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authorJakov Smolić <jsmolic@gentoo.org>2022-03-28 11:34:30 +0200
committerJakov Smolić <jsmolic@gentoo.org>2022-03-28 11:34:30 +0200
commit7e02f5e90dc6463bd249131c9b8307343e481147 (patch)
treea2126e7f68c1ca20f384bafc748ac872fe811096 /sci-chemistry/mm-align
parentnet-fs/smbtad: treeclean (diff)
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sci-chemistry/mm-align: treeclean
Closes: https://bugs.gentoo.org/834301 Closes: https://bugs.gentoo.org/723194 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
Diffstat (limited to 'sci-chemistry/mm-align')
-rw-r--r--sci-chemistry/mm-align/Manifest1
-rw-r--r--sci-chemistry/mm-align/files/CMakeLists.txt5
-rw-r--r--sci-chemistry/mm-align/metadata.xml26
-rw-r--r--sci-chemistry/mm-align/mm-align-20120321.ebuild23
4 files changed, 0 insertions, 55 deletions
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
-}