# ChangeLog for sci-chemistry/pdb2pqr
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.46 2015/01/04 19:15:11 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.47 2015/01/04 19:17:35 jlec Exp $
+
+ 04 Jan 2015; Justin Lecher <jlec@gentoo.org> -pdb2pqr-1.7.0.ebuild,
+ -pdb2pqr-1.7.0-r2.ebuild, -pdb2pqr-1.8.0-r1.ebuild, -pdb2pqr-1.9.0.ebuild:
+ Drop old
04 Jan 2015; Justin Lecher <jlec@gentoo.org> pdb2pqr-1.9.0-r1.ebuild:
Drop obsolete dep
AUX pdb2pqr-1.9.0-flags.patch 1392 SHA256 478b86cf3871e39b9d231a10474abbcade07eceb32db2a83c0e68bbd2c1f5f32 SHA512 deed0aef88dc43515745204f2b4209bd6b42702d9004d48797d642b8f497229424bd0bb92017982cec54c448ea35de563bd42017cd5dc042840acae8495d135b WHIRLPOOL 7280c677dbfeb309c6c66d495c857a581fbac80801f9241c20ff17a2c6f4e051929f675807ec30f8dce1fd5337937c76e857b955570f2c1f134855a2b7c0ec2c
AUX pdb2pqr-1.9.0-install-py.patch 578 SHA256 c82c11eb421a839710d40bfb3de4d99852ef69dc9b35b1ac31f7b51b36ff512d SHA512 902ad717e32790e9c691851dc4b92412f07ac79caf74b2b5794a10fa75cca7fa19e8814df4d8ba71bd2ecc98a3d777d0b79e6e43009171a32e8c99756d81d4d2 WHIRLPOOL 94348fe88a1910e916ca0d428a78636e5fe8371582a80dbbbda07d433d1fb8a35157a73d525eac88bd9dac6dc1c3a913288fdb7bd06f7584553b0b5c17aa17da
DIST pdb2pqr-1.5.tar.gz 5747178 SHA256 2a83433b50a57aa0a05102c425cd7b4bb6750487327195ab719992f4186281c5
-DIST pdb2pqr-1.7.tar.gz 6906538 SHA256 8d27f2df430c40b99cde7952d0e96e72e433871a289d39c970b5eefe34345757 SHA512 64938ad08f2e86e0e1a121a2401aa599ffeecd313e5e69dd832e6b5afd698995aba3e96aec5e7c27c433d1429cbaa41d4bae1200e380fd2b954c08fbcd6a1484 WHIRLPOOL 5e937daa3a18c08988bc58167227c8143e7176ccb98cc041f7ec0138a0f991c94e38500bba5f196f4c1486085cb782017cdaa344ac5e8503a18087697ff2269d
-DIST pdb2pqr-1.8.tar.gz 6781507 SHA256 78470c21e5dc7afa12d782559b11d2cb04b755d93086bb80a43bd09fa0c3521f SHA512 3f640979d21511c4b08ab20c49f4662d959dddf67d9fedfb5e528d0869d897cd5770e77059b78a16c9778760593f410caf39eaaae2b664113af6875052873316 WHIRLPOOL bd582efba5544ec6450cf94e06f9449ba9d6a2861d64d0f88616302e3f93bf16332f210eecb01e268e2b1022bf6c5cbce3667b006b8e9345c9d18cebca373e74
DIST pdb2pqr-src-1.9.0.tar.gz 9051969 SHA256 d9d91bf27a023732be33d1d780ef283ae28d3b0e256c53e86c37ac001dd7ef53 SHA512 7f3f191cca9879a0e166e82700c706f8c99bb66558a218e54845f10c3324b6c45d413da80b0782d96a8d56df1463262609db075aba3768db3942cb928ee7b98f WHIRLPOOL 4a4b883200dad3e7467392e508c2372ad6876e78005da14e5747f3b7b12d0e3d5695e3cc590812b835ae67703819b201620809dff05af0a7c363c23d22046bae
EBUILD pdb2pqr-1.5.0-r2.ebuild 3668 SHA256 09b59ed6461c60ca7fdcdca1604306579f054db992b1833226cce00566f05a7a SHA512 2d1ce04378e15d814dfc73d407149465e61b04d646710b918708e4f8eb1a6f1973c85cfca0d63dfa8f85aa6cf1e61b3a950c82833ff7853e2d6d3bc223890f6d WHIRLPOOL 3e4da41f599befa813ec693c8fd2b42ffda163047a43ecbe8f83a3fd63e1066a61e05e56993b2fa3fcc507e652ad60ad3aeca7c6fbb1e967edcc1ead362b943d
