commit: 7e02f5e90dc6463bd249131c9b8307343e481147 Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> AuthorDate: Mon Mar 28 09:34:30 2022 +0000 Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> CommitDate: Mon Mar 28 09:34:30 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7e02f5e9
sci-chemistry/mm-align: treeclean Closes: https://bugs.gentoo.org/834301 Closes: https://bugs.gentoo.org/723194 Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org> profiles/package.mask | 5 ----- 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 | 23 ---------------------- 5 files changed, 60 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 12dc681fb20b..d90ab8b095ca 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -351,11 +351,6 @@ sci-chemistry/votca-ctp # Bug #834317. Removal on 2022-03-31. dev-libs/injeqt -# Sam James <s...@gentoo.org> (2022-02-27) -# Fails to build with modern GCC, stuck on cmake-utils.eclass too. -# bug #723194, bug #834301. Removal on 2022-03-27. -sci-chemistry/mm-align - # Andreas Sturmlechner <ast...@gentoo.org> (2022-02-27) # No revdeps since begin of gentoo.git history, outdated and unmaintained. # Bug #834307. Removal on 2022-03-29. diff --git a/sci-chemistry/mm-align/Manifest b/sci-chemistry/mm-align/Manifest deleted file mode 100644 index 97e91d4c9433..000000000000 --- a/sci-chemistry/mm-align/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST MM-align-20120321.tar.xz 20072 BLAKE2B be53cff43b220c9c44bbd600e4e2870e3987da25744a4bf3da0bc8cf7bc2619c93839e27327d23b5ef3bfbf9aca86b865717c48eb5d91a9da7b977909fb3bc39 SHA512 193c3b16b2d9fb0aaacf18b203fcf0240de7b11b4c0ce99fc571c277aa6e624b7b8b4df625e34433a5dec4349bb5bf6ae0368609c1738337923cf3b4d06428bc diff --git a/sci-chemistry/mm-align/files/CMakeLists.txt b/sci-chemistry/mm-align/files/CMakeLists.txt deleted file mode 100644 index 635ffdd67418..000000000000 --- a/sci-chemistry/mm-align/files/CMakeLists.txt +++ /dev/null @@ -1,5 +0,0 @@ -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 deleted file mode 100644 index 03c48e987ffb..000000000000 --- a/sci-chemistry/mm-align/metadata.xml +++ /dev/null @@ -1,26 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemis...@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 deleted file mode 100644 index d2b42fe2547e..000000000000 --- a/sci-chemistry/mm-align/mm-align-20120321.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# 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 -}
