9e57b256ce822a64df420ebf3ab7391722757caeaa7e615526242043e9375fee8f4ee86fb4eb8de7a50d5cfc8f8d973ace5fa082e6f9010eb692cd6ee51 WHIRLPOOL 3f87d24ad0ca7eb60e0ae3d561da7c61e0caa9fe8bb71cd3a06731228926d4c16ee03699d80adf02e2c9b263f96ea8d5b096e64e3e94b0208b1cb618c8a8a7ca +DIST vmd-1.9.2.src.tar.gz 34903084 SHA256 870ee1e483ad23eb7f3bb6ac816cb7be5df893879dddc0bda8423a011993ccdb SHA512 b232b743d4ea97dcf76e3005e1c8716d7138602edc078c4846026ab67759c8559af956182cb1acf3c85890db10b6f658ac9c269d432f2595612cf376d6d505ef WHIRLPOOL e2489b4bd8f28359ee959d6ebec3a9e775fbaf7a25baa1324c99dd04c7768e002924c671c11830ec6e9589ecc9de4864f2bcf3dfaf9eb36f5a1d03d5e5841f17 +EBUILD vmd-1.9.2.ebuild 7144 SHA256 d6d38d62c6b8001bbf0a43a96bb1dafc80025addd1faa98f0abe1a492825876d SHA512 d3432b08ea1b5888a05e49911daabaaac64f265940fb639c1677532c7828431735e89119ca450f8983ddf961857a866ba5e2cb288b960b8f386746e87ae9411e WHIRLPOOL 571a6f8832b61f6fa120fc8c876a1d06592ec3ba7eea5af4b39a572d46a04afde3c169efa181e9773ee0cb03bc19bfd657c9f1e1eb16f29517855b017f6ffe7a +MISC ChangeLog 2551 SHA256 e9fb995684082a287b3209a9d642c652499b9bab26da73f4a28fd6e03b8407ac SHA512 c28866e3cf85f8c1ff40408da7ea6a2c08b449a516d5b73e7fafb936901e4b086d2d7145f3b27557546a88ed45efa66bc2ca29188ac058cf82a0476600545925 WHIRLPOOL 41002b5fa58cee1d9ecefa015636ec32d55904425e9fdbd81b57bb910553ea47c272beacbabb9b881c2e8c3214023bd85d614c7b6b9f285800be415cfb520326 +MISC ChangeLog-2015 10735 SHA256 a86018bbed7e1a61b0c80a738ec7d1bc5684d3f90769045be55714c187a46857 SHA512 210b17a4758411bf7344e7c235ff5c16a7f538bb031aaa53bcd134014ddcf497335863870fb4fb237dc2724528ba0e847d1d53d4e28f4d1383af93859f02d60c WHIRLPOOL 2854f8e671cb5bc4f203de6995b896485521bce7119adeda55756d545fe6e33ce9ba4e280f171081693dd7728cdd39c141550fb7d425fafa93cdbb7f7f645bad +MISC metadata.xml 778 SHA256 79ee62bd7447526f07950c756d31d87e2c52d6f79773bbf95f806717926b40ce SHA512 8ac6f9bf6f78c1da366fa5e61950be887ce7aafe479e359e18448de2ad422b977ef3a2d44a36434f36701aa7c0447f2a041dedb91102b2628a09379e664f46df WHIRLPOOL 6795ec883c6137f16510816bacf7cd0fd0262bf5da774af31adf4c0411f3d0b04d8213dd1e8b7591ce4426e59e9612a1baea4b6cab3a2412b4853e023040dd09 diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch new file mode 100644 index 000000000000..ce842448decf --- /dev/null +++ b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch @@ -0,0 +1,28 @@ + vmd-1.9.1/src/CUDAMarchingCubes.cu | 1 + + vmd-1.9.1/src/CUDAQuickSurf.cu | 1 + + 2 files changed, 2 insertions(+) + +diff --git a/vmd-1.9.1/src/CUDAMarchingCubes.cu b/vmd-1.9.1/src/CUDAMarchingCubes.cu +index 5bfe7bf..36faaf0 100755 +--- a/vmd-1.9.1/src/CUDAMarchingCubes.cu ++++ b/vmd-1.9.1/src/CUDAMarchingCubes.cu +@@ -45,6 +45,7 @@ + #include "CUDAMarchingCubes.h" + #include <thrust/scan.h> + #include <thrust/functional.h> ++#include <thrust/device_ptr.h> + + // The number of threads to use for triangle generation + // (limited by shared memory size) +diff --git a/vmd-1.9.1/src/CUDAQuickSurf.cu b/vmd-1.9.1/src/CUDAQuickSurf.cu +index a21ebde..56a42c8 100755 +--- a/vmd-1.9.1/src/CUDAQuickSurf.cu ++++ b/vmd-1.9.1/src/CUDAQuickSurf.cu +@@ -22,6 +22,7 @@ + #include <stdlib.h> + #include <string.h> + #include <cuda.h> ++#include <thrust/device_ptr.h> + + #if CUDART_VERSION < 4000 + #error The VMD QuickSurf feature requires CUDA 4.0 or later diff --git a/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch b/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch new file mode 100644 index 000000000000..3f9ea5c8c2ef --- /dev/null +++ b/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch @@ -0,0 +1,16 @@ + plugins/molfile_plugin/src/maeffplugin.cxx | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/plugins/molfile_plugin/src/maeffplugin.cxx b/plugins/molfile_plugin/src/maeffplugin.cxx +index cfe1223..41d92bb 100644 +--- a/plugins/molfile_plugin/src/maeffplugin.cxx ++++ b/plugins/molfile_plugin/src/maeffplugin.cxx +@@ -1979,7 +1979,7 @@ namespace { + } + } + catch (std::exception &e) { +- fprintf(stderr, e.what()); ++ fprintf(stderr, "%s", e.what()); + return MOLFILE_ERROR; + } + return MOLFILE_SUCCESS; diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml new file mode 100644 index 000000000000..1b24082830f2 --- /dev/null +++ b/sci-chemistry/vmd/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="cuda">Use nvidia cuda toolkit for speeding up computations</flag> + <flag name="gromacs">Add support for TNG file format</flag> + <flag name="msms">Add support for MSMS SAS calcualtion tool</flag> + <flag name="povray">Add support for povray raytracer for HQ images</flag> + <flag name="tachyon">Add support for tachyon raytracer for HQ images</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/vmd/vmd-1.9.2.ebuild b/sci-chemistry/vmd/vmd-1.9.2.ebuild new file mode 100644 index 000000000000..347a8c9a751f --- /dev/null +++ b/sci-chemistry/vmd/vmd-1.9.2.ebuild @@ -0,0 +1,251 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cuda eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs + +DESCRIPTION="Visual Molecular Dynamics" +HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" +SRC_URI=" + https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz + ${P}.src.tar.gz" + +SLOT="0" +LICENSE="vmd" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cuda gromacs msms povray sqlite tachyon xinerama" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RESTRICT="fetch" + +# currently, tk-8.5* with USE=truetype breaks some +# tk apps such as Sequence Viewer or Timeline. +CDEPEND=" + >=dev-lang/tk-8.6.1 + dev-lang/perl + dev-libs/expat + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/netcdf:0= + virtual/opengl + >=x11-libs/fltk-1.1.10-r2:1 + x11-libs/libXft + x11-libs/libXi + ${PYTHON_DEPS} + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) + gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1[tng] ) + sqlite? ( dev-db/sqlite:3= ) + tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) + xinerama? ( x11-libs/libXinerama )" +DEPEND="${CDEPEND} + virtual/pkgconfig + dev-lang/swig" +RDEPEND="${CDEPEND} + sci-biology/stride + sci-chemistry/surf + x11-terms/xterm + msms? ( sci-chemistry/msms-bin ) + povray? ( media-gfx/povray ) + " + +VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" +# Binary only plugin!! +QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" +QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" +QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" + +pkg_nofetch() { + elog "Please download ${P}.src.tar.gz from" + elog "${VMD_DOWNLOAD}" + elog "after agreeing to the license and get" + elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" + elog "Place both in ${DISTDIR}" +} + +src_prepare() { + use cuda && cuda_sanitize + + epatch "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch + + cd "${WORKDIR}"/plugins || die + + epatch \ + "${WORKDIR}"/${P}-gentoo-plugins.patch \ + "${FILESDIR}"/${P}-format-security.patch + + [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) + + sed \ + -e "s:CC = gcc:CC = $(tc-getCC):" \ + -e "s:CXX = g++:CXX = $(tc-getCXX):" \ + -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ + -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ + -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ + -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ + -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ + -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ + -e "s:-ltcl8.5:-ltcl:" \ + -i Make-arch || die "Failed to set up plugins Makefile" + + sed \ + -e '/^AR /s:=:?=:g' \ + -e '/^RANLIB /s:=:?