sci-chemistry/relax: New addition

Package-Manager: portage-2.2.0_alpha120/cvs/Linux x86_64

5 files changed, 142 insertions, 0 deletions

diff --git a/sci-chemistry/relax/ChangeLog b/sci-chemistry/relax/ChangeLog
new file mode 100644
index 000000000000..557f781a3ed9
--- /dev/null
+++ b/sci-chemistry/relax/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/relax
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/relax/ChangeLog,v 1.1 2012/07/19 16:05:51 jlec Exp $
+
+*relax-2.1.0 (19 Jul 2012)
+
+  19 Jul 2012; Justin Lecher <jlec@gentoo.org> +relax-2.1.0.ebuild,
+  +files/relax-2.1.0-gentoo.patch, +metadata.xml:
+  New addition
+
diff --git a/sci-chemistry/relax/Manifest b/sci-chemistry/relax/Manifest
new file mode 100644
index 000000000000..b21fa602dd4d
--- /dev/null
+++ b/sci-chemistry/relax/Manifest
@@ -0,0 +1,16 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
+AUX relax-2.1.0-gentoo.patch 910 SHA256 2e85e979fa61e950def08e5a71e0d61662d5d8755a50fa6f4210000760778dbe SHA512 45c537b69b84e67fbadfcc30ae51f8f2d86d897c6187a1008b974899e8464cc638ad21b7e43eb2395887a962dcd6a751e24e4d46fec3639413a90de7fbfb98e6 WHIRLPOOL fd3ffa8d5926586b2d8ff56e3e3e20cf816987a23358e823c39ed4217d53fbea43185c5bcc1abb9bbcb0703e84f1243cbca5db7cb26d432755b488950db72171
+DIST relax-2.1.0.src.tar.bz2 22054720 SHA256 e7908dbf774e1eb866f45fc222d14935624ce9fe4453da979d1b6cb7e1204dd4 SHA512 e42fb050097de6c79751477e1b9e8ff76f8d495fae446380785d8bf8a0e384df4837b283d95c6988e9e5a2aec9af54369a53cc5584d233c58448882f07235dd0 WHIRLPOOL 51b62e2515780248345c14e1fd11511e8dba1832c69178dca1afb0784b2d411ddb21d3f305e04216ef8e041ea1ce560a40135617f91a5bb5e94d19c76ec0cab6
+EBUILD relax-2.1.0.ebuild 1144 SHA256 8d8955bb6bad56e10a9028ffff89b3c57b64db418cecb893f01b5e04acae20f3 SHA512 bb3e66a8a94d2f4df8eef3b031054656c6ed19f363ae583c1aea82385b68daa462870d530789f852adbc100ff346e1b66b5ee5831ee29841c0b664be0f10b0fd WHIRLPOOL 8bafd92268d8aa3acc650769a378d73ae493b1102a52546e884f2d18b3ba92ee7c35e98e4896e807ad1d72c289fc6fb50a32c7c374896df5c3257ecab37f1414
+MISC ChangeLog 371 SHA256 fc5cbd7631b30f7882068827823bd5bab7a0796d071fa6395a8f35dd4bc479bf SHA512 c9faa810e9ad2b4dd7e9cf5fe112b154285d31df0186f729e112a823d26d69c83f3cfdd1fcde2819e960694cbe9d2ab0432498e47492b88eb33228d1fef25b96 WHIRLPOOL 2a9ae808350d9ebf5cc58d274e41ff14be273c3912812cc23de2de2c9c8db601fab6cbea023863ba513d992790273dfc5fe2eacc5d3581402621b23c8eae032f
+MISC metadata.xml 1309 SHA256 a4efc57396e2e72aefa0b878bcc594ddf36c0836dd541d1368e8a5343a25de29 SHA512 c60a2123c136915a51d383ac99b384c5eab87af3e42d93f433ab1906d71f1b9d37009e85bf6e9c58fb24d98026592cf4c3a6dfc34b1e433e139921e8adfd2d75 WHIRLPOOL 009442176479969658126d69976a2f4198f877d0f44045dbc16a65d9f8315f7f20f8938f22eed570f679cd14aba62c569a2b50b1b879619b2ad2ae7612816811
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.19 (GNU/Linux)
+Comment: GPGTools - http://gpgtools.org
+
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diff --git a/sci-chemistry/relax/files/relax-2.1.0-gentoo.patch b/sci-chemistry/relax/files/relax-2.1.0-gentoo.patch
new file mode 100644
index 000000000000..3edbfb287a1b
--- /dev/null
+++ b/sci-chemistry/relax/files/relax-2.1.0-gentoo.patch
@@ -0,0 +1,27 @@
+ sconstruct |    6 +++++-
+ 1 files changed, 5 insertions(+), 1 deletions(-)
+
+diff --git a/sconstruct b/sconstruct
+index c0fab95..c9d5e2c 100644
+--- a/sconstruct