-EBUILD pdb2pqr-1.7.0-r2.ebuild 3859 SHA256 3c0213ade23aa4a13f9091ca96d69dc1c4f2eb2b80195759b1b4eb7b3ac5072e SHA512 61f4c29714a428fb956c7cb47c47c8a7d50d4796ef5dd406f88a9336494732d732cef13608fabfd055a78407eaf091fdc548e3c91a0e4547e55c7775e33e83ea WHIRLPOOL 34f203002dded65e8723b9220a310f183fdff28df8069aab1f6f464f6cc3a3a3c44f07fe6e51e043c9d2dcfc2cc98da2bed95eaf73ffc0645746f2640f56b8b7
-EBUILD pdb2pqr-1.7.0.ebuild 3661 SHA256 83a908824110516331cb4e7a8acce26c3992971af13d2514ca0345ab14d3b44f SHA512 f6a942958f120eeee05b9e70751cca487ba06c29a39127f65075936b41521575e089b8c764f53e06a2c286899d4fdf16be9eefc46c0e9942c03ac1c74803c093 WHIRLPOOL dc3c3292217517bb3503fd53313e055ccf008f556eea319b738f88fb82cbc18be1c76099a6dcde4cc32861b8ecf9362554a0039fae896aeacf802e0ae2b05eb4
-EBUILD pdb2pqr-1.8.0-r1.ebuild 2710 SHA256 0e9a72ee39aefb50240535fd8c3e63dc10d6780ddfa4c351faca04d681798221 SHA512 06343ea03459c63d16b2217c88ede20bceb3c55f9b9ff59608a81f5f443168ac358948dfa5e6628910e654830fba6a1587f13d46d021e411cea79402215e12f6 WHIRLPOOL 3bc926750815c591c94a83c7c7cbadd638da6b4c499a067d9273b5168454637e0b37f99e736f801dc55adee1f9610b43133b2989d3b1c72eb8093aa0c7bcaa57
EBUILD pdb2pqr-1.9.0-r1.ebuild 3034 SHA256 4b1aa523c69bd312c61aa59f3c7cc5767d9aabf419a13366c249008fa5a6ab42 SHA512 85edccc6a3699f1f45d961c39ad451b782c516c74caf4ae15baf484e424c95652d8cf6e6a7e333dac5a477a48503b575a20c5652573b1726dfb163326a259df5 WHIRLPOOL 6887ffd80639828c98b62989fd719659151dba04a43693950d35a33fce44a00fea62fe63f9db0d5dc8270cb8ee1a71d346b1fbd5784fb13714b46e435e8a4c8a
-EBUILD pdb2pqr-1.9.0.ebuild 2928 SHA256 b91fd804c3dcfb6321d3924a438622f011101270a364814c5da05f2c89b639d5 SHA512 e575f33dcb0c3c1a0156aa95866ee811c26ae0e3600e3b0bbfff96fd1a3c26e2f3b79d9ff426b97fb3e7d7e0806e91be582afc3a92c9e836a5c3feb9a97a2c57 WHIRLPOOL bd39ced8cf6e53af40c419b0599f4cb76d15f843fc468d5acbb1056bb6135085d2097c58be3629b020649493dbc650c015e1baa597600de4e571f0a696d2b99c
-MISC ChangeLog 7353 SHA256 676f471df1ad0206587308e3a644ad1e08bb008de4db4d351bdcc23a08c0881c SHA512 483f04dbe1df4785035618d4c196e97e8cbbbe9b7a25ecc23f428815c8e43ff49e2bd19663caee196b8dd9b34ed23105afff38782e4cdf3138be4a7a801a9619 WHIRLPOOL 8b704e8da59024d3ea12498864f31182e318b08dba1b2a1fa3a44972253136d1db350c49aa32b428777a6e94beeb23bff22283a740894d228210812deab10f65
+MISC ChangeLog 7512 SHA256 0f69f6fe20510ab388cbd04420335510c942e3845f8899de9467611cd5cd5616 SHA512 ef214446229995bab6ecfbd376f48cb9847dafca47094a267c7ff0d491b5f5836a8ee31bf637c9336b15f8a23b4a24a22794d131313c9035bd3823a3a7ccad5c WHIRLPOOL 022055b295f11cbc0dc03a26702880f47843e0488902223e5ef00ea5d51e284a6a551345edb919fb1b3df2f678c70eba2ecc8120993b16f62fb97a3995aac768
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+++ /dev/null
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0-r2.ebuild,v 1.2 2012/10/19 10:10:18 jlec Exp $
-
-EAPI=4
-
-PYTHON_DEPEND="2:2.5"
-SUPPORT_PYTHON_ABIS="1"
-PYTHON_EXPORT_PHASE_FUNCTIONS="1"
-RESTRICT_PYTHON_ABIS="2.4 3.* 2.7-pypy-*"
-
-inherit autotools eutils fortran-2 flag-o-matic python toolchain-funcs versionator
-
-MY_PV=$(get_version_component_range 1-2)
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-LICENSE="BSD"
-HOMEPAGE="http://pdb2pqr.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-SLOT="0"