=:g' \ + -i ../plugins/*/Makefile || die + + tc-export AR RANLIB + + sed \ + -e "s:\$(CXXFLAGS)::g" \ + -i hesstrans/Makefile || die + + # prepare vmd itself + cd "${S}" || die + + epatch "${WORKDIR}"/${P}-gentoo-base.patch + + # PREFIX + sed \ + -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ + -i configure || die + + sed \ + -e "s:gentoo-bindir:${ED}/usr/bin:g" \ + -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ + -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ + -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -e "s:gentoo-gcc:$(tc-getCC):g" \ + -e "s:gentoo-g++:$(tc-getCXX):g" \ + -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ + -e "s:gentoo-cflags:${CFLAGS}:g" \ + -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ + -e "s:gentoo-nvflags::g" \ + -e "s:gentoo-ldflags:${LDFLAGS}:g" \ + -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ + -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ + -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ + -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ + -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -i configure || die + + if use cuda; then + sed \ + -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ + -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ + -i configure src/Makefile || die + sed \ + -e '/compute_/d' \ + -i configure || die + sed \ + -e 's:-gencode .*code=sm_..::' \ + -i src/Makefile || die + fi + + sed \ + -e "s:LINUXPPC:LINUX:g" \ + -e "s:LINUXALPHA:LINUX:g" \ + -e "s:LINUXAMD64:LINUX:g" \ + -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ + -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ + -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ + -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" + + EMAKEOPTS=( + TCLINC="-I${EPREFIX}/usr/include" + TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" + TCLLDFLAGS="-shared" + NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf) ${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" + NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf) ${EPREFIX}/usr/include" + NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" + NETCDFDYNAMIC=1 + EXPATINC="-I${EPREFIX}/usr/include" + EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" + EXPATLDFLAGS="-shared" + EXPATDYNAMIC=1 + ) + if use gromacs; then + EMAKEOPTS+=( + TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" + TNGINC="-I${EPREFIX}/usr/include" + TNGLDFLAGS="-shared" + TNGDYNAMIC=1 + ) + fi + if use sqlite; then + EMAKEOPTS+=( + SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" + SQLITEINC="-I${EPREFIX}/usr/include" + SQLITELDFLAGS="-shared" + SQLITEDYNAMIC=1 + ) + fi +} + +src_configure() { + local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" + rm -f configure.options && echo $myconf >> configure.options + + use cuda && myconf+=" CUDA" +# use mpi && myconf+=" MPI" + use tachyon && myconf+=" LIBTACHYON" && append-cflags -I"${EPREFIX}/usr/include/tachyon" + use xinerama && myconf+=" XINERAMA" + + export \ + PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ + PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ + PYTHON_LIBRARY="$(python_get_LIBS)" \ + NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ + NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" + + perl ./configure LINUX \ + ${myconf} || die +} + +src_compile() { + # build plugins + cd "${WORKDIR}"/plugins || die + + emake \ + ${EMAKEOPTS[@]} \ + LINUX + + # build vmd + cd "${S}"/src || die + emake +} + +src_install() { + # install plugins + cd "${WORKDIR}"/plugins || die + emake \ + PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ + distrib + + # install vmd + cd "${S}"/src || die + emake install + + # install docs + cd "${S}" || die + dodoc Announcement README doc/ig.pdf doc/ug.pdf + + # remove some of the things we don't want and need in + # /usr/lib + cd "${ED}"/usr/$(get_libdir)/vmd || die + rm -fr doc README Announcement LICENSE || \ + die "failed to clean up /usr/lib/vmd directory" + + # adjust path in vmd wrapper + sed \ + -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ + -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ + || die "failed to set up vmd wrapper script" + + # install icon and generate desktop entry + insinto /usr/share/pixmaps + doins "${WORKDIR}"/vmd.png + eprefixify "${WORKDIR}"/vmd.desktop + sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die + domenu "${WORKDIR}"/vmd.desktop +} diff --git a/sci-chemistry/votca-csg/Manifest b/sci-chemistry/votca-csg/Manifest new file mode 100644 index 000000000000..db532eea7f2f --- /dev/null +++ b/sci-chemistry/votca-csg/Manifest @@ -0,0 +1,12 @@ +DIST votca-csg-1.4.1.tar.gz 347702 SHA256 1ff9fc5ad95cd57e7c1d2c8adad5b32f81a978e2bea34f14f7defcdd11a05ec7 SHA512 87f2798c9b5f2d82ae1c158238f7a3b7007c7ceb7ce82503f0b002f605f2cc0b5ca4c8ef24fab571efae63a81e7a60bc476b5433962c239de4f5d42bae3c10ea WHIRLPOOL 26946d54dd2c1665f411ae0424150ef93db7cf71984377a04a6bb1154d66ba8676f54a4b10f0e8167cee3ae5a4ad26f702a67da2be356c08e5e6a626e2483864 +DIST votca-csg-1.4.tar.gz 346527 SHA256 713702613b1e51459a18eb1ef83116eb3dbfd25f05d32e5772ee300a674cdc74 SHA512 26318644c7af2dfa1b81242b27ffac98f2180c3a1f05581bc50a00f644cec4b19ffbaf41c9d941a4714171b56ae93fe41f1a663cd0593ae2b0be2da379119d9b WHIRLPOOL 15c7749b1fa003e92e94f4f3f4ac7698667e5a06f739d4e97686aa904b8433a1e1628fae1c1f718bc4bfd2108d515cb12098852a0ebecb213e478874997f3148 +DIST votca-csg-manual-1.4.1.pdf 1282641 SHA256 8358bf7640d30f3dce75c7c2463383d6c5ca37aca4cb3f4b638a02dbcc806c7b SHA512 e89f41af05eaeb9ea499e8625cc98e2632ec647ec2d8c9c9052dcd4d2935d082b29b51495514e3e06e73ce42b8cda7017fc523a013569378e2bc86bf88ad32d4 WHIRLPOOL 2b8e903fc4ceddb58af8c3d7b78b8c2091aca473154dc613736f39f757e6a546058b16d5272ebbaad441eb143cc2f7edd8afd82fa884aff140aa7102d5b3b417 +DIST votca-csg-manual-1.4.pdf 1281983 SHA256 e2e235473a64dc674a373eacaade4922e02a64274c1f28bcf3b443fbf425d1da SHA512 2e1f4a4375d83df9bd357d4d17e79d26a3a31c9177f008de86721427ffc6f43a5000ec840691108b52a8aecf962321ba6363cd975c7445d7230ee5b0b151b3fa WHIRLPOOL 24580fe71202daad3d4f627657c6aa24175df807462e5c03a05de39f5b2ba38a44a51ee7cfc50416795fc4dfbc8041a4360a3dd680ea339464e1097782b71ac9 +DIST votca-csg-tutorials-1.4.1.tar.gz 6339417 SHA256 029e7f033c21ed37d8428c363133326744ff088bdcf3cd6b843a9b60dba268ef SHA512 896ec9d6b2537a06301046a74c1957708eb96d9854b3ec855fe3457208c142f6fb26a03e323a2644862a1efd0030fcceb1189f73655b984462f0f7127a02de90 WHIRLPOOL b540802743eff6c988f00dd8c4f449021f4ca257541394194ef48d0fc364d73d90a1c3845472769c82cfdc20c6dbf8671440fa4c5cc623ab179b2459e87bc078 +DIST votca-csg-tutorials-1.4.tar.gz 6348417 SHA256 f5082f57575f09e9a0035f428603946676b251b7cb45b4332ded833be4dca649 SHA512 f3eb28a133ebc04eed07f84d5962943cb9c547c1099638127f15e0015dfdf3f0b25aab4c97d009d6040bf1d69d408cc178edd6e803d33bf1d831e12dca0671c7 WHIRLPOOL da02cda090eb46dd74d6f2bec8adec70ca7a05796ed0d05772133f566e091f794e2d7fa2640ca775e249248624d0f022212444fa3425c3f715a4dea94a300225 +EBUILD votca-csg-1.4.1.ebuild 3195 SHA256 83c2cbfe82b0b6ecb3d64d96db8bc0d2bbb116bac6057b0786546f5ccdb65ed3 SHA512 988bb34ccb1a96c4548a582ba99fc1097c696f647fc810f2fb3a026145de306b24c392494fe1aa33a0bab91212167f845cb339ab8fd13dbf4af2dcd5c23c6529 WHIRLPOOL 80b9cf6eba07bce95e63784bf0675214b87459fe40b4e5a7e74f1512445e2c2981669118f63fa3f2658648c31305f498abac4b39e52c3280b7caf652356b5607 +EBUILD votca-csg-1.4.ebuild 3191 SHA256 792c3cf375bc7daa4d8f2376f8a818eede8ae497f1fc7aae862e3b3ebf51c550 SHA512 4c65b4853bab1b6f67aba56020569f70db10727d28e3775688a59a6901bc3d48e22483bf9f6b622ec2ee2cd51c70073d622f62188c0c172b6a0c18a437169504 WHIRLPOOL 6560607ff74f32cd8e74ef27ff06080c5324b6644457f6225dbddb92b20176b376e900efd24601a9236444500be2fdb160fbef5ae1c3ea277f78ae0fd606e053 +EBUILD votca-csg-9999.ebuild 2519 SHA256 43dffa34ebc4781e51e30629003fb2fae4ea000602186d34f77d69f004e1407d SHA512 ce773a44becac5b667c99103e4be733cc136c7642b1ca5944f7c93b39ac04ae6b8b4fe722c58037da33c53e6c3ff2d9c7f3267d045371cfa7580f483dd01b434 WHIRLPOOL 1363723e507a0d9ea77e87c00ea440bb741aea6a2127bdc29a202a5df80cd088be8299bc831d71dbc31fb46f58966512185ff1f1ed93f51478140a1cb1af1407 +MISC ChangeLog 5347 SHA256 be65e7d45f20ad7111b215941f7ae0aa45490108f600ced2d84c7c9a479a949f SHA512 1d1685c1584188fbb44f6dc87448ed4aafb45609c6f37e8c1cb8cdedc1e2797922b9e829c3b7edc97cee6cf6880663c7d136959f1b3ad085bc0fc99fd46194d7 WHIRLPOOL 36a08ad6aa9ce713b59f48af25a88a941601bfd1c61b1e16b38c5a4ada082544bcb2c29dcad735fc6bba721a58e2894c665c1565157351305815ebcc0ed6b913 +MISC ChangeLog-2015 3867 SHA256 70f287208a04ef13cecb9739bfc90779191f8efa53cf27d99af57811d0bdb3b5 