From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001 From: "Robin H. Johnson" Date: Sat, 8 Aug 2015 13:49:04 -0700 Subject: proj/gentoo: Initial commit MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson X-Thanks: Alec Warner - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring - wrote much python to improve cvs2svn X-Thanks: Rich Freeman - validation scripts X-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed --- sci-chemistry/mm-align/Manifest | 1 + sci-chemistry/mm-align/files/CMakeLists.txt | 5 +++++ sci-chemistry/mm-align/metadata.xml | 26 +++++++++++++++++++++++++ sci-chemistry/mm-align/mm-align-20120321.ebuild | 22 +++++++++++++++++++++ 4 files changed, 54 insertions(+) create mode 100644 sci-chemistry/mm-align/Manifest create mode 100644 sci-chemistry/mm-align/files/CMakeLists.txt create mode 100644 sci-chemistry/mm-align/metadata.xml create mode 100644 sci-chemistry/mm-align/mm-align-20120321.ebuild (limited to 'sci-chemistry/mm-align') diff --git a/sci-chemistry/mm-align/Manifest b/sci-chemistry/mm-align/Manifest new file mode 100644 index 000000000000..a1e08c44269c --- /dev/null +++ b/sci-chemistry/mm-align/Manifest @@ -0,0 +1 @@ +DIST MM-align-20120321.tar.xz 20072 SHA256 0158a93a06257b885630ab7bed3b7bf8dca2ee12217c84d019829a1e34f3eeb3 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..2634f696a953 --- /dev/null +++ b/sci-chemistry/mm-align/metadata.xml @@ -0,0 +1,26 @@ + + + + sci-chemistry + + jlec@gentoo.org + + +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. + + 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..c0ef57c832af --- /dev/null +++ b/sci-chemistry/mm-align/mm-align-20120321.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit cmake-utils fortran-2 + +DESCRIPTION="Protein Complex Structural Alignment" +HOMEPAGE="http://zhanglab.ccmb.med.umich.edu/MM-align/" +SRC_URI="http://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 +} -- cgit v1.2.3-18-g5258