sci-chemistry/mustang: Version Bump

Package-Manager: portage-2.2.23
Signed-off-by: Justin Lecher <jlec@gentoo.org>

3 files changed, 51 insertions, 55 deletions

diff --git a/sci-chemistry/mustang/Manifest b/sci-chemistry/mustang/Manifest
index 278238854069..f8d1b591405d 100644
--- a/sci-chemistry/mustang/Manifest
+++ b/sci-chemistry/mustang/Manifest
@@ -1 +1,2 @@
 DIST mustang_v3.2.1.tgz 161216 SHA256 38f8ec10f15466a42ade770eb6c3ed0ed2449bb070a53b5e8d3125f2596b1556 SHA512 aee37bb77edbdc601cdc735db8602d0a3804065200df1b36b6956e74dfd5f85b554a655be1bfbe673aada1abd5e1aee1c0f59fb2ff0380bfcb725e38439d41ff WHIRLPOOL 521edce7648c28c067dae4462e432c8b5f2b9a60be4248ba78280067254fdfb9f584c18ce9afc5c99927f6227e1e650989cd7d65df1b3c6e7494d617b89a74fe
+DIST mustang_v3.2.2.tgz 141940 SHA256 6fe274a93b54ba3c46e262fc6d7114bad239d1cbd2dadec8a92a7194328373a2 SHA512 cb862f860f3cdb3349743c6005a29acc14cde5269df9d61f1100ffdc9a22c1d8e3dd46771371557b823724e79783f8fcb7356c63c6f0c0a09aac09bee407a26d WHIRLPOOL 63e7b6f881274c20df59e85699b1f1a07506f0dd20082e898001c163fb02b60336c0ee6b629bf19f773f86b3479f4ae1344cf1ea6b7f6052d1407db3f05910bb
diff --git a/sci-chemistry/mustang/files/mustang-3-gcc43.patch b/sci-chemistry/mustang/files/mustang-3-gcc43.patch
deleted file mode 100644
index ef2818b92ed8..000000000000
--- a/sci-chemistry/mustang/files/mustang-3-gcc43.patch
+++ /dev/null
@@ -1,55 +0,0 @@
-diff -u MUSTANG_v.3.orig/src/ew_2.cpp MUSTANG_v.3/src/ew_2.cpp
---- MUSTANG_v.3.orig/src/ew_2.cpp	2008-01-15 11:18:34.000000000 -0700
-+++ MUSTANG_v.3/src/ew_2.cpp	2008-12-09 10:47:22.000000000 -0700
-@@ -36,6 +36,7 @@
- using std::ifstream;
- 
- #include<math.h>
-+#include <cstdlib>
- #include "macros.h"
- #include "globals.h"
- #include "ew.h"
-diff -u MUSTANG_v.3.orig/src/multiple_superposition.cpp MUSTANG_v.3/src/multiple_superposition.cpp
---- MUSTANG_v.3.orig/src/multiple_superposition.cpp	2008-01-15 11:18:34.000000000 -0700
-+++ MUSTANG_v.3/src/multiple_superposition.cpp	2008-12-09 10:49:00.000000000 -0700
-@@ -51,6 +51,7 @@
- #include "alloc_routines.h"
- #include "de_alloc_routines.h"
- #include <cmath>
-+#include <cstdlib>
- #define THRESH 0.0001
- 
- void MOVE_TO_CENTER_OF_GRAVITY( int NSTRUC , int NRES , float ***R , float **CMs )
-diff -u MUSTANG_v.3.orig/src/multiple_superposition.h MUSTANG_v.3/src/multiple_superposition.h
---- MUSTANG_v.3.orig/src/multiple_superposition.h	2008-01-15 11:18:34.000000000 -0700
-+++ MUSTANG_v.3/src/multiple_superposition.h	2008-12-09 10:48:11.000000000 -0700
-@@ -25,3 +25,4 @@
- #define MULT_SUPERPOSE
- void  M_SUPERPOSE( int , int , float***, float** , float*** ) ;
- #endif
-+#include <cstdlib>
-diff -u MUSTANG_v.3.orig/src/pdb_ripper.h MUSTANG_v.3/src/pdb_ripper.h
---- MUSTANG_v.3.orig/src/pdb_ripper.h	2008-01-15 11:18:34.000000000 -0700
-+++ MUSTANG_v.3/src/pdb_ripper.h	2008-12-09 10:46:47.000000000 -0700
-@@ -29,4 +29,5 @@
- void PARSE_ENTIRE_PDB_STRUCTURE( char * , int ) ;
- 
- #endif
-+#include <cstdlib>
- 
-diff -u MUSTANG_v.3.orig/src/progress_align.h MUSTANG_v.3/src/progress_align.h
---- MUSTANG_v.3.orig/src/progress_align.h	2008-01-15 11:18:34.000000000 -0700
-+++ MUSTANG_v.3/src/progress_align.h	2008-12-09 10:47:50.000000000 -0700
-@@ -25,3 +25,4 @@
- #define PROG_ALGN_H
- void PROGRESSIVE_ALIGNMENT_USING_EXTENDED_EDGE_WEIGHTS() ;
- #endif
-+#include <cstdlib>
-diff -u MUSTANG_v.3.orig/src/read_structures.h MUSTANG_v.3/src/read_structures.h
---- MUSTANG_v.3.orig/src/read_structures.h	2008-01-15 11:18:34.000000000 -0700
-+++ MUSTANG_v.3/src/read_structures.h	2008-12-09 10:46:22.000000000 -0700
-@@ -26,3 +26,4 @@
- void READ_STRUCTURES( char **paths );
- void READ_ENTIRE_PDBS( char **paths) ;
- #endif
-+#include <cstdlib>
diff --git a/sci-chemistry/mustang/mustang-3.2.2.ebuild b/sci-chemistry/mustang/mustang-3.2.2.ebuild
new file mode 100644
index 000000000000..fdc300fd2b0b
--- /dev/null
+++ b/sci-chemistry/mustang/mustang-3.2.2.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+MY_PN="MUSTANG"
+SRC_P="${PN}_v${PV}"
+MY_P="${MY_PN}_v${PV}"
+
+DESCRIPTION="MUltiple STructural AligNment AlGorithm"
+HOMEPAGE="http://www.csse.monash.edu.au/~karun/Site/mustang.html"
+SRC_URI="http://www.csse.monash.edu.au/~karun/${PN}/${PN}_v${PV}.tgz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-3.2.1-gcc-4.7.patch
+	sed -e 's:3.2.1:3.2.2:g' -i Makefile || die
+}
+
+src_compile() {
+	emake \
+		CPP=$(tc-getCXX) \
+		CPPFLAGS="${CXXFLAGS}" \
+		LDFLAGS="${LDFLAGS}"
+}
+
+src_test() {
+	./bin/${P} -f ./data/test/test_zf-CCHH || die
+}
+
+src_install() {
+	newbin bin/${P} ${PN}
+	doman man/${PN}.1
+	dodoc README
+}
+
+pkg_postinst() {
+	elog "If you use this program for an academic paper, please cite:"
+	elog "Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey, and Arthur M. Lesk"
+	elog "Proteins: Structure, Function, and Bioinformatics. 64(3):559-574, Aug. 2006"
+}