SHA512 de6d49f7da10339b1c31784bbc898c227c917653dbed6ac24a590caf655aa6fb45771a6f3ed5b300cbd8cc0a0b6096816e09d6121d7d4b306227bc3bdb7abe67 WHIRLPOOL 6f1cc0b40e04a5f0722e64b7b6b58f69793969043e9afd8924e32ae3091d79dc6943cad0f5684ef4c51d2fe393d5f3d0357e2c75fbb8c5e9cd94406a150bda5a +MISC metadata.xml 676 SHA256 ef882f6f0dc5c8ad1e35f655494811ad7bf1447d07dae8d51f4f9cfb46559b76 SHA512 14ecd498eeeed1576923d8da9bc5dc98e47c1d162173b7f2419ad367fa84e227555bd0365709be8a456dc5388ea6fa6734fa7df3c82fd4efcd1cf3460c7e12a1 WHIRLPOOL 606c78879ca5d06204446b6f781f611f0d7edb238f383063f32762a9838bc8dc07ca6e6899303ecd5581c60ec23d72e73083fb171c846a9f7f9f5fd69341f897 diff --git a/sci-chemistry/votca-csg/metadata.xml b/sci-chemistry/votca-csg/metadata.xml new file mode 100644 index 000000000000..795272141d7f --- /dev/null +++ b/sci-chemistry/votca-csg/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>junghans@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="gromacs">Add support for gromacs file formats through <pkg>sci-chemistry/gromacs</pkg></flag> + <flag name="extras">Pull in extra applications from <pkg>sci-chemistry/votca-csgapps</pkg></flag> + </use> + <upstream> + <remote-id type="github">votca/csg</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/votca-csg/votca-csg-1.4.1.ebuild b/sci-chemistry/votca-csg/votca-csg-1.4.1.ebuild new file mode 100644 index 000000000000..533b017fe2b9 --- /dev/null +++ b/sci-chemistry/votca-csg/votca-csg-1.4.1.ebuild @@ -0,0 +1,113 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils multilib + +IUSE="doc examples extras +gromacs hdf5" +PDEPEND="extras? ( =sci-chemistry/${PN}apps-${PV} )" +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz + doc? ( https://github.com/${PN/-//}-manual/releases/download/v${PV}/${PN}-manual-${PV}.pdf ) + examples? ( https://github.com/${PN/-//}-tutorials/archive/v${PV}.tar.gz -> ${PN}-tutorials-${PV}.tar.gz )" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="~amd64 ~x86" +fi + +DESCRIPTION="Votca coarse-graining engine" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" + +RDEPEND=" + =sci-libs/votca-tools-${PV} + gromacs? ( sci-chemistry/gromacs:= ) + hdf5? ( sci-libs/hdf5 ) + dev-lang/perl + app-shells/bash:*" + +DEPEND="${RDEPEND} + doc? ( + app-doc/doxygen[dot] + dev-texlive/texlive-latexextra + virtual/latex-base + dev-tex/pgf + ) + >=app-text/txt2tags-2.5 + virtual/pkgconfig" + +DOCS=( README.md NOTICE CHANGELOG.md ) + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use doc; then + EGIT_REPO_URI="https://github.com/${PN/-//}-manual.git" + EGIT_BRANCH="master" + EGIT_CHECKOUT_DIR="${WORKDIR}/${PN}-manual"\ + git-r3_src_unpack + fi + if use examples; then + EGIT_REPO_URI="https://github.com/${PN/-//}-tutorials.git" + EGIT_BRANCH="master" + EGIT_CHECKOUT_DIR="${WORKDIR}/${PN#votca-}-tutorials"\ + git-r3_src_unpack + fi + fi +} + +src_configure() { + mycmakeargs=( + -DWITH_GMX=$(usex gromacs) + -DWITH_H5MD=$(usex hdf5) + -DWITH_RC_FILES=OFF + -DLIB=$(get_libdir) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + newbashcomp scripts/csg-completion.bash csg_call + for i in "${ED}"/usr/bin/csg_*; do + [[ ${i} = *csg_call ]] && continue + bashcomp_alias csg_call "${i##*/}" + done + if use doc; then + if [[ ${PV} = *9999* ]]; then + #we need to do that here, because we need an installed version of csg to build the manual + [[ ${CHOST} = *-darwin* ]] && \ + emake -C "${WORKDIR}/${PN}"-manual PATH="${PATH}${PATH:+:}${ED}/usr/bin" DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)" \ + || emake -C "${WORKDIR}/${PN}"-manual PATH="${PATH}${PATH:+:}${ED}/usr/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}${LD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)" + newdoc "${WORKDIR}/${PN}"-manual/manual.pdf "${PN}-manual-${PV}.pdf" + else + dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" + fi + cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html + dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html + fi + if use examples; then + insinto "/usr/share/doc/${PF}/tutorials" + docompress -x "/usr/share/doc/${PF}/tutorials" + rm -rf "${WORKDIR}/${PN#votca-}"-tutorials*/CMake* + doins -r "${WORKDIR}/${PN#votca-}"-tutorials*/* + fi +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA, J. Chem. Theory Comput. 5, 3211 (2009). " + einfo "https://dx.doi.org/10.1021/ct900369w" + einfo +} diff --git a/sci-chemistry/votca-csg/votca-csg-1.4.ebuild b/sci-chemistry/votca-csg/votca-csg-1.4.ebuild new file mode 100644 index 000000000000..f8a45defd418 --- /dev/null +++ b/sci-chemistry/votca-csg/votca-csg-1.4.ebuild @@ -0,0 +1,113 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils multilib + +IUSE="doc examples extras +gromacs hdf5" +PDEPEND="extras? ( =sci-chemistry/${PN}apps-${PV} )" +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz + doc? ( https://github.com/${PN/-//}-manual/releases/download/v${PV}/${PN}-manual-${PV}.pdf ) + examples? ( https://github.com/${PN/-//}-tutorials/archive/v${PV}.tar.gz -> ${PN}-tutorials-${PV}.tar.gz )" + KEYWORDS="amd64 x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="amd64 x86" +fi + +DESCRIPTION="Votca coarse-graining engine" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" + +RDEPEND=" + =sci-libs/votca-tools-${PV} + gromacs? ( sci-chemistry/gromacs:= ) + hdf5? ( sci-libs/hdf5 ) + dev-lang/perl + app-shells/bash:*" + +DEPEND="${RDEPEND} + doc? ( + app-doc/doxygen[dot] + dev-texlive/texlive-latexextra + virtual/latex-base + dev-tex/pgf + ) + >=app-text/txt2tags-2.5 + virtual/pkgconfig" + +DOCS=( README.md NOTICE CHANGELOG.md ) + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use doc; then + EGIT_REPO_URI="https://github.com/${PN/-//}-manual.git" + EGIT_BRANCH="master" + EGIT_CHECKOUT_DIR="${WORKDIR}/${PN}-manual"\ + git-r3_src_unpack + fi + if use examples; then + EGIT_REPO_URI="https://github.com/${PN/-//}-tutorials.git" + EGIT_BRANCH="master" + EGIT_CHECKOUT_DIR="${WORKDIR}/${PN#votca-}-tutorials"\ + git-r3_src_unpack + fi + fi +} + +src_configure() { + mycmakeargs=( + -DWITH_GMX=$(usex gromacs) + -DWITH_H5MD=$(usex hdf5) + -DWITH_RC_FILES=OFF + -DLIB=$(get_libdir) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + newbashcomp scripts/csg-completion.bash csg_call + for i in "${ED}"/usr/bin/csg_*; do + [[ ${i} = *csg_call ]] && continue + bashcomp_alias csg_call "${i##*/}" + done + if use doc; then + if [[ ${PV} = *9999* ]]; then + #we need to do that here, because we need an installed version of csg to build the manual + [[ ${CHOST} = *-darwin* ]] && \ + emake -C "${WORKDIR}/${PN}"-manual PATH="${PATH}${PATH:+:}${ED}/usr/bin" DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)" \ + || emake -C "${WORKDIR}/${PN}"-manual PATH="${PATH}${PATH:+:}${ED}/usr/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}${LD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)" + newdoc "${WORKDIR}/${PN}"-manual/manual.pdf "${PN}-manual-${PV}.pdf" + else + dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" + fi + cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html + dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html + fi + if use examples; then + insinto "/usr/share/doc/${PF}/tutorials" + docompress -x "/usr/share/doc/${PF}/tutorials" + rm -rf "${WORKDIR}/${PN#votca-}"-tutorials*/CMake* + doins -r "${WORKDIR}/${PN#votca-}"-tutorials*/* + fi +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA, J. Chem. Theory Comput. 