Added support for psb2pka

(Portage version: 2.2.0_alpha3/cvs/Linux x86_64)

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"
+}