-IUSE="doc examples opal +pdb2pka"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="
- dev-python/numpy
- sci-chemistry/openbabel
- opal? ( dev-python/zsi )
- pdb2pka? ( sci-chemistry/apbs[python,-mpi] )"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
- if [[ -z ${MAXATOMS} ]]; then
- einfo "If you like to have support for more then 10000 atoms,"
- einfo "export MAXATOMS=\"your value\""
- else
- einfo "Allow usage of ${MAXATOMS} during calculations"
- fi
- python_pkg_setup
- fortran-2_pkg_setup
-}
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/${PN}-1.4.0-ldflags.patch \
- "${FILESDIR}"/${PN}-1.4.0-automagic.patch \
- "${FILESDIR}"/${PV}-install.patch
- sed \
- -e '50,200s:CWD:DESTDIR:g' \
- -i Makefile.am || die
-
- python_src_prepare
-
- preparation() {
- sed \
- -e "s:python\$PY_VERSION:$(PYTHON):g" \
- -i configure.ac || die
-
- eautoreconf
- }
- python_execute_function -s preparation
-
- tc-export CC
-}
-
-src_configure() {
- # we need to compile the *.so as pic
- append-flags -fPIC
- FFLAGS="${FFLAGS} -fPIC"
-
- configuration() {
- # Avoid automagic to numeric
- econf \
- --enable-propka \
- --with-max-atoms=${MAXATOMS:-10000} \
- $(use_enable pdb2pka) \
- $(use_with opal) \
- NUMPY="${EPREFIX}/$(python_get_sitedir)" \
- F77="$(tc-getFC)"
- }
- python_execute_function -s configuration
-}
-
-src_compile() {
- python_execute_function -d -s
-}
-
-src_test() {
- testing() {
- emake -j1 test
- }
- python_execute_function -s testing
-}
-
-src_install() {
- installation() {
- dodir $(python_get_sitedir)/${PN}
- emake -j1 DESTDIR="${ED}$(python_get_sitedir)/${PN}" \
- PREFIX="" install
-
- INPATH="$(python_get_sitedir)/${PN}"
-
- # generate pdb2pqr wrapper
- cat >> "${T}"/${PN}-$(python_get_version) <<-EOF
- #!/bin/sh
- $(PYTHON) ${EPREFIX}${INPATH}/${PN}.py \$*
- EOF
-
- cat >> "${T}"/pdb2pka-$(python_get_version) <<-EOF
- #!/bin/sh
- $(PYTHON) ${EPREFIX}${INPATH}/pdb2pka/pka.py \$*
- EOF
-
- dobin "${T}"/{${PN},pdb2pka}-$(python_get_version)
-
- insinto "${INPATH}" && doins __init__.py
-
- exeinto "${INPATH}" && doexe ${PN}.py
-
- insinto "${INPATH}"/dat && doins dat/*
-
- exeinto "${INPATH}"/extensions && doexe extensions/*
-
- insinto "${INPATH}"/src && doins src/*.py
-
- exeinto "${INPATH}"/propka && doexe propka/_propkalib.so
-
- insinto "${INPATH}"/propka && doins propka/propkalib.py propka/__init__.py
-
- insinto "${INPATH}"/pdb2pka && doins pdb2pka/*.{py,so,DAT,h}
-
- dosym ../../apbs/_apbs.so "${INPATH}"/pdb2pka/_apbslib.so
- dosym ../../apbs/apbslib.py "${INPATH}"/pdb2pka/apbslib.py
- dosym ../../apbs/apbslib.pyc "${INPATH}"/pdb2pka/apbslib.pyc
- dosym ../../apbs/apbslib.pyo "${INPATH}"/pdb2pka/apbslib.pyo
- }
- python_execute_function -s installation
-
- dosym ${PN}-$(python_get_version -f) /usr/bin/${PN}
- dosym pdb2pka-$(python_get_version -f) /usr/bin/pdb2pka
-
- if use doc; then
- pushd doc > /dev/null
- sh genpydoc.sh || die "genpydoc failed"
- dohtml -r *.html images pydoc
- popd > /dev/null
- fi
-
