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# 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-r1.ebuild,v 1.1 2014/10/28 09:00:32 jlec Exp $
EAPI=5
PYTHON_COMPAT=( python2_7 )
inherit autotools scons-utils fortran-2 flag-o-matic python-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[${PYTHON_USEDEP}]
sci-chemistry/openbabel[python]
sci-chemistry/openbabel-python[${PYTHON_USEDEP}]
opal? ( dev-python/zsi[${PYTHON_USEDEP}] )
pdb2pka? ( sci-chemistry/apbs[${PYTHON_USEDEP},-mpi] )"
DEPEND="${RDEPEND}
dev-lang/swig:0"
PATCHES=(
"${FILESDIR}"/${P}-flags.patch
"${FILESDIR}"/${P}-install-py.patch
)
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
}
src_prepare() {
find -type f \( -name "*\.pyc" -o -name "*\.pyo" \) -delete || die
export CXXFLAGS="${CXXFLAGS}"
export LDFLAGS="${LDFLAGS}"
epatch ${PATCHES[@]}
tc-export CXX
rm -rf scons || die
python_copy_sources
}
src_configure() {
python_configure() {
cd "${BUILD_DIR}" || 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
}
python_foreach_impl python_configure
}
src_compile() {
python_compile() {
cd "${BUILD_DIR}" || die
escons
}
python_foreach_impl python_compile
}
src_test() {
python_test() {
local myesconsargs=( -j1 )
cd "${BUILD_DIR}" || die
escons test
escons advtest
escons complete-test
}
python_foreach_impl python_test
}
src_install() {
dodir /usr/share/doc/${PF}/html
python_install() {
local lib
cd "${BUILD_DIR}" || die
escons install
find "${ED}"$(python_get_sitedir)/${PN}/{jmol,examples,doc,contrib} -delete || die
python_doscript "${FILESDIR}"/{${PN},pdb2pka}
for lib in apbslib.py{,c,o}; do
dosym ../../apbs/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib}
done
dosym ../../_apbslib.so $(python_get_sitedir)/${PN}/pdb2pka/_apbslib.so
python_optimize
}
python_foreach_impl python_install
if use doc; then
pushd doc > /dev/null
docinto html
dodoc -r *.html images pydoc
popd > /dev/null
fi
use examples && \
insinto /usr/share/${PN}/ && \
doins -r examples
dodoc *md NEWS
}
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