5, 3211 (2009). " + einfo "https://dx.doi.org/10.1021/ct900369w" + einfo +} diff --git a/sci-chemistry/votca-csg/votca-csg-9999.ebuild b/sci-chemistry/votca-csg/votca-csg-9999.ebuild new file mode 100644 index 000000000000..ea6ac3506f7f --- /dev/null +++ b/sci-chemistry/votca-csg/votca-csg-9999.ebuild @@ -0,0 +1,100 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils multilib + +IUSE="doc examples extras +gromacs hdf5" +PDEPEND="extras? ( =sci-chemistry/${PN}apps-${PV} )" +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz + doc? ( https://github.com/${PN/-//}-manual/releases/download/v${PV}/${PN}-manual-${PV}.pdf ) + examples? ( https://github.com/${PN/-//}-tutorials/archive/v${PV}.tar.gz -> ${PN}-tutorials-${PV}.tar.gz )" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="" + PDEPEND="${PDEPEND} doc? ( =app-doc/${PN}-manual-${PV} )" +fi + +DESCRIPTION="Votca coarse-graining engine" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" + +RDEPEND=" + =sci-libs/votca-tools-${PV} + gromacs? ( sci-chemistry/gromacs:= ) + hdf5? ( sci-libs/hdf5 ) + dev-lang/perl + app-shells/bash:*" + +DEPEND="${RDEPEND} + doc? ( + app-doc/doxygen[dot] + dev-texlive/texlive-latexextra + virtual/latex-base + dev-tex/pgf + ) + >=app-text/txt2tags-2.5 + virtual/pkgconfig" + +DOCS=( README.md NOTICE CHANGELOG.md ) + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use examples; then + EGIT_REPO_URI="https://github.com/${PN/-//}-tutorials.git" + EGIT_BRANCH="master" + EGIT_CHECKOUT_DIR="${WORKDIR}/${PN#votca-}-tutorials"\ + git-r3_src_unpack + fi + fi +} + +src_configure() { + mycmakeargs=( + -DWITH_GMX=$(usex gromacs) + -DWITH_H5MD=$(usex hdf5) + -DWITH_RC_FILES=OFF + -DLIB=$(get_libdir) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + newbashcomp scripts/csg-completion.bash csg_call + for i in "${ED}"/usr/bin/csg_*; do + [[ ${i} = *csg_call ]] && continue + bashcomp_alias csg_call "${i##*/}" + done + if use doc; then + [[ ${PV} != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" + cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html + dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html + fi + if use examples; then + insinto "/usr/share/doc/${PF}/tutorials" + docompress -x "/usr/share/doc/${PF}/tutorials" + rm -rf "${WORKDIR}/${PN#votca-}"-tutorials*/CMake* + doins -r "${WORKDIR}/${PN#votca-}"-tutorials*/* + fi +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA, J. Chem. Theory Comput. 5, 3211 (2009). " + einfo "https://dx.doi.org/10.1021/ct900369w" + einfo +} diff --git a/sci-chemistry/votca-csgapps/Manifest b/sci-chemistry/votca-csgapps/Manifest new file mode 100644 index 000000000000..552c227a0222 --- /dev/null +++ b/sci-chemistry/votca-csgapps/Manifest @@ -0,0 +1,8 @@ +DIST votca-csgapps-1.4.1.tar.gz 21066 SHA256 e3b46ad80f20d543f7c87eca0cd1f140ba040270340516f3b1fc91584bf6651a SHA512 80881ac173b56b07825c484f98c598de8d74bb8a54b888f06cc3a20d15670b49059e50adc210308e21ee4ea9038cf564c08d7ab33c4a43864acb1de97bc3fcef WHIRLPOOL d9c3c1aa98060353e1f63fbb4d2e403e4860afd9130578c753a4bbbbb17a67762f90e3c8e10c267d25189885dfc4c95cf3cafbf51284191b5eabd22a2b94de1e +DIST votca-csgapps-1.4.tar.gz 21072 SHA256 6636412db0a23c12fb67e7958050d0bc484f3f615faa95a9b98f4d4696c67243 SHA512 325c99606f17d7bb00e2cc3b1545f31dd4cf1fbc0d216f2da2c48e06b2011c9f99096643a6c6efd794a169de056f803f791c156afec4a73e41c58bc4ca1055f9 WHIRLPOOL e05c17218ad85c9b8f6cfbd892646492519ec3ab6e99102c3be94fbfac1fdcf8a08389b6b56921941e7186d93298120cb367e24ae3dbf66fbaf3670b9d8a5fc0 +EBUILD votca-csgapps-1.4.1.ebuild 653 SHA256 9fd15d63faa84e6293e8d3295d44a727b37969f84191bcde2142768739f2c94c SHA512 13ab1d118aea4f16664566f4e13965cc46a9e67e37157e23ad8c76a68d5db89b8db5b95104c23cf9cc16f78315dc9f632708cbd3920a545d964e2226dc6f9ff2 WHIRLPOOL eab76e2cd895d05b0941505691e5f7877962cb704c6908628474a3e3dd6896371b3dbf34cf192da7093fd210608a44a921f1689302069293e59feb3e49726530 +EBUILD votca-csgapps-1.4.ebuild 649 SHA256 37c2f61f459883b4055e9b35f4e95750214fe839277eb4a401a6d8116e3ca821 SHA512 b6400f2a28ce0c2953495c00aeaab0bfd15c52df28a5e6575b0f568c9a777678495b591cbce58fa61e1d54149fa3f684c6f9f99aaa82127e2eedcc67f6259ed8 WHIRLPOOL 2a507a86e01b2395c3389b1511a2531fb5a64ae648e6cf7f77c145145cde2062c5599bea1eab19715a8a14fcb19c6ab9110c0cc7785ad4f2095285384346e333 +EBUILD votca-csgapps-9999.ebuild 642 SHA256 75bceace892b253aeafb4cb2d9c0a763148dc30ffc8a064fedc60a03af7c5b8b SHA512 1863c5340ada5919f9d4734d4d10bb8ea237b88e110a7b454ec944819149d8a52da5d4a9a7e22e1a82499278a690e5fbc970c6f4595f15c391100c24d3bd0416 WHIRLPOOL 6970b1828b1a360e35d17f6bdc6256420b5bdb1ccd7456a9c25cb147db43f5b234f9a67bf4673bf0757e53d2577fd9133fcaf630c541fc327641a32069e5a158 +MISC ChangeLog 4933 SHA256 b227d67b5c1b3353d748d9cccd38c3c46e057e829001a82811c2ec499d19ef61 SHA512 59f2be5e1d25532ebaf8abffb2769a55263b4b981cc714f667cb2c7a7ac7ef3e05441836851daaa0e847292dd5ee58f8d11367185fc386348c5f6f6a8e7d90ce WHIRLPOOL d97ad326029be00632a87632450f245b5a2a99a3cc0f59d489e279ccd8e27aac814007f768d36241678ec2b8c2f5bd6bd2102576fd0c306b95eb9e4ac4cdf5e3 +MISC ChangeLog-2015 2160 SHA256 e707eb2e57e3d9f0bd9a277b3b8cc8fa093cfc6d0cb701a5f77bd5f56fe1a418 SHA512 4a476b46d6234015c6dfe9bd1cfd57ce03c994623ee1aca061104aaf48dfa9a62d53f7aecbd0bdf6c25609b85ca84d41efc27e153ca5d346f142096722f053ed WHIRLPOOL 30c28f5f7d180c138272a8cf148be72e1bf96f515afbec60061a1b894e602c699cd1309fad78421914639498684a1e83d795df97073741e7ae951df542b95447 +MISC metadata.xml 457 SHA256 0496180e0b82f56c00e90b587743bba3f2dcc393827c15adeb2a2e0e4718461b SHA512 42a8ccad09d35dd4677b70005606582207747ae39d62a7ea75e2f5de28f887fee4265c8ae3b38e5cdb3017cc84c8902e2a525ae31fa5dd0aa00369e9b428f563 WHIRLPOOL 2b1d69cb0d4f9f927716d37e43ca216935761dc34aea5629acdba45ad1f7b4673395200721c25c7053ae9e75a3380be31f0d04d0db352a7c176c2296348e9b9d diff --git a/sci-chemistry/votca-csgapps/metadata.xml b/sci-chemistry/votca-csgapps/metadata.xml new file mode 100644 index 000000000000..b555f7427afd --- /dev/null +++ b/sci-chemistry/votca-csgapps/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>junghans@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="github">votca/csgapps</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-1.4.1.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-1.4.1.ebuild new file mode 100644 index 000000000000..4112759a2d55 --- /dev/null +++ b/sci-chemistry/votca-csgapps/votca-csgapps-1.4.1.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit cmake-utils + +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="~amd64 ~x86" +fi + +DESCRIPTION="Extra applications for votca-csg" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="" + +RDEPEND="~sci-chemistry/${PN%apps}-${PV}" + +DEPEND="${RDEPEND}" + +DOCS=( README ) diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-1.4.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-1.4.ebuild new file mode 100644 index 000000000000..9c82b843b301 --- /dev/null +++ b/sci-chemistry/votca-csgapps/votca-csgapps-1.4.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit cmake-utils + +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="amd64 x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="amd64 x86" +fi + +DESCRIPTION="Extra applications for votca-csg" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="" + +RDEPEND="~sci-chemistry/${PN%apps}-${PV}" + +DEPEND="${RDEPEND}" + +DOCS=( README ) diff --git a/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild b/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild new file mode 100644 index 000000000000..3fb54fe5504e --- /dev/null +++ b/sci-chemistry/votca-csgapps/votca-csgapps-9999.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit cmake-utils + +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="" +fi + +DESCRIPTION="Extra applications for votca-csg" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="" + +RDEPEND="~sci-chemistry/${PN%apps}-${PV}" + +DEPEND="${RDEPEND}" + +DOCS=( README ) diff --git a/sci-chemistry/votca-ctp/Manifest b/sci-chemistry/votca-ctp/Manifest new file mode 100644 index 000000000000..a52bb500d9a3 --- /dev/null +++ b/sci-chemistry/votca-ctp/Manifest @@ -0,0 +1,2 @@ +EBUILD votca-ctp-9999.ebuild 1012 SHA256 b89cdab2de96d00c455b25af5de51612a373b13c9306a52557380ff9becb74b9 SHA512 192e30c106f1c43d8edb784b497b830bf4fa8df8c2b9e704f1d76068dea254f3a418338318c1cef2d718a30fa322626550b68fbf604183e33e6ca06f801e58bb WHIRLPOOL a23c432761ebbecb01999bfe92f5d2c32926d23a21bf2d41881fe1837b5808ced648d900fcdd9599afb963b62a0e3b6e837ea078882aafcf4b7693474b6db1ea +MISC metadata.xml 453 SHA256 1450296640fecbb233a5fca2ea5fda8327bf842033ee963fdedabbe25d157005 SHA512 53ace87a281559ae8881b8b010c76801696521de930dcfaf12a5e320456cb4a21a55a7873d173bdb5cc740f3cdbccf1daf62bc83579342f4f23329df7dbd2dba WHIRLPOOL e8e17461069cde6ddef1de7122d7e0db18ffc8452bf659ee3c57dcdfd22168682c70baae7f810bcbc9c402912d6c38547d9050371a7eab907fe4f2816ed034b9 diff --git a/sci-chemistry/votca-ctp/metadata.xml b/sci-chemistry/votca-ctp/metadata.xml new file mode 100644 index 000000000000..7b7ecf654688 --- /dev/null +++ b/sci-chemistry/votca-ctp/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>junghans@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="github">votca/ctp</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/votca-ctp/votca-ctp-9999.ebuild b/sci-chemistry/votca-ctp/votca-ctp-9999.ebuild new file mode 100644 index 000000000000..ba7ad052c5aa --- /dev/null +++ b/sci-chemistry/votca-ctp/votca-ctp-9999.