- use examples && \
- insinto /usr/share/${PN}/ && \
- doins -r examples
-
- dodoc ChangeLog NEWS README AUTHORS
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
+++ /dev/null
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0.ebuild,v 1.9 2012/10/19 10:10:18 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-SUPPORT_PYTHON_ABIS="1"
-PYTHON_EXPORT_PHASE_FUNCTIONS="1"
-RESTRICT_PYTHON_ABIS="2.4 3.*"
-
-inherit autotools eutils fortran-2 flag-o-matic python toolchain-funcs versionator
-
-MY_PV=$(get_version_component_range 1-2)
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-LICENSE="BSD"
-HOMEPAGE="http://pdb2pqr.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-SLOT="0"
-IUSE="doc examples opal"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="
- dev-python/numpy
- sci-chemistry/openbabel
- opal? ( dev-python/zsi )"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
- fortran-2_pkg_setup
- python_pkg_setup
-}
-
-src_prepare() {
- epatch "${FILESDIR}"/${PN}-1.4.0-ldflags.patch
- epatch "${FILESDIR}"/${PN}-1.4.0-automagic.patch
- epatch "${FILESDIR}"/${PV}-install.patch
- sed '50,200s:CWD:DESTDIR:g' -i Makefile.am \
- || die "Failed to fix Makefile.am"
- python_src_prepare
- preparation() {
- eautoreconf
- }
- python_execute_function -s preparation
-}
-
-src_configure() {
- # we need to compile the *.so as pic
- append-flags -fPIC
- FFLAGS="${FFLAGS} -fPIC"
-
- configuration() {
- # Avoid automagic to numeric
- NUMPY="${EPREFIX}/$(python_get_sitedir)" \
- F77="$(tc-getFC)" \
- econf \
- $(use_with opal)
- }
- python_execute_function -s configuration
-}
-
-src_compile() {
- compilation() {
- emake || die
- }
- python_execute_function -s compilation
-}
-
-src_test() {
- testing() {
- emake -j1 test \
- || die "tests failed"
- }
- python_execute_function -s testing
-}
-
-src_install() {
- installation() {
- dodir $(python_get_sitedir)/${PN}
- emake -j1 DESTDIR="${ED}$(python_get_sitedir)/${PN}" \
- PREFIX="" install || die "install failed"
-
- INPATH="$(python_get_sitedir)/${PN}"
-
- # generate pdb2pqr wrapper
- cat >> "${T}"/${PN}-$(python_get_version) <<-EOF
- #!/bin/sh
- $(PYTHON) ${EPREFIX}/${INPATH}/${PN}.py \$*
- EOF
-
- dobin "${T}"/${PN}-$(python_get_version) || die "Failed to install pdb2pqr wrapper."
-
- insinto "${INPATH}"
- doins __init__.py || \
- die "Setting up the pdb2pqr site-package failed."
-
- exeinto "${INPATH}"
- doexe ${PN}.py || die "Installing pdb2pqr failed."
-
- insinto "${INPATH}"/dat
- doins dat/* || die "Installing data failed."
-
- exeinto "${INPATH}"/extensions
- doexe extensions/* || \
- die "Failed to install extensions."
-
- insinto "${INPATH}"/src
- doins src/*.py || die "Installing of python scripts failed."
-
- exeinto "${INPATH}"/propka
- doexe propka/_propkalib.so || \
- die "Failed to install propka."
-
- insinto "${INPATH}"/propka
- doins propka/propkalib.py propka/__init__.py || \
- die "Failed to install propka."
-
- insinto "${INPATH}"/pdb2pka
- doins pdb2pka/*.{py,so,DAT,h} || \
- die "Failed to install pdb2pka."
