reduce: bump to 3.14.080821.

4 files changed, 155 insertions, 0 deletions

diff --git a/sci-chemistry/reduce/ChangeLog b/sci-chemistry/reduce/ChangeLog
new file mode 100644
index 0000000..c05552f
--- /dev/null
+++ b/sci-chemistry/reduce/ChangeLog
@@ -0,0 +1,85 @@
+# ChangeLog for sci-chemistry/reduce
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/reduce/ChangeLog,v 1.18 2010/09/20 06:57:54 jlec Exp $
+
+  20 Sep 2010; Justin Lecher <jlec@gentoo.org>
+  -files/2.21.030604-gcc4.patch,
+  -files/3.02.060709-remove-extra-qualification.patch,
+  +files/3.13.080428-CFLAGS.patch, reduce-3.13.080428-r1.ebuild:
+  Respect CFLAGS, removed old patches
+
+  15 Jul 2010; Markus Meier <maekke@gentoo.org>
+  reduce-3.13.080428-r1.ebuild:
+  x86 stable, bug #325999
+
+  14 Jul 2010; Justin Lecher <jlec@gentoo.org> reduce-3.13.080428-r1.ebuild:
+  You should not use EPREFIX with helpers
+
+  28 Jun 2010; Christoph Mende <angelos@gentoo.org>
+  reduce-3.13.080428-r1.ebuild:
+  Stable on amd64 wrt bug #325999
+
+  22 Apr 2010; Justin Lecher <jlec@gentoo.org> reduce-3.13.080428-r1.ebuild:
+  Keyworded for ~*-linux
+
+*reduce-3.13.080428-r1 (05 Feb 2010)
+
+  05 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/3.13.080428-LDFLAGS.patch, -reduce-2.21.030604.ebuild,
+  -reduce-3.02.060709.ebuild, +reduce-3.13.080428-r1.ebuild:
+  Clean old versions, fix for 280857 & 280858
+
+  29 May 2009; Donnie Berkholz <dberkholz@gentoo.org>;
+  reduce-3.13.080428.ebuild:
+  Stable on amd64.
+
+*reduce-3.13.080428 (07 Jul 2008)
+
+  07 Jul 2008; Donnie Berkholz <dberkholz@gentoo.org>;
+  +reduce-3.13.080428.ebuild:
+  (#230693) Bump. Keyword ~amd64. Thanks to Philipp Psurek for doing the
+  initial investigation on what changes happened.
+
+  23 Oct 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  reduce-2.21.030604.ebuild, reduce-3.02.060709.ebuild:
+  (#152424) Missing dep on unzip.
+
+  20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
+  (#148281) Change herd to sci-chemistry from sci.
+
+  30 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  reduce-3.02.060709.ebuild:
+  Directory names changed in the tarball, causing breakage. Fix it.
+
+  20 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/3.02.060709-remove-extra-qualification.patch:
+  (#143858) Add a forgotten patch.
+
+*reduce-3.02.060709 (09 Aug 2006)
+
+  09 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  +reduce-3.02.060709.ebuild:
+  Bump.
+
+  09 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  reduce-2.21.030604.ebuild:
+  Update SRC_URI.
+
+  05 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
+  Remove myself as maintainer, anyone feel free to work on this, although I'll
+  continue to do so as well.
+
+  09 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  reduce-2.21.030604.ebuild:
+  x86/ppc stable.
+
+  07 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
+  Update to my new email address.
+
+*reduce-2.21.030604 (04 Jun 2006)
+
+  04 Jun 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/2.21.030604-gcc4.patch, +metadata.xml, +reduce-2.21.030604.ebuild:
+  New package to add hydrogens to a Protein Data Bank (PDB) molecule structure
+  file.
+
diff --git a/sci-chemistry/reduce/Manifest b/sci-chemistry/reduce/Manifest
new file mode 100644
index 0000000..5e2d737
--- /dev/null
+++ b/sci-chemistry/reduce/Manifest
@@ -0,0 +1,4 @@
+DIST reduce.3.14.080821.src.tgz 5199731 RMD160 5ffb105e0cb9bc6b2c0d6dc995e9ffdf7c3695e7 SHA1 294be6bcf69c72df8645e8ba4194aa790af4b739 SHA256 0c32f3e9f818b976e0996f088639a194cde63f227eff32c35e14526ec05c930a
+EBUILD reduce-3.14.080821.ebuild 1467 RMD160 2fa72a86b07efe74238ee2952a04e25008987e92 SHA1 9895e76f6c5d737c53ffa2f8e1163ff381b9e053 SHA256 f325befa43a4d428b45a6e9687a8d45ecaa0f1b2223b73c794f3698334772d41
+MISC ChangeLog 2949 RMD160 5aef737a01c1e39ab93e86fd1d84580960a05646 SHA1 f4aa73673aca8f8b347dbd11145efa45d564616a SHA256 74c6823f1b069d536c711c18fc0966e55451982afb8a3df415cbad589093a9dc
+MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-chemistry/reduce/metadata.xml b/sci-chemistry/reduce/metadata.xml
new file mode 100644
index 0000000..9ac9ffd
--- /dev/null
+++ b/sci-chemistry/reduce/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-chemistry</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/reduce/reduce-3.14.080821.ebuild b/sci-chemistry/reduce/reduce-3.14.080821.ebuild
new file mode 100644
index 0000000..068a619
--- /dev/null
+++ b/sci-chemistry/reduce/reduce-3.14.080821.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild,v 1.6 2010/09/20 06:57:54 jlec Exp $
+
+EAPI="3"
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}.${PV}.src"
+
+DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php"
+SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/reduce31/${MY_P}.tgz"
+
+LICENSE="richardson"
+SLOT="0"
+KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	app-arch/unzip"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	sed \
+		-e "s:CFLAGS:CXXFLAGS:g" \
+		-e 's:$(CXX) -o:$(CXX) $(LDFLAGS) -o:g' \
+		-i reduce_src/Makefile \
+		|| die
+	emake clean || die
+}
+
+src_compile() {
+	DICT_DIR="/usr/share/reduce"
+	DICT_FILE="reduce_het_dict.txt"
+
+	emake \
+		CC="$(tc-getCC)" \
+		CXX="$(tc-getCXX)" \
+		OPT="${CXXFLAGS}" \
+		DICT_HOME="${EPREFIX}/${DICT_DIR}/${DICT_FILE}" \
+		|| die "make failed"
+}
+
+src_install() {
+	dobin "${S}"/reduce_src/reduce || die
+	insinto ${DICT_DIR}
+	doins "${S}"/${DICT_FILE} "${S}"/reduce_wwPDB_het_dict.txt || die
+	dodoc README.usingReduce.txt || die
+}
+
+pkg_info() {
+	elog "To use the PDBv3 dictionary instead of PDBv2, set the environment"
+	elog "variable REDUCE_HET_DICT to ${EPREFIX}/usr/share/reduce/reduce_wwPDB_het_dict.txt"
+}
+
+pkg_postinst() {
+	pkg_info
+}