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit cmake-utils multilib + +IUSE="" +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="" +fi + +DESCRIPTION="Votca charge transport module" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" + +RDEPEND=" + =sci-libs/votca-tools-${PV}[sqlite] + =sci-libs/votca-moo-${PV} + =sci-chemistry/votca-csg-${PV}" + +DEPEND="${RDEPEND} + virtual/pkgconfig" + +DOCS=( README NOTICE CHANGELOG.md ) + +src_configure() { + mycmakeargs=( + -DLIB=$(get_libdir) + ) + cmake-utils_src_configure +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA-CTP, J. Chem. Theo. Comp. 7, 3335-3345 (2011)" + einfo "https://dx.doi.org/10.1021/ct200388s" + einfo +} diff --git a/sci-chemistry/votca-xtp/Manifest b/sci-chemistry/votca-xtp/Manifest new file mode 100644 index 000000000000..3ce655cefd71 --- /dev/null +++ b/sci-chemistry/votca-xtp/Manifest @@ -0,0 +1,9 @@ +DIST votca-xtp-1.4.1.tar.gz 15214413 SHA256 3c1d7b94e8c34ceb74310c7c1661f570dbe3a3ad58c118e9c62913c416452978 SHA512 1a3f5df3dc9a7f532464ef84ff4f4f8e60b9495529f349ab5e496595e73fff8f4678b8276b2c5733dd3f692ca03220e7d0bc4a82163017572428c0d1dd5f91fd WHIRLPOOL 2249cebd9cf03f42d0e82d7ab45c04853894ed563d04716fa1b22f472ac6fa8edb6ffce8be3e52cd29489cdbfb17784b2c9a9860bbda113c972a131d2f8caea0 +DIST votca-xtp-1.4.tar.gz 15214266 SHA256 a52bc19ce6168a16a8d3e1e6b6b35de10a266b3b5dccd8afa9c1708629699ddc SHA512 ffc32260331862393e199f7ab643b1008ee4f800cd017f175550a079afaa20e5c929cb8599bc0c2a2328253051895de7b979f5fec044243abc680a0dc87a69b9 WHIRLPOOL 7a28f99d0fc06cbd571c075ec813d085eaa2c8e3cbb0e632b1b38c01c630a75730279ab362764f5ba682324cc1866a7ba87d2b93ab9eb812b9ff7f31eb3ae84a +DIST votca-xtp-manual-1.4.1.pdf 1066873 SHA256 20a4f121c0a3f7f9c139058fb0057d82772cb48ed896d428cc6cb3a3088667e6 SHA512 fdf1147f24785524f5e96020fcd29c32bbeef520eebf6afba32b59d7e777d586c452919478d2734c3f021e558b1147b945cdbc0833402be2b16e5af3a8e37f5f WHIRLPOOL 82778fef7d2ed7d1671d068eab641c4afb5ee7bea851b01cdc25c2ef92b2ec4f33ae1606ab94841304eef886d053e7c122352b0d0b0a95ce4b55fda339e5493a +DIST votca-xtp-manual-1.4.pdf 1064006 SHA256 332fe5ccbbcea0c26f7542a50adbffcbb34e9aec555b67c60102094ae7119c81 SHA512 96d7f59dbcc3a6efdc297237025217d5a56d2c81e491d90680786ea4769a5ebbea379df3b06c4847307ee30accd7415e316dee4730361262f5aff73d2f5d387e WHIRLPOOL 974854581b104d0018d304452fe3d2fbfcfe4c873c3adb4c35139e0413c13aff5364538ac9521ee2e6f65cc256674ba7960d43fddd74cb78e66d893f357b8200 +EBUILD votca-xtp-1.4.1.ebuild 1622 SHA256 451f4f4041e49ddcacc0236a68c225c9ba260e11a1a7c4f16f50d3794249f7fd SHA512 69344b5ebf673b9636006e74e60b810ed193475a95588359c3c20d370048340d054ba5529e82df6d43a6d6fb742ae24c7c8e5f3adc3ba2bd58d205f10a67e14b WHIRLPOOL 6d6c51c1b3a72df9dc9566e12866c4c157531f1b861eb7c24106b89f405874a83219087e5ad14290326b1d2ce16a86d7d74eaefbbbfcb2221d17eb7959bf5832 +EBUILD votca-xtp-1.4.ebuild 1618 SHA256 d447da43e8f2fe3a933965e0a5ddd2aa927467613ac2f977b69e1aed84fc3fb2 SHA512 9388708981c3cd4469ceb7dbc4a1b67780ddc2318f1316ff5fee3824b9f7e03b27c019218af9a9c623839555b05caef32aeef37d58b2b19d643cc775a7caf363 WHIRLPOOL 0306ebeceb61c5548048ad166b70836235bec836724c10022d9003192c78a2501782fb5bf14b1e78b56d6db1e63c20d4f055604ee9e6bcc7f7efa2d2f0746bc7 +EBUILD votca-xtp-9999.ebuild 1564 SHA256 9c1b7aaad72bfde42b77984405d312b0fac520061b5277005a52363227354fa5 SHA512 1c252dd3fea745732263c9c2d284c44794b895ac44c345d0bd7c07c54c0c88f2a1bab79723a3c9f61e850b42a6dceab6790b86b346ba6885c1ef348cf64ee0b7 WHIRLPOOL c2ab78b8a3b6620e7c528315aff77b4da29bd02d00bcb13e676cb0a0bd40659578f8e0e5959e6d558260093aa4572b9b2f854fc2c526c8a1b5214c83f8166f10 +MISC ChangeLog 853 SHA256 09284565012283a07fda2ecc7e485d73fb820a02e3cba9e5006817bbf80ed6d0 SHA512 3cca7abbc0c9a6379448ad262aaab1365d3c64d9288522c6a1e79702e99735a09c59733c94e1351c25e3235019095fa7075ffc2caa5544a645ea6d520fb4037b WHIRLPOOL a0e247fad531ea96308296012b1611eb19cc22a9987e79a9f43b4221e9303bbe146e9d84a4ffd4d4c6e5800402fa2d55ed685e37641fb612fa9c1c63c10a7d54 +MISC metadata.xml 453 SHA256 5f2ab750f2eea2eb3d7372d719f0abf0daf7035aff7512c5825dd7cc6dff1b2d SHA512 892c8f84df6bd19e969b372def9a485be9121d8f7ab410b532529980298e57d0705f73fac409d8f251449cf2119dd3f28133e08d21d0e73b27d5ec0e9a3f205e WHIRLPOOL 8ac49a91cb4ffa734f0ea9c08bf80e3ace99a27eafaac2736bcb978be1bb6a77484c852ba51db181c0e1b9f61ffeba886441538685722550168d1c79530f229b diff --git a/sci-chemistry/votca-xtp/metadata.xml b/sci-chemistry/votca-xtp/metadata.xml new file mode 100644 index 000000000000..1b28210e37ef --- /dev/null +++ b/sci-chemistry/votca-xtp/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>junghans@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="github">votca/xtp</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-chemistry/votca-xtp/votca-xtp-1.4.1.ebuild b/sci-chemistry/votca-xtp/votca-xtp-1.4.1.ebuild new file mode 100644 index 000000000000..6f4425ac7182 --- /dev/null +++ b/sci-chemistry/votca-xtp/votca-xtp-1.4.1.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils multilib + +IUSE="doc" +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz + doc? ( https://github.com/${PN/-//}/releases/download/v${PV}/${PN}-manual-${PV}.pdf )" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="~amd64 ~x86" +fi + +DESCRIPTION="Votca excitation and charge properties module" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" + +RDEPEND=" + =sci-libs/votca-tools-${PV}[sqlite] + =sci-chemistry/votca-csg-${PV}" + +DEPEND="${RDEPEND} + doc? ( + app-doc/doxygen[dot] + dev-texlive/texlive-latexextra + virtual/latex-base + dev-tex/pgf + ) + >=app-text/txt2tags-2.5 + virtual/pkgconfig" + +DOCS=( README NOTICE CHANGELOG.md ) + +src_configure() { + mycmakeargs=( + -DLIB=$(get_libdir) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + if use doc; then + if [[ ${PV} = *9999* ]]; then + cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" manual + newdoc "${S}"/manual/xtp-manual.pdf "${PN}-manual-${PV}.pdf" + else + dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" + fi + cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html + dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html + fi +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA-CTP, J. Chem. Theo. Comp. 7, 3335-3345 (2011)" + einfo "https://dx.doi.org/10.1021/ct200388s" + einfo +} diff --git a/sci-chemistry/votca-xtp/votca-xtp-1.4.ebuild b/sci-chemistry/votca-xtp/votca-xtp-1.4.ebuild new file mode 100644 index 000000000000..17eef63d0d82 --- /dev/null +++ b/sci-chemistry/votca-xtp/votca-xtp-1.4.