1 |
commit: 7e02f5e90dc6463bd249131c9b8307343e481147 |
2 |
Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> |
3 |
AuthorDate: Mon Mar 28 09:34:30 2022 +0000 |
4 |
Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> |
5 |
CommitDate: Mon Mar 28 09:34:30 2022 +0000 |
6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7e02f5e9 |
7 |
|
8 |
sci-chemistry/mm-align: treeclean |
9 |
|
10 |
Closes: https://bugs.gentoo.org/834301 |
11 |
Closes: https://bugs.gentoo.org/723194 |
12 |
Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org> |
13 |
|
14 |
profiles/package.mask | 5 ----- |
15 |
sci-chemistry/mm-align/Manifest | 1 - |
16 |
sci-chemistry/mm-align/files/CMakeLists.txt | 5 ----- |
17 |
sci-chemistry/mm-align/metadata.xml | 26 ------------------------- |
18 |
sci-chemistry/mm-align/mm-align-20120321.ebuild | 23 ---------------------- |
19 |
5 files changed, 60 deletions(-) |
20 |
|
21 |
diff --git a/profiles/package.mask b/profiles/package.mask |
22 |
index 12dc681fb20b..d90ab8b095ca 100644 |
23 |
--- a/profiles/package.mask |
24 |
+++ b/profiles/package.mask |
25 |
@@ -351,11 +351,6 @@ sci-chemistry/votca-ctp |
26 |
# Bug #834317. Removal on 2022-03-31. |
27 |
dev-libs/injeqt |
28 |
|
29 |
-# Sam James <sam@g.o> (2022-02-27) |
30 |
-# Fails to build with modern GCC, stuck on cmake-utils.eclass too. |
31 |
-# bug #723194, bug #834301. Removal on 2022-03-27. |
32 |
-sci-chemistry/mm-align |
33 |
- |
34 |
# Andreas Sturmlechner <asturm@g.o> (2022-02-27) |
35 |
# No revdeps since begin of gentoo.git history, outdated and unmaintained. |
36 |
# Bug #834307. Removal on 2022-03-29. |
37 |
|
38 |
diff --git a/sci-chemistry/mm-align/Manifest b/sci-chemistry/mm-align/Manifest |
39 |
deleted file mode 100644 |
40 |
index 97e91d4c9433..000000000000 |
41 |
--- a/sci-chemistry/mm-align/Manifest |
42 |
+++ /dev/null |
43 |
@@ -1 +0,0 @@ |
44 |
-DIST MM-align-20120321.tar.xz 20072 BLAKE2B be53cff43b220c9c44bbd600e4e2870e3987da25744a4bf3da0bc8cf7bc2619c93839e27327d23b5ef3bfbf9aca86b865717c48eb5d91a9da7b977909fb3bc39 SHA512 193c3b16b2d9fb0aaacf18b203fcf0240de7b11b4c0ce99fc571c277aa6e624b7b8b4df625e34433a5dec4349bb5bf6ae0368609c1738337923cf3b4d06428bc |
45 |
|
46 |
diff --git a/sci-chemistry/mm-align/files/CMakeLists.txt b/sci-chemistry/mm-align/files/CMakeLists.txt |
47 |
deleted file mode 100644 |
48 |
index 635ffdd67418..000000000000 |
49 |
--- a/sci-chemistry/mm-align/files/CMakeLists.txt |
50 |
+++ /dev/null |
51 |
@@ -1,5 +0,0 @@ |
52 |
-cmake_minimum_required (VERSION 2.6) |
53 |
-project (MM-align Fortran) |
54 |
-add_executable(MMalign MM-align.f) |
55 |
- |
56 |
-install (TARGETS MMalign DESTINATION bin) |
57 |
|
58 |
diff --git a/sci-chemistry/mm-align/metadata.xml b/sci-chemistry/mm-align/metadata.xml |
59 |
deleted file mode 100644 |
60 |
index 03c48e987ffb..000000000000 |
61 |
--- a/sci-chemistry/mm-align/metadata.xml |
62 |
+++ /dev/null |
63 |
@@ -1,26 +0,0 @@ |
64 |
-<?xml version="1.0" encoding="UTF-8"?> |
65 |
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> |
66 |
-<pkgmetadata> |
67 |
- <maintainer type="project"> |
68 |
- <email>sci-chemistry@g.o</email> |
69 |
- <name>Gentoo Chemistry Project</name> |
70 |
- </maintainer> |
71 |
- <longdescription> |
72 |
-MM-align is an algorithm for structurally aligning multiple-chain |
73 |
-protein-protein complexes. The algorithm is built on a heuristic |
74 |
-iteration of a modified Needleman-Wunsch dynamic programming (DP) |
75 |
-algorithm, with the alignment score specified by the inter-complex residue |
76 |
-distances. The multiple chains in each complex are first joined, in every |
77 |
-possible order, and then simultaneously aligned with cross-chain alignments |
78 |
-prevented. The alignments of interface residues are enhanced by an |
79 |
-interface-specific weighting factor. An optimal alignment between two complexes, |
80 |
-as well as the overall TM-score, will be reported for each comparison. |
81 |
-What is the difference between TM-align and MM-align? TM-align is for aligning |
82 |
-monomer protein structures while MM-align is designed for aligning |
83 |
-multiple-chain protein complex structures. Although one can still use TM-align |
84 |
-to align protein complexes after manually joining the chains, this will lead |
85 |
-to suboptimal alignments with unphysical cross alignments. Therefore, the |
86 |
-best result will be obtained if one uses TM-align to monomer structures and |
87 |
-MM-align for multimer structures. |
88 |
-</longdescription> |
89 |
-</pkgmetadata> |
90 |
|
91 |
diff --git a/sci-chemistry/mm-align/mm-align-20120321.ebuild b/sci-chemistry/mm-align/mm-align-20120321.ebuild |
92 |
deleted file mode 100644 |
93 |
index d2b42fe2547e..000000000000 |
94 |
--- a/sci-chemistry/mm-align/mm-align-20120321.ebuild |
95 |
+++ /dev/null |
96 |
@@ -1,23 +0,0 @@ |
97 |
-# Copyright 1999-2017 Gentoo Foundation |
98 |
-# Distributed under the terms of the GNU General Public License v2 |
99 |
- |
100 |
-EAPI=6 |
101 |
- |
102 |
-inherit cmake-utils fortran-2 |
103 |
- |
104 |
-DESCRIPTION="Protein Complex Structural Alignment" |
105 |
-HOMEPAGE="http://zhanglab.ccmb.med.umich.edu/MM-align/" |
106 |
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/MM-align-${PV}.tar.xz" |
107 |
- |
108 |
-SLOT="0" |
109 |
-LICENSE="tm-align" |
110 |
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
111 |
-IUSE="" |
112 |
- |
113 |
-S="${WORKDIR}" |
114 |
- |
115 |
-src_prepare() { |
116 |
- cp "${FILESDIR}"/CMakeLists.txt . || die |
117 |
- |
118 |
- cmake-utils_src_prepare |
119 |
-} |