New addition, written by me

Package-Manager: portage-2.2.0_alpha93/cvs/Linux x86_64

5 files changed, 78 insertions, 0 deletions

diff --git a/sci-chemistry/mm-align/ChangeLog b/sci-chemistry/mm-align/ChangeLog
new file mode 100644
index 000000000000..013740b098e4
--- /dev/null
+++ b/sci-chemistry/mm-align/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/mm-align
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mm-align/ChangeLog,v 1.1 2012/03/21 12:28:50 jlec Exp $
+
+*mm-align-20120321 (21 Mar 2012)
+
+  21 Mar 2012; Justin Lecher <jlec@gentoo.org> +mm-align-20120321.ebuild,
+  +files/CMakeLists.txt, +metadata.xml:
+  New addition, written by me
+
diff --git a/sci-chemistry/mm-align/Manifest b/sci-chemistry/mm-align/Manifest
new file mode 100644
index 000000000000..6424887bf71f
--- /dev/null
+++ b/sci-chemistry/mm-align/Manifest
@@ -0,0 +1,15 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
+AUX CMakeLists.txt 142 RMD160 88da2f65bb9b44b074fa2c8afb3352b108e13a1c SHA1 86242c8dd99f74c5e3d91889f9b2069f60b134d7 SHA256 29f1003a81107cc60a17f0fe26fb59b91a28fb3e46224552b856bf505f777ae0
+DIST MM-align-20120321.tar.xz 20072 RMD160 3bf453c062f9f06e5b4da2f2a174fb15403e9df5 SHA1 94c9633511794e1b71e2d2cbc9447c6f3fde9d2f SHA256 0158a93a06257b885630ab7bed3b7bf8dca2ee12217c84d019829a1e34f3eeb3
+EBUILD mm-align-20120321.ebuild 602 RMD160 d3e2382fea6ce314696974d79ea32c013c9a20ee SHA1 79e0d8e779a2e2f4de5fc9f47afd344979f8cd4d SHA256 f48c01817346d88328f8c4a4c94bf6a0a500578d057b902a40cf65980441eea5
+MISC ChangeLog 394 RMD160 766297fd6fdfe0e689987af7a5e5bd781a86c57a SHA1 8963804f6f8b10181a739db58fbe5b87fc2ad563 SHA256 fd35983f54951fb3a904968411724d18995d8b6c45989f65b4d1b5c13fd22f20
+MISC metadata.xml 1407 RMD160 a54114b0bf812198ccf5e2a49288c0f403a2b483 SHA1 6f80e88b1cdfd9de0b5031ab83ed297c8c794482 SHA256 7de95c3976eb176863f4356e10193beedd1563bd98f62998d6573986c71b5edc
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.18 (GNU/Linux)
+
+iEYEAREKAAYFAk9pyYcACgkQgAnW8HDreRZZ0gCfRFhldW2NSGSS86RqalWpWXZt
+mQQAn3ufdp0i3uflGXQmjxdqktBUuYo3
+=1YPY
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/mm-align/files/CMakeLists.txt b/sci-chemistry/mm-align/files/CMakeLists.txt
new file mode 100644
index 000000000000..635ffdd67418
--- /dev/null
+++ b/sci-chemistry/mm-align/files/CMakeLists.txt
@@ -0,0 +1,5 @@
+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
new file mode 100644
index 000000000000..6a27c1a3ac5f
--- /dev/null
+++ b/sci-chemistry/mm-align/metadata.xml
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-chemistry</herd>
+	<maintainer>
+		<email>jlec@gentoo.org</email>
+	</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
new file mode 100644
index 000000000000..e5b3c19faddf
--- /dev/null
+++ b/sci-chemistry/mm-align/mm-align-20120321.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mm-align/mm-align-20120321.ebuild,v 1.1 2012/03/21 12:28:50 jlec Exp $
+
+EAPI=4
+
+inherit cmake-utils fortran-2
+
+DESCRIPTION="Protein Complex Structural Alignment"
+HOMEPAGE="http://zhanglab.ccmb.med.umich.edu/MM-align/"
+SRC_URI="http://dev.gentoo.org/~jlec/distfiles/MM-align-${PV}.tar.xz"
+
+SLOT="0"
+LICENSE="as-is"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+S="${WORKDIR}"
+
+src_prepare() {
+	cp "${FILESDIR}"/CMakeLists.txt . || die
+}