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils multilib + +IUSE="doc" +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz + doc? ( https://github.com/${PN/-//}/releases/download/v${PV}/${PN}-manual-${PV}.pdf )" + KEYWORDS="amd64 x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="amd64 x86" +fi + +DESCRIPTION="Votca excitation and charge properties module" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" + +RDEPEND=" + =sci-libs/votca-tools-${PV}[sqlite] + =sci-chemistry/votca-csg-${PV}" + +DEPEND="${RDEPEND} + doc? ( + app-doc/doxygen[dot] + dev-texlive/texlive-latexextra + virtual/latex-base + dev-tex/pgf + ) + >=app-text/txt2tags-2.5 + virtual/pkgconfig" + +DOCS=( README NOTICE CHANGELOG.md ) + +src_configure() { + mycmakeargs=( + -DLIB=$(get_libdir) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + if use doc; then + if [[ ${PV} = *9999* ]]; then + cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" manual + newdoc "${S}"/manual/xtp-manual.pdf "${PN}-manual-${PV}.pdf" + else + dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" + fi + cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html + dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html + fi +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA-CTP, J. Chem. Theo. Comp. 7, 3335-3345 (2011)" + einfo "https://dx.doi.org/10.1021/ct200388s" + einfo +} diff --git a/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild b/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild new file mode 100644 index 000000000000..d2c60640d4a0 --- /dev/null +++ b/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit bash-completion-r1 cmake-utils multilib + +IUSE="doc" +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz + doc? ( https://github.com/${PN/-//}/releases/download/v${PV}/${PN}-manual-${PV}.pdf )" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="" +fi + +DESCRIPTION="Votca excitation and charge properties module" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" + +RDEPEND=" + =sci-libs/votca-tools-${PV}[sqlite] + =sci-libs/votca-moo-${PV} + =sci-chemistry/votca-csg-${PV} + =sci-chemistry/votca-ctp-${PV}" + +DEPEND="${RDEPEND} + doc? ( + app-doc/doxygen[dot] + dev-texlive/texlive-latexextra + virtual/latex-base + dev-tex/pgf + ) + >=app-text/txt2tags-2.5 + virtual/pkgconfig" + +DOCS=( README NOTICE CHANGELOG.md ) + +src_configure() { + mycmakeargs=( + -DLIB=$(get_libdir) + -DBUILD_XTP_MANUAL=$(usex doc) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + if use doc; then + [[ ${PV} != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf" + cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html + dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html + fi +} + +pkg_postinst() { + einfo + einfo "Please read and cite:" + einfo "VOTCA-CTP, J. Chem. Theo. Comp. 7, 3335-3345 (2011)" + einfo "https://dx.doi.org/10.1021/ct200388s" + einfo +} diff --git a/sci-chemistry/wxmacmolplt/Manifest b/sci-chemistry/wxmacmolplt/Manifest new file mode 100644 index 000000000000..e250d7b49fe9 --- /dev/null +++ b/sci-chemistry/wxmacmolplt/Manifest @@ -0,0 +1,6 @@ +AUX wxmacmolplt-7.5-glew.patch 415 SHA256 3c9f186bcc26a8ad055303be34d407d842b2ca51fec604989af11c1c560c068e SHA512 4d15247fbb5c2d9a60e7427b2c2f91d8a8f82cc457c681687f3046eda8e913125a0e041fd5d28744e0b12fe96b71280432b27bcdea5b7a8af7718b2f2d820d9e WHIRLPOOL f988892efd78d4f3ac9dcfdc048434802941731683db7a5d094bee65fd58bba46d884ea305130daba8004ef258edcb90d0e3a3b7cc8ad830fec962a2a3ec7b1c +DIST wxmacmolplt-7.5.tar.gz 1965376 SHA256 df74762d106e4b44bba8ced84d2df78848052fea543937c51297479fa98fc787 SHA512 a1064d5068136b2a91328c7f912ff57d4741081d6d61437e7b4567fbf732917485b391493d637b8892bdad50b539363cfa9c778bb35407a9c0a2bfed20e42bc0 WHIRLPOOL 9cda289232f7323819b7426dc17532396e633514e292e11f71404f380f174c1439b788bffff594f8d9a72cc0ddca48d799a173ff14a9b783edb8bc64f0b4e04c +EBUILD wxmacmolplt-7.5-r1.ebuild 968 SHA256 ef56ef59d7cd05d940d4f71e2292554fff444a7e152b8620f7fc4468dfbfd7b1 SHA512 a9b24d109de51684443e398ee3841ade82f76c1ae4513480cdfb2e71cbad3bdeebf508db38457bee4a6cc811b4a41c643a027c3d9dcd69a2ff0daa532d9ba51e WHIRLPOOL 2444d871fb91c458ff22739b2d089be99130f6f7a14c8255540978c666567d4130176cbaca0ed9aae63333c08d89866849b90603ee7b523ec047fc0c39b651f8 +MISC ChangeLog 3178 SHA256 03ed5a36bf3935d1fb1ae5dddd4d181af606fa78a5d3a194307e15b64a4b6500 SHA512 3dfe6f81a84db20806b65a101b1e95510c9f61436fa043c5e1896701ede03b3b4d3807337cacfec7d584365ffb208c4ec2a3b17163982aadb98f0e472036a60a WHIRLPOOL 9232d61a70647b3f56b0dab1d12d83d26d9c4613ffd48f703ade3d32c61fc669e37d9218823e3c8b959006bb715530ef032abef33ab0c62dc73d734be2bcaf56 +MISC ChangeLog-2015 2459 SHA256 e939561b045dd78a7068e824654c0a8fbd91345b3b8647c10ccdbb6d46bdf283 SHA512 010620184797f97e6adb5c143b7a31b66115097074f99f837656db09fe2a5ba3eebf3825ed18a7582e2f471605af23d24ad691bc005191a174dfbcca42d8425b WHIRLPOOL 5f01f8d40ad67c368023a3a962a53e07d57002b3959cf66965d1f3380842277adca9e4a393d2ae680ad24fefd7831dc2357026def12f6b29c84ed4e2ee46b6e6 +MISC metadata.xml 754 SHA256 e27039d0fdccc5306638f2a20d2f88c9408e0250c7e55db6dd02a4f959343066 SHA512 b5cd355851122f768fe0670518df7d4dbc2bd0a04c057acd95d25c3beedd8483d40dbd95b3d3090904b4e4d6289153731d8b0aa0c4753ee9614f1d693a409486 WHIRLPOOL bfc3572592dac86464690d3bb973ef811cb2ef6f0fb1de46f8effe433315cf44b7c215952b340be7192ac1c217376706c86defe193f04d401b2b40b482c18336 diff --git a/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch b/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch new file mode 100644 index 000000000000..08986db5bff2 --- /dev/null +++ b/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch @@ -0,0 +1,12 @@ +diff -urN wxmacmolplt-7.4.2.orig/configure.ac wxmacmolplt-7.4.2/configure.ac +--- wxmacmolplt-7.4.2.orig/configure.ac 2010-12-05 02:48:29.000000000 +0300 ++++ wxmacmolplt-7.4.2/configure.ac 2010-12-06 19:30:24.000000000 +0300 +@@ -20,7 +20,7 @@ + ;; + *) + HOST=LINUX +- LIBGL="-lGL -lGLU" ++ LIBGL=`pkg-config --libs glu glew` + ;; + esac + AM_CONDITIONAL(HOST_IS_MSW, [test "x$HOST" == xMSW]) diff --git a/sci-chemistry/wxmacmolplt/metadata.xml b/sci-chemistry/wxmacmolplt/metadata.xml new file mode 100644 index 000000000000..4fa3624287b4 --- /dev/null +++ b/sci-chemistry/wxmacmolplt/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +wxMacMolPlt is a program for plotting 3D molecular structures and normal modes (vibrations), various orbitals and electron density maps. It reads a variety of file formats including any GAMESS input, log or IRC file directly to create animations. It has a simple GAMESS input (.inp) builder and a primitive molecule builder. +</longdescription> + <use> + <flag name="flash">Add support for flash movie generation using <pkg>media-libs/ming</pkg></flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild b/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild new file mode 100644 index 000000000000..17f69a8387ae --- /dev/null +++ b/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +WX_GTK_VER=3.0 + +inherit autotools eutils wxwidgets + +DESCRIPTION="Chemical 3D graphics program with GAMESS input builder" +HOMEPAGE="http://www.scl.ameslab.gov/MacMolPlt/" +SRC_URI="https://wxmacmolplt.googlecode.com/files/${P}.tar.gz" + +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86" +SLOT="0" +IUSE="flash" + +RDEPEND=" + media-libs/glew:0= + media-libs/mesa + x11-libs/wxGTK:${WX_GTK_VER}[X,opengl] + flash? ( media-libs/ming )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + need-wxwidgets unicode + epatch "${FILESDIR}"/${P}-glew.patch + sed \ + -e "/^dist_doc_DATA/d" \ + -i Makefile.am || die "Failed to disable installation of LICENSE file" + eautoreconf +} + +src_configure() { + econf \ + --with-glew \ + $(use_with flash ming) +} + +src_install() { + default + doicon resources/${PN}.png + make_desktop_entry ${PN} wxMacMolPlt ${PN} "Science;DataVisualization;" +} diff --git a/sci-chemistry/xds-bin/Manifest b/sci-chemistry/xds-bin/Manifest new file mode 100644 index 000000000000..f04011e1c646 --- /dev/null +++ b/sci-chemistry/xds-bin/Manifest @@ -0,0 +1,6 @@ +DIST XDS-INTEL64_Linux_x86_64-20170930.tar.gz 9501598 SHA256 f0fb97c25283e0c2502b5ebb0839e207de7402d0c8f1b8afab6abb9881a74bea SHA512 8da1d75633e8bf8495c30926a622f57aa0a51ea3b724101c96da6fae0a303860a4a4a8eaf3ecdf66948f18e702211aab3800760ca498c4562e947e3f94c25a4d WHIRLPOOL df7a32b3d9119a2d82d64899e534a0439b41145021147b7a0ebcc5b0892dd70103dac4ed9f2cd06e1ef7a937e743dc3e099607739abcbcc15d9e8996fd4b68c7 +DIST XDS_html_doc-20170930.tar.gz 117249 SHA256 33f39d2e4daa9ad40732ca827e905ef4f0190a532cf27fc2f5193749c098bf78 SHA512 bbc24eeb0f8a63e6186906b0c0ee67efa83d1cdd169b091878c323455e2448ee6cb1667467bc9701b4e1839af2d10d4cb3e8f8d080b7dd5e449fda03c2aa8f89 WHIRLPOOL de7ca492f4789f93f0e430022a5c9890008f53d0997d36895aea6eee214f98551c92f659331195441573aa40f5d54699bdae14d987b2f37ea5feecebb27989a5 +EBUILD xds-bin-20170930.ebuild 