From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-chemistry/pymol-plugins-msms/Manifest | 6 +++ .../pymol-plugins-msms/files/100415-msms.patch | 33 +++++++++++++++++ sci-chemistry/pymol-plugins-msms/metadata.xml | 17 +++++++++ .../pymol-plugins-msms-100415-r1.ebuild | 43 ++++++++++++++++++++++ 4 files changed, 99 insertions(+) create mode 100644 sci-chemistry/pymol-plugins-msms/Manifest create mode 100644 sci-chemistry/pymol-plugins-msms/files/100415-msms.patch create mode 100644 sci-chemistry/pymol-plugins-msms/metadata.xml create mode 100644 sci-chemistry/pymol-plugins-msms/pymol-plugins-msms-100415-r1.ebuild (limited to 'sci-chemistry/pymol-plugins-msms') 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 @@ + + + + + sci-chemistry@gentoo.org + Gentoo Chemistry Project + + +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 + + 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 +} -- cgit v1.2.3