[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mm-align/, profiles/, sci-chemistry/mm-align/files/

[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mm-align/, profiles/, sci-chemistry/mm-align/files/

[Jakov Smolić]

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 <sam@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 <asturm@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 # No revdeps since begin of gentoo.git history, outdated and unmaintained.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-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
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
-}