++++ b/sconstruct
+@@ -26,7 +26,7 @@
+ 
+ # Import statements.
+ from numpy import get_include
+-from os import getcwd, path, remove, sep, walk
++from os import getcwd, path, remove, sep, walk, environ
+ import platform
+ from re import search
+ from shutil import rmtree
+@@ -586,6 +586,10 @@ class Main:
+         for file in files:
+             nodes.append(env.SharedObject(dir + path.sep + file, CCFLAGS=cflags))
+ 
++        env.Append(LINKFLAGS = environ['LDFLAGS'])
++        env.Append(CFLAGS = environ['CFLAGS'])
++        env.Replace(CC = environ['CC'])
++
+         # Build the relaxation curve fitting module.
+         self.relax_fit_object = env.SharedLibrary(target=dir + path.sep + 'relax_fit', source=nodes, SHLIBPREFIX=prefix, SHLIBSUFFIX=suffix)
+ 
diff --git a/sci-chemistry/relax/metadata.xml b/sci-chemistry/relax/metadata.xml
new file mode 100644
index 000000000000..b1c325bde991
--- /dev/null
+++ b/sci-chemistry/relax/metadata.xml
@@ -0,0 +1,30 @@
+<?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>
+The program relax is a software package designed for the study of molecular 
+dynamics through the analysis of experimental NMR data. Organic molecules, 
+proteins, RNA, DNA, sugars, and other biomolecules are all supported. It 
+was originally written for the model-free analysis of protein dynamics, 
+though its scope has been significantly expanded.
+
+relax is a community driven project created by NMR spectroscopists for 
+NMR spectroscopists. It supports a diverse range of analyses:
+
+Model-free analysis - the Lipari and Szabo model-free analysis of NMR 
+	relaxation data.
+R1 and R2 - the exponential curve fitting for the calculation of the 
+	Rx NMR relaxation rates.
+NOE - the calculation of the steady-state NOE NMR relaxation data.
+Consistency testing of multiple field NMR relaxation data.
+RSDM - Reduced Spectral Density Mapping.
+Frame order and N-state model - study of domain motions via the N-state 
+	model and frame order dynamics theories using anisotropic 
+	NMR parameters such as RDCs and PCSs.
+Stereochemistry investigations.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-chemistry/relax/relax-2.1.0.ebuild b/sci-chemistry/relax/relax-2.1.0.ebuild
new file mode 100644
index 000000000000..6d8f10a6e160
--- /dev/null
+++ b/sci-chemistry/relax/relax-2.1.0.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/relax/relax-2.1.0.ebuild,v 1.1 2012/07/19 16:05:51 jlec Exp $
+
+EAPI=4
+
+PYTHON_DEPEND="2"
+
+WX_GTK_VER="2.8"
+
+inherit eutils python scons-utils toolchain-funcs wxwidgets
+
+DESCRIPTION="Molecular dynamics by NMR data analysis"
+HOMEPAGE="http://www.nmr-relax.com/"
+SRC_URI="http://download.gna.org/relax/${P}.src.tar.bz2"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	dev-python/numpy
+	sci-libs/bmrblib
+	sci-libs/minfx
+	sci-libs/scipy
+	x11-libs/wxGTK:2.8[X]"
+DEPEND="${RDEPEND}"
+
+pkg_setup() {
+	wxwidgets_pkg_setup
+	python_pkg_setup
+	python_set_active_version 2
+}
+
+src_prepare() {
+	rm -rf minfx bmrblib
+	epatch "${FILESDIR}"/${P}-gentoo.patch
+	tc-export CC
+}
+
+src_compile() {
+	escons
+}
+
+src_test() {
+	$(PYTHON) ./${PN}.py -s || die
+	$(PYTHON) ./${PN}.py -x || die
+}
+
+src_install() {
+	dodoc README
+	rm ${PN} README || doe
+
+	insinto $(python_get_sitedir)/${PN}
+	doins -r *
+
+	make_wrapper ${PN} "$(PYTHON) $(python_get_sitedir)/${PN}/${PN}.py $@"
+}