sci-chemistry/pdb2pqr: Version Bump

(Portage version: 2.2.14/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

3 files changed, 160 insertions, 1 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index 6b70f1fa377b..d475c25007f7 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pdb2pqr
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.40 2014/10/24 12:06:42 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.41 2014/10/27 17:03:21 jlec Exp $
+
+*pdb2pqr-1.9.0 (27 Oct 2014)
+
+  27 Oct 2014; Justin Lecher <jlec@gentoo.org> +pdb2pqr-1.9.0.ebuild,
+  +files/pdb2pqr-1.9.0-flags.patch:
+  Version Bump
 
 *pdb2pqr-1.8.0-r1 (24 Oct 2014)
 
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch
new file mode 100644
index 000000000000..fac32b233e6b
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch
@@ -0,0 +1,45 @@
+ pdb2pka/SConscript           | 9 ++++++++-
+ pdb2pka/substruct/SConscript | 6 ++++++
+ 2 files changed, 14 insertions(+), 1 deletion(-)
+
+diff --git a/pdb2pka/SConscript b/pdb2pka/SConscript
+index 583cdc5..6c30011 100644
+--- a/pdb2pka/SConscript
++++ b/pdb2pka/SConscript
+@@ -1,4 +1,11 @@
+ Import('env')

++import os

++

++env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())

++env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())

++env['CXX'] = os.environ['CXX']

++env['LINK'] = os.environ['CXX']

++

+ 

+ if env['REBUILD_SWIG']:

+     pyc = env.LoadableModule('_pMC_mult', ['pMC_mult.cpp', 'pMC_mult.i'])

+@@ -9,4 +16,4 @@ Default(pyc)
+     

+ algorithms_module = SConscript('substruct/SConscript')

+ 

+-Return('pyc algorithms_module')
+\ No newline at end of file
++Return('pyc algorithms_module')

+diff --git a/pdb2pka/substruct/SConscript b/pdb2pka/substruct/SConscript
+index 7dbcdb0..56fb577 100644
+--- a/pdb2pka/substruct/SConscript
++++ b/pdb2pka/substruct/SConscript
+@@ -1,7 +1,13 @@
+ import distutils

+ import numpy

++import os

+ Import('env')

+ 

++env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())

++env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())

++env['CXX'] = os.environ['CXX']

++env['LINK'] = os.environ['CXX']

++

+ env.Append(CPPPATH=[distutils.sysconfig.get_python_inc(), numpy.get_include()])

+ 

+ algorithms_pyc = env.LoadableModule('Algorithms', ['Algorithms.cpp'])

diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0.ebuild
new file mode 100644
index 000000000000..360ae3fbd21e
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0.ebuild
@@ -0,0 +1,108 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0.ebuild,v 1.1 2014/10/27 17:03:21 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools scons-utils fortran-2 flag-o-matic python-single-r1 toolchain-funcs
+
+DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
+HOMEPAGE="http://www.poissonboltzmann.org/"
+SRC_URI="https://github.com/Electrostatics/apbs-${PN}/releases/download/${P}/${PN}-src-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+IUSE="doc examples opal +pdb2pka"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-chemistry/openbabel[python]
+	opal? ( dev-python/zsi[${PYTHON_USEDEP}] )
+	pdb2pka? ( sci-chemistry/apbs[${PYTHON_USEDEP},-mpi] )"
+DEPEND="${RDEPEND}
+	dev-lang/swig:0"
+
+pkg_setup() {
+	if [[ -z ${MAXATOMS} ]]; then
+		einfo "If you like to have support for more then 10000 atoms,"
+		einfo "export MAXATOMS=\"your value\""
+		export MAXATOMS=10000
+	else
+		einfo "Allow usage of ${MAXATOMS} during calculations"
+	fi
+	fortran-2_pkg_setup
+	python-single-r1_pkg_setup
+}
+
+src_prepare() {
+	find -type f \( -name "*\.pyc" -o -name "*\.pyo" \) -delete || die
+
+	cat > build_config.py <<- EOF
+	PREFIX="${ED}/$(python_get_sitedir)/${PN}"
+	#URL="http://<COMPUTER NAME>/pdb2pqr/"
+	APBS="${EPREFIX}/usr/bin/apbs"
+	#OPAL="http://nbcr-222.ucsd.edu/opal2/services/pdb2pqr_1.8"
+	#APBS_OPAL="http://nbcr-222.ucsd.edu/opal2/services/apbs_1.3"
+	MAX_ATOMS=${MAXATOMS}
+	BUILD_PDB2PKA=$(usex pdb2pka True False)
+	REBUILD_SWIG=True
+	EOF
+
+	export CXXFLAGS="${CXXFLAGS}"
+	export LDFLAGS="${LDFLAGS}"
+
+	epatch "${FILESDIR}"/${P}-flags.patch
+	tc-export CXX
+	rm -rf scons || die
+}
+
+src_compile() {
+	escons
+}
+
+src_test() {
+	local myesconsargs=( -j1 )
+	escons test
+	escons advtest
+	escons complete-test
+}
+
+src_install() {
+	escons install
+
+	local lib
+
+	make_wrapper ${PN} "${PYTHON} /$(python_get_sitedir)/${PN}/${PN}.py"
+	make_wrapper pdb2pka "${PYTHON} /$(python_get_sitedir)/${PN}/pdb2pka/pka.py"
+
+	for lib in apbslib.py{,c,o}; do
+		dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib}
+	done
+	dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so
+
+	if use doc; then
+		pushd doc > /dev/null
+		dohtml -r *.html images pydoc
+		popd > /dev/null
+	fi
+
+	use examples && \
+		insinto /usr/share/${PN}/ && \
+		doins -r examples
+
+	dodir /usr/share/doc/${PF}/html
+	mv "${ED}"$(python_get_sitedir)/${PN}/doc/pydoc/* "${ED}"/usr/share/doc/${PF}/html || die
+	rmdir "${ED}"$(python_get_sitedir)/${PN}/doc/pydoc || die
+	mv "${ED}"$(python_get_sitedir)/${PN}/doc/* "${ED}"/usr/share/doc/${PF}/ || die
+
+	dodoc *md NEWS
+
+	find "${ED}"$(python_get_sitedir)/${PN}/contrib -delete || die
+
+	python_optimize
+}