diff options
Diffstat (limited to 'sci-chemistry/tm-align')
| -rw-r--r-- | sci-chemistry/tm-align/Manifest | 8 | ||||
| -rw-r--r-- | sci-chemistry/tm-align/files/CMakeLists.txt | 6 | ||||
| -rw-r--r-- | sci-chemistry/tm-align/metadata.xml | 24 | ||||
| -rw-r--r-- | sci-chemistry/tm-align/tm-align-20140601.ebuild | 24 | ||||
| -rw-r--r-- | sci-chemistry/tm-align/tm-align-20150914.ebuild | 24 |
5 files changed, 86 insertions, 0 deletions
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 +} |