-
- insinto "${INPATH}"/pdb2pka/
- doins pdb2pka/*.{py,so,DAT,h} || \
- die "Failed to install pdb2pka."
- }
- python_execute_function -s installation
-
- dosym ${PN}-$(python_get_version -f) /usr/bin/${PN}
-
- if use doc; then
- cd doc
- sh genpydoc.sh \
- || die "genpydoc failed"
- dohtml -r *.html images pydoc \
- || die "failed to install html docs"
- cd -
- fi
-
- if use examples; then
- insinto /usr/share/${PN}/
- doins -r examples || die "Failed to install examples."
- fi
-
- dodoc ChangeLog NEWS README AUTHORS || \
- die "Failed to install docs"
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
+++ /dev/null
-# 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-1.8.0-r1.ebuild,v 1.1 2014/10/24 12:06:42 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools eutils fortran-2 flag-o-matic python-single-r1 toolchain-funcs versionator
-
-MY_PV=$(get_version_component_range 1-2)
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-LICENSE="BSD"
-HOMEPAGE="http://www.poissonboltzmann.org/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-SLOT="0"
-IUSE="doc examples opal +pdb2pka"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-
-REQUIRED_USE="${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="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
- if [[ -z ${MAXATOMS} ]]; then
- einfo "If you like to have support for more then 10000 atoms,"
- einfo "export MAXATOMS=\"your value\""
- else
- einfo "Allow usage of ${MAXATOMS} during calculations"
- fi
- fortran-2_pkg_setup
- python-single-r1_pkg_setup
-}
-
-src_prepare() {
- rm -rf contrib/* || die
- epatch \
- "${FILESDIR}"/${P}-ldflags.patch \
- "${FILESDIR}"/${PN}-1.4.0-automagic.patch \
- "${FILESDIR}"/1.7.0-install.patch
- sed \
- -e '50,200s:CWD:DESTDIR:g' \
- -i Makefile.am || die
-
- eautoreconf
-
- tc-export CC
-}
-
-src_configure() {
- # we need to compile the *.so as pic
- append-flags -fPIC
- FFLAGS="${FFLAGS} -fPIC"
- econf \
- --with-max-atoms=${MAXATOMS:-10000} \
- --with-python="${PYTHON}" \
- $(usex pdb2pka "" --disable-pdb2pka) \
- $(use_with opal) \
- NUMPY="${EPREFIX}/$(python_get_sitedir)" \
- F77="$(tc-getFC)"
-}
-
-src_compile() {
- default
- if use doc; then
- pushd doc > /dev/null
- sh genpydoc.sh || die "genpydoc failed"
- popd > /dev/null
- fi
-}
-
-src_test() {
- emake -j1 test
-}
-
-src_install() {
- local lib
- dodir $(python_get_sitedir)/${PN}
- emake -j1 \
- DESTDIR="${ED}$(python_get_sitedir)/${PN}" \
- PREFIX="" install
- INPATH="$(python_get_sitedir)/${PN}"
-
- make_wrapper ${PN} "${PYTHON} /$(python_get_sitedir)/${PN}/${PN}.py"
- make_wrapper pdb2pka "${PYTHON} /$(python_get_sitedir)/${PN}/pdb2pka/pka.py"
-
- for lib in _apbs.so apbslib.py{,c,o}; do
- dosym /usr/share/apbs/tools/python/${lib} $(python_get_sitedir)/${PN}/pdb2pka/${lib}
- done
-
- if use doc; then
- pushd doc > /dev/null
- dohtml -r *.html images pydoc
- popd > /dev/null
- fi
-
- use examples && \
- insinto /usr/share/${PN}/ && \
- doins -r examples
-
- dodoc ChangeLog NEWS README AUTHORS
-
- python_optimize
-}
+++ /dev/null
-# 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 1.3 2014/10/29 02:42:21 patrick Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit 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[${PYTHON_USEDEP}]
- sci-chemistry/openbabel[python]
- sci-chemistry/openbabel-python[${PYTHON_USEDEP}]
- opal? ( dev-python/zsi[${PYTHON_USEDEP}] )
- pdb2pka? ( sci-chemistry/apbs[${PYTHON_USEDEP},-mpi] )"
-DEPEND="${RDEPEND}
- dev-lang/swig:0"
-
-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
-}
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