1233 SHA256 93c2698135e2b7f3ff6767d464e9f17b8b5bb0deac653b79e46be57611418623 SHA512 1edab97138ecfa5dd75f4eabe1498b7db18a88b45cb4da1639551dd5e05822c7517bf1b79d5a4651c9a0872dde2330add629d946aa209b8eb4144eab8947faa5 WHIRLPOOL 2160c46876b31b407e59dde01f6ef6362dae976943f1b4136d1e751c56f4a56fb8ec260461997e82eb1f5ab302e855c19d41295680bfbd4c9f77e12fdf43b97c +MISC ChangeLog 2901 SHA256 938caa8b9dfc449b7765461f5115079c42fe4948003b21099447380fbc7f61e7 SHA512 d69622a4257539fcd88638f7e9a58fa1414553ace7ae3a5e14db9e563a61691a012a68c9ba346880347900f46420e54d776352fb6e254f9cb8257aac6ab77afa WHIRLPOOL d050c231f9a73f7c587589947c51001d4c8deff55e4ba7e650e3d7ebbe8fcee294dc01a6a3a0ddc2a1a923adbbf85acc7b1a3024eedf2d83f2b2e5479997c943 +MISC ChangeLog-2015 2857 SHA256 dd4545770b75abd879bc2c3e19e35045fbc37039548e3071eab0b98cfd6a0092 SHA512 ea3f1ef457faf38cb1d9f4431d8b63366fe7fe154db5b89c7ef71672269a443a3d38be2945597d1a6de90f0880cbb68e559d0719caef25b1f96d7d3dfdd67409 WHIRLPOOL b3dd63f60ebd70e715f74ff96a5464c313adf33a74b7dd8aac81e735663dda26aa6c0f0b46ed21a4b3b4acd46a179133f4f28872330737b94ff062d947db0686 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/xds-bin/metadata.xml b/sci-chemistry/xds-bin/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/xds-bin/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/xds-bin/xds-bin-20170930.ebuild b/sci-chemistry/xds-bin/xds-bin-20170930.ebuild new file mode 100644 index 000000000000..9478c991983f --- /dev/null +++ b/sci-chemistry/xds-bin/xds-bin-20170930.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="Software for processing single-crystal X-ray monochromatic diffraction data" +HOMEPAGE="http://xds.mpimf-heidelberg.mpg.de/" +SRC_URI=" + ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz -> XDS-INTEL64_Linux_x86_64-${PV}.tar.gz + ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS_html_doc.tar.gz -> XDS_html_doc-${PV}.tar.gz" + +LICENSE="free-noncomm" +SLOT="0" +KEYWORDS="-* ~amd64" +IUSE="smp X" + +RDEPEND="X? ( sci-visualization/xds-viewer )" +DEPEND="" + +QA_PREBUILT="opt/xds-bin/*" + +src_unpack() { + default + mv XDS-* "${S}" || die +} + +src_install() { + local HTML_DOCS=( "${WORKDIR}"/XDS_html_doc/. ) + einstalldocs + + local i suffix=$(usex smp '_par' '') + exeinto /opt/${PN} + doexe * + + for i in xds mintegrate mcolspot xscale; do + dosym ../${PN}/${i}${suffix} /opt/bin/${i} + done + + for i in 2cbf cellparm forkcolspot forkintegrate merge2cbf pix2lab xdsconv; do + dosym ../${PN}/${i} /opt/bin/${i} + done + + insinto /usr/share/${PN}/INPUT_templates + doins -r "${WORKDIR}"/XDS_html_doc/html_doc/INPUT_templates/. +} + +pkg_postinst() { + elog "This package will expire on September 30, 2017" +} diff --git a/sci-chemistry/xdsgui/Manifest b/sci-chemistry/xdsgui/Manifest new file mode 100644 index 000000000000..727411a1b717 --- /dev/null +++ b/sci-chemistry/xdsgui/Manifest @@ -0,0 +1,6 @@ +DIST xdsgui-0_p130530.32 10372936 SHA256 f9af76a1e4ef96ac5930a0f51f0052ecf02b0a2496ce832403c31b216a033ebd SHA512 f9ef5d914afb8e6a64f936508fee2e84f4e579898726774dc995e920e5a953341c48022e8078eb60f9a2a288190765949da03f394f221a48916d12dc26a898b1 WHIRLPOOL d7792edfcd273c37569c303e6c4f5acf9d832d4bc4f67048a063a25894e375f1dc1b612f879edc14e3c7fdc6ddda84f25990cb8a3d3fbea35f1784835a3febc5 +DIST xdsgui-0_p130530.64 12220790 SHA256 333de2bc7dd88051a43a912dc6e0903bdc17d0d32c16f8c175fa9ec27289f76a SHA512 bd54ddacf44a9156306354249c5b1b61deb9b1f9ebdad879b98d01354ccb51ab60c183e3c58c2be2bb1a42b55b96cea470ee70538110f0fc1b9e3b46ffce3d40 WHIRLPOOL 1002646b1e22cfad35f81287602c496d8d5c323cf9285604ceb9f3717e2a2b1416e9d1f9ef730e0284d972e4f090752a0d41b9bfcefa403a8d746bbc84b3feb2 +EBUILD xdsgui-0_p130530.ebuild 906 SHA256 c0e52a347c0ac1b86eb69d9d10871cf56758ea8a08774924743927ce80c63219 SHA512 335a7fd6d15f03e475712738a88fc5554cba9ae5a3589557ddf9afaf4100399946ccd0a4a20a4937cfa10d9e436690cf3113a7b94d8f09a96a12bcd88342d0b0 WHIRLPOOL 5184db1e66082e241283f4a2330130935a043f5ac88ad9951b8a29af41b0d29ccb7b3ca9be5f6384d7cb75e661ced90d25fc6ac91b03dbe364747f6faafe1588 +MISC ChangeLog 2760 SHA256 6ddce00efe4f6f112b223a0a7b35b0ec3f6282da381c22310b41b97a7959b79f SHA512 54ab65ee449cc4a7f5d60a6980ea1e328a545780c1b9c6947bc83a2198554b159b7f8b25ffabbd0903989bf8cf6a8ed1afaeee1f3a8c3a8a25023a5f1ed063de WHIRLPOOL deac9aceec4b9fd40e86fa87b98e17f115526ea00f52dee28d8579b94b0672999edf372869b3364a3c6fa22c5f2617980eafb0309761f1c758cca43311fbed8e +MISC ChangeLog-2015 614 SHA256 d6309b7b2d449796ba2e4056041a83345d17cdecf4b173afd8028bfcd0f66813 SHA512 83c981f446b1025f09408ea0c589217184e7f2f31ba8f491505199ec8cdfc55e38facf1d450a0bff85c4232cfc8efeddec7e28b68abdee5ede6b5d8f1cac13a7 WHIRLPOOL 7ca2b95360ca89060499fc3ab3f389c8f64fe0b7ddbc2282b271131cf2c67657ce8c534a24d383e989b875b11986295795bb9b841c8ea9f5f9f5cfabd7959bc4 +MISC metadata.xml 687 SHA256 a0f92d3fb9e3302ef9696e7f4617b2d59dc1019f86dcc05d86417033d4de3d8d SHA512 ea98e543b3b037ab8e94099dc0a6cd69e1423fb622bb87ccd4b44569e1878bfa400f1a0e0c1f8f3325ec12d6c43c2dba3379f24de2734de866a02e595c771c35 WHIRLPOOL 07ab48e717e88e579b062942eba4ccb7fc07656fd42e659632590dbbe67a2ade1960b6b7d48155c0f5ed205cdcbbcae2ca3491fc909a4eb86fb3a36cd4a3687c diff --git a/sci-chemistry/xdsgui/metadata.xml b/sci-chemistry/xdsgui/metadata.xml new file mode 100644 index 000000000000..6eab78d31188 --- /dev/null +++ b/sci-chemistry/xdsgui/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +XDSgui is a GUI (graphical user interface) for XDS that is supposed to help both +novice and experienced users. It graphically displays the ASCII and cbf files +that XDS writes, and can run useful shell commands with a simple mouse click. +The design goal of the program is to enable XDS data processing without the +commandline, and to supply additional graphical information. +</longdescription> +</pkgmetadata> diff --git a/sci-chemistry/xdsgui/xdsgui-0_p130530.ebuild b/sci-chemistry/xdsgui/xdsgui-0_p130530.ebuild new file mode 100644 index 000000000000..116ce867545b --- /dev/null +++ b/sci-chemistry/xdsgui/xdsgui-0_p130530.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +DESCRIPTION="GUI for XDS that is supposed to help both novice and experienced users" +HOMEPAGE="http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XdsGUI" +SRC_URI=" + amd64? ( ftp://turn5.biologie.uni-konstanz.de/pub/xdsGUI.rhel6.64 -> ${P}.64 ) + x86? ( ftp://turn5.biologie.uni-konstanz.de/pub/xdsGUI.rhel6.32 -> ${P}.32 )" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="-* ~amd64 ~amd64-linux" +IUSE="" + +RDEPEND=" + dev-qt/qtcore:4 + dev-qt/qtgui:4 + dev-util/xxdiff + sci-chemistry/xds-bin + sci-chemistry/xdsstat-bin + sci-visualization/xds-viewer" +DEPEND="" + +S="${WORKDIR}" + +QA_PREBUILT="opt/bin/*" + +src_unpack() { + if use amd64; then + cp -rf "${DISTDIR}"/${P}.64 ${PN} || die + elif use x86; then + cp -rf "${DISTDIR}"/${P}.32 ${PN} || die + fi +} + +src_install() { + exeinto /opt/bin + doexe ${PN} +} diff --git a/sci-chemistry/xdsstat-bin/Manifest b/sci-chemistry/xdsstat-bin/Manifest new file mode 100644 index 000000000000..c822d701d529 --- /dev/null +++ b/sci-chemistry/xdsstat-bin/Manifest @@ -0,0 +1,6 @@ +DIST xdsstat-linux32.bz2 235255 SHA256 366b9565a172b9ab756e1669a353003c74b9e0341bba5b1822fef775a35e1290 SHA512 233c25b60501f794887a09960e2e8377c0443bce661c769624d8afcde288b58968b3406cc7e1bb02f0de010f4e6555ef0641fd5ebcfdd5f6396ec21a22c32985 WHIRLPOOL a304fd23eaf3d8292f3bc414e6bc1c1b5895590b4235e637d357a4a462c91939195fd99764b4233775f1dd6d65601391d4c6328fe578734dae498e6f382e96f7 +DIST xdsstat-linux64.bz2 256555 SHA256 45408d09cb13ec664e863863ec66a1cece204308e074f29f54f922d804f042f9 SHA512 d5b3043bec30a17f6960308d642a3721f7a73bc851a71ec28a813b5a98f2de4f215d3603e8da4a9bcb949cfa15030c3eac108bc5549ebdef6737885e60dbd626 WHIRLPOOL 5d81ba5998e6c527978f10e0aa2ded7c8ada53beb6340ba592d74b34a64a81e17c0184d101dc7698d4771458d0e27559fb857fd329be8eb95a4f75136f549790 +EBUILD xdsstat-bin-140225.ebuild 699 SHA256 a52d5d15347b8d3b79427907bc3f3c227444de8944388789f685973f42644357 SHA512 2bf1fff52d13808c572730a81b07bc8ee60d83acdd1b51e86ef30e9ba0a8a20694ca50a724d3d765aec7fc2e46cbb306ec926564f2821601bc95991b4a169a6a