diff options
Diffstat (limited to 'sci-chemistry/pdb2pqr')
| -rw-r--r-- | sci-chemistry/pdb2pqr/ChangeLog | 8 | ||||
| -rw-r--r-- | sci-chemistry/pdb2pqr/metadata.xml | 3 | ||||
| -rw-r--r-- | sci-chemistry/pdb2pqr/pdb2pqr-1.7.0-r1.ebuild | 163 |
3 files changed, 172 insertions, 2 deletions
diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog index 07f912ac9f9e..41728a45d3ae 100644 --- a/sci-chemistry/pdb2pqr/ChangeLog +++ b/sci-chemistry/pdb2pqr/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-chemistry/pdb2pqr # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.28 2010/10/15 18:56:50 ranger Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.29 2010/11/04 09:35:19 jlec Exp $ + +*pdb2pqr-1.7.0-r1 (04 Nov 2010) + + 04 Nov 2010; Justin Lecher <jlec@gentoo.org> +pdb2pqr-1.7.0-r1.ebuild, + metadata.xml: + Added support for psb2pka 15 Oct 2010; Brent Baude <ranger@gentoo.org> pdb2pqr-1.5.0-r2.ebuild: stable ppc, bug 321897 diff --git a/sci-chemistry/pdb2pqr/metadata.xml b/sci-chemistry/pdb2pqr/metadata.xml index 03e1d8b50494..a99cdb01d6af 100644 --- a/sci-chemistry/pdb2pqr/metadata.xml +++ b/sci-chemistry/pdb2pqr/metadata.xml @@ -3,6 +3,7 @@ <pkgmetadata> <herd>sci-chemistry</herd> <use> - <flag name='opal'>Add web interface via opal</flag> + <flag name='opal'>Add web interface via opal</flag> + <flag name='pdb2pka'>Install experimental pdb2pka interface</flag> </use> </pkgmetadata> diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0-r1.ebuild new file mode 100644 index 000000000000..26010325ccd9 --- /dev/null +++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0-r1.ebuild @@ -0,0 +1,163 @@ +# Copyright 1999-2010 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-r1.ebuild,v 1.1 2010/11/04 09:35:20 jlec Exp $ + +EAPI="3" + +SUPPORT_PYTHON_ABIS="1" +PYTHON_EXPORT_PHASE_FUNCTIONS="1" +RESTRICT_PYTHON_ABIS="2.4 3.*" + +inherit eutils fortran multilib flag-o-matic distutils python versionator toolchain-funcs + +FORTRAN="g77 gfortran" + +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}/${MY_P}.tar.gz" + +SLOT="0" +IUSE="doc examples opal +pdb2pka" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=" + dev-python/numpy + sci-chemistry/openbabel + opal? ( dev-python/zsi ) + pdb2pka? ( sci-chemistry/apbs[python,-mpi] )" +DEPEND="${DEPEND}" + +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 ${MAXATOMS} during calculations" + fi + python_pkg_setup +} + +src_prepare() { + epatch "${FILESDIR}"/${PN}-1.4.0-ldflags.patch + epatch "${FILESDIR}"/${PN}-1.4.0-automagic.patch + epatch "${FILESDIR}"/${PV}-install.patch + sed '50,200s:CWD:DESTDIR:g' -i Makefile.am \ + || die "Failed to fix Makefile.am" + python_src_prepare + preparation() { + eautoreconf + } + python_execute_function -s preparation + tc-export CC +} + +src_configure() { + # we need to compile the *.so as pic + append-flags -fPIC + FFLAGS="${FFLAGS} -fPIC" + + configuration() { + # Avoid automagic to numeric + NUMPY="${EPREFIX}/$(python_get_sitedir)" \ + F77="${FORTRANC}" \ + econf \ + --enable-propka \ + --with-max-atoms=${MAXATOMS:-10000} \ + $(use_enable pdb2pka) \ + $(use_with opal) || \ + die "econf failed" + } + python_execute_function -s configuration +} + +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}/${PN}.py \$* + EOF + + cat >> "${T}"/pdb2pka-$(python_get_version) <<-EOF + #!/bin/sh + $(PYTHON) ${EPREFIX}${INPATH}/pdb2pka/pka.py \$* + EOF + + dobin "${T}"/{${PN},pdb2pka}-$(python_get_version) || die "Failed to install pdb2pqr wrapper." + + insinto "${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 "${INPATH}"/pdb2pka + doins pdb2pka/*.{py,so,DAT,h} || \ + die "Failed to install pdb2pka." + + dosym ../../apbs/_apbslib.so "${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 + 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" +} |