From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 8921C15808C for ; Mon, 28 Mar 2022 09:35:45 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id A177BE095E; Mon, 28 Mar 2022 09:35:44 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 57E82E095E for ; Mon, 28 Mar 2022 09:35:44 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 1A121340CFB for ; Mon, 28 Mar 2022 09:35:43 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 1459E34E for ; Mon, 28 Mar 2022 09:35:40 +0000 (UTC) From: "Jakov Smolić" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Jakov Smolić" Message-ID: <1648460070.7e02f5e90dc6463bd249131c9b8307343e481147.jsmolic@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/mm-align/, profiles/, sci-chemistry/mm-align/files/ X-VCS-Repository: repo/gentoo X-VCS-Files: profiles/package.mask sci-chemistry/mm-align/Manifest sci-chemistry/mm-align/files/CMakeLists.txt sci-chemistry/mm-align/metadata.xml sci-chemistry/mm-align/mm-align-20120321.ebuild X-VCS-Directories: sci-chemistry/mm-align/files/ profiles/ sci-chemistry/mm-align/ X-VCS-Committer: jsmolic X-VCS-Committer-Name: Jakov Smolić X-VCS-Revision: 7e02f5e90dc6463bd249131c9b8307343e481147 X-VCS-Branch: master Date: Mon, 28 Mar 2022 09:35:40 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: b4ee77e8-c5da-4a62-9cbd-b01829d92672 X-Archives-Hash: 281e6ddf534c175dc9f5f5e369481268 commit: 7e02f5e90dc6463bd249131c9b8307343e481147 Author: Jakov Smolić gentoo org> AuthorDate: Mon Mar 28 09:34:30 2022 +0000 Commit: Jakov Smolić gentoo 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 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 (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 (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 @@ - - - - - sci-chemistry@gentoo.org - Gentoo Chemistry Project - - -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 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 -}