WHIRLPOOL be70b77dacf1c83be7154763c72fd05b9a3c6f65eb65c98de6b9e1b5767752f001d82ec13a8d4f81e0c7fd4b0898d97d8ce79ca57c0c73c2d402e96c1d22024e +MISC ChangeLog 2771 SHA256 d0e801bf1dd595f9f6adcb2cde6ebed42a4cef5d14d79374f08e7db946280d47 SHA512 1a8c53f4a4d3b9ffff458f20b512238f3378b653f3ea30022dd6c19b94cf55f6de674048f0a48aa50f39d70a9b5ad2e2c6d57c15352c162220c5a13697e03a2a WHIRLPOOL b4efa1eafa64c2a77565db20b8cb372bea69e718d49bb02addf0cf00972ac22221b9e0fb80b20c40ebf275ff70908e0a376fe879ddb820159e5f3780dc72d789 +MISC ChangeLog-2015 919 SHA256 91c1648f1a136eeb46bc930a02bc5fc9f41a50eab3f74aee75333c082d66de26 SHA512 c7019a73f3e4bc8983c5477bb77b156ecc7760f59e3cafaf5d82ecb7dd98bdbafafeee0e04157349b0bcf7b1927e9a401e1b26e0c3ec9b00ea489d1ecd31ce8f WHIRLPOOL 88339131750b47fe36c0e8f356afbc13105a82ad88a513d2507d9de95aaf30237c451663641f161bcde51929cf08cd9d69448de81c13a9c3bdf9d93349721aff +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/xdsstat-bin/metadata.xml b/sci-chemistry/xdsstat-bin/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/xdsstat-bin/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/xdsstat-bin/xdsstat-bin-140225.ebuild b/sci-chemistry/xdsstat-bin/xdsstat-bin-140225.ebuild new file mode 100644 index 000000000000..57619af5341b --- /dev/null +++ b/sci-chemistry/xdsstat-bin/xdsstat-bin-140225.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +MY_PN="${PN/-bin}" + +DESCRIPTION="Prints various statistics (that are not available from XDS itself)" +HOMEPAGE="http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSSTAT" +SRC_URI=" + amd64? ( ftp://turn5.biologie.uni-konstanz.de/pub/${MY_PN}-linux64.bz2 ) + x86? ( ftp://turn5.biologie.uni-konstanz.de/pub/${MY_PN}-linux32.bz2 ) +" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64 ~amd64-linux" +IUSE="" + +RDEPEND="sci-chemistry/xds-bin" +DEPEND="" + +RESTRICT="mirror" + +QA_PREBUILT="opt/bin/*" + +S="${WORKDIR}" + +src_install() { + exeinto /opt/bin + newexe ${MY_PN}* ${MY_PN} +} diff --git a/sci-chemistry/xyza2pipe/Manifest b/sci-chemistry/xyza2pipe/Manifest new file mode 100644 index 000000000000..55327cbbc958 --- /dev/null +++ b/sci-chemistry/xyza2pipe/Manifest @@ -0,0 +1,6 @@ +AUX xyza2pipe-20121001-gentoo.patch 3974 SHA256 3886b6e12fc799eac67e2405ab298328a9f91c6eee868e8fe0ad8b2302024133 SHA512 7b8be1fd799d65e9a600766afb21e95a4722eff8a657f88d0adaf5aaf11ed369f6d8a27f3e003337570837abc45cfa9e758d1219af275773f79b81d1c1c322c4 WHIRLPOOL f59c5cb20c4546e96ce4a0fe88109306f99fd8f9f8218f50d592afa05327d5e3b74e910d00785e9070dd6af131b20799248112883edbee708203a7e7620334ad +DIST xyza2pipe-20121001.tgz 61002 SHA256 c2e2d83dc6f0424afe519aa0ba83922f1c6d1b90933edf5d62722ac56af3b1de SHA512 b64abf46a8d7f3530eecaeec3bc8b143600c6823174a22727868087c2f7f17af0b538a0521e3a29806dc608b003948a1e31296ab395bc3c0089c5dc7a391d855 WHIRLPOOL fec47032811c81709d996712b938ed315e67435d72ae91c1ce2a01546c62eae4868d7e430585cd4f1830e158a8a994e23af02e6f23a897d44f98a81b2889baac +EBUILD xyza2pipe-20121001.ebuild 686 SHA256 dacf176f29a0807ca83d774d2fca0f9d74edd4231ac7bb58004c96d3956b87f4 SHA512 407fcfd20d9bc7c4ed85b6a8838996ec014d5c631f355be88d67f3cd42376617716286f43ecb01d1acba866f49d232ddf8c1d7e3b44975b1d552baaaa9fc9fe2 WHIRLPOOL 6ac54e032185056b89d1f75b6aad4aeaa6d95d5f981d2957f0a7f6a9dc940a5d8f6b66ffa230bcfab5994ea3c61a0b5e4efcdf98244a7458302ec3e830c14dcd +MISC ChangeLog 2718 SHA256 20b3a8c4b767761b81ad6dca4f74f10cecdf8ad3c038654ca9507eca00c95916 SHA512 3bd7ad3f7844f74e1ec60fed1a5606e69fe77275bce43eccbcb7b4c5fdec5a54be47358538ede704c0cf778d6f55b4c23b0100f910580eb223cf2f580a007cb8 WHIRLPOOL 0effcc713b1f9661f84b1a9834db9627377525a8d392737d570ac5e33f4df61384ef07c1d7a44c384ac0f96c9309bd4ddf6bfa40e0a10623b796fc4debe0452c +MISC ChangeLog-2015 572 SHA256 19e878f0ec6aac0ffb6d8cbc33f5cbde29622ffba731bccf003a7c3834fefb3b SHA512 1c5e958721108b493d6b772e7d3af99e24467e2e62c6f42e61535b6e270e88085f78535af78d662a1d48689aa1c2fbafb76d7a4fd67871402ee14e05a01080d3 WHIRLPOOL f6fb2a77aa3ef702d9d5c1d9383240f8686c630c087ceda83cfad049d08ada6a3b995153b10cd6b2edb56a24f570078c6764311cb122adbd9456cb67b9241432 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch b/sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch new file mode 100644 index 000000000000..ec4220dd0695 --- /dev/null +++ b/sci-chemistry/xyza2pipe/files/xyza2pipe-20121001-gentoo.patch @@ -0,0 +1,168 @@ + Makefile | 106 +++++++++++++++++++++++++++++++++++++-------------------------- + 1 file changed, 63 insertions(+), 43 deletions(-) + +diff --git a/Makefile b/Makefile +index 15d4bd3..e738ec2 100644 +--- a/Makefile ++++ b/Makefile +@@ -4,7 +4,7 @@ + # Last modified: Feb/22/2012 + # + +-CFLAGS = -O3 ++CFLAGS ?= -O3 + MFLAGS = -lm + + TARGETS = xyza2pipe ucsf2pipe nv2pipe xeasy2pipe azara2pipe vnmr2pipe xwnmr2pipe\ +@@ -62,89 +62,109 @@ clean: + rm -f $(TARGETS) addxyza2pipe + + $(OBJECTS_MATH): +- $(CC) $*.c -c -o $@ $(CFLAGS) -D__XYZA2PIPE__ ++ $(CC) $(CPPFLAGS) -D__XYZA2PIPE__ $(CFLAGS) $*.c -c -o $@ + + .o: +- $(CC) $< -c -o $@ $(CFLAGS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $< -c -o $@ + + xyza2pipe: $(OBJECTS_C) $(OBJECTS_XP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + pipe2xyza: $(OBJECTS_C) $(OBJECTS_PX) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + ucsf2pipe: $(OBJECTS_C) $(OBJECTS_UP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + pipe2ucsf: $(OBJECTS_C) $(OBJECTS_PU) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + nv2pipe: $(OBJECTS_C) $(OBJECTS_NP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + pipe2nv: $(OBJECTS_C) $(OBJECTS_PN) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + xeasy2pipe: $(OBJECTS_C) $(OBJECTS_EP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + pipe2xeasy: $(OBJECTS_C) $(OBJECTS_PE) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + azara2pipe: $(OBJECTS_C) $(OBJECTS_AP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + pipe2azara: $(OBJECTS_C) $(OBJECTS_PA) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + vnmr2pipe: $(OBJECTS_C) $(OBJECTS_VP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + xwnmr2pipe: $(OBJECTS_C) $(OBJECTS_BP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + pipe2proj: $(OBJECTS_C) $(OBJECTS_PJ) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + add2pipe: $(OBJECTS_C) $(OBJECTS_DXP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + rm -f addxyza2pipe + ln -s add2pipe addxyza2pipe + + adducsf2pipe: $(OBJECTS_C) $(OBJECTS_DUP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + addnv2pipe: $(OBJECTS_C) $(OBJECTS_DNP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + addxeasy2pipe: $(OBJECTS_C) $(OBJECTS_DEP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + addazara2pipe: $(OBJECTS_C) $(OBJECTS_DAP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + addvnmr2pipe: $(OBJECTS_C) $(OBJECTS_DVP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ + + addxwnmr2pipe: $(OBJECTS_C) $(OBJECTS_DBP) +- $(CC) $@.c $^ -o $@ \ +- $(CFLAGS) $(MFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $@.c $^ -o $@ \ ++ $(MFLAGS) ++ mv -v $@ bin/ diff --git a/sci-chemistry/xyza2pipe/metadata.xml b/sci-chemistry/xyza2pipe/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/xyza2pipe/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild b/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild new file mode 100644 index 000000000000..033619474de5 --- /dev/null +++ b/sci-chemistry/xyza2pipe/xyza2pipe-20121001.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Cross conversion environment of NMR spectra" +HOMEPAGE="http://fermi.pharm.hokudai.ac.jp/olivia/api/index.php/Xyza2pipe_src" +SRC_URI="http://fermi.pharm.hokudai.ac.jp/olivia/documents/xyza2pipe.tgz -> ${P}.tgz" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="olivia" +IUSE="" + +S="${WORKDIR}"/${PN} + +PATCHES=( "${FILESDIR}"/${P}-gentoo.patch ) + +src_prepare() { + default + tc-export CC + mkdir bin || die +} + +src_install() { + local i + dodoc README FEEDBACK + cd bin || die + for i in *; do + newbin ${i}{,-olivia} + done +} |