Added support for psb2pka

Package-Manager: portage-2.2.0_alpha3/cvs/Linux x86_64

5 files changed, 194 insertions, 10 deletions

diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
index c2f76c5be1ca..cbd7b581223a 100644
--- a/sci-chemistry/apbs/Manifest
+++ b/sci-chemistry/apbs/Manifest
@@ -5,7 +5,7 @@ AUX apbs-1.2.0-contrib.patch 382 RMD160 4c0c75e57fb6a0c298606d87785a5b9daa8db457
 AUX apbs-1.2.0-link.patch 1716 RMD160 904e7123d32f628171aa728a761c9d7fd95e967d SHA1 63265d0c7c636749292d90efe6a989e7e48251b6 SHA256 37faa758d6439f22853aa9d4524e3e8770437d3986e00649a193b0a97f369bba
 AUX apbs-1.2.1b-autoconf-2.64.patch 952 RMD160 80ed2f351c52764b1c3221b4f5f0e152652c8637 SHA1 dbe725035299182efe82d6ab4a8dcb721601592c SHA256 d9855b84b5b3ca404c463ad9ada7d75d7076d11a929b53bd61f42ed427be9984
 AUX apbs-1.2.1b-install-fix.patch 1467 RMD160 0ed57415822554b888f642b4e3afb296418ead1e SHA1 b7de15116e16c440c7b689182fa465c55fb4a628 SHA256 f67dfdbdff6f89c616c01890efcb059e104be94a33bc8a538275fa4360831d9f
-AUX apbs-1.2.1b-multilib.patch 762 RMD160 24093fa4dec54c95882c77113dd37e59fc0ba5f1 SHA1 3de61489da2cacbef395602ec41596d26f7a88b3 SHA256 d55b62bdade6077e848d3b56f5d38fe937b8ed2779ac639ced5555cf4a6792db
+AUX apbs-1.2.1b-multilib.patch 545 RMD160 c9c103a99c9cedc1e158c4c851b70871e23bf09a SHA1 607c409f46b7fadc0ce0ba0b9353812eb9b0d99b SHA256 f7906454f096c90814418a57cf4796f0bad6be7f7f08d6fc81242ca59f99329f
 AUX apbs-1.2.1b-openmp.patch 1471 RMD160 456d2b1b74a3cb403c7e77814bcb017e7726b578 SHA1 386ffbe0e68398168ede30a33706227e6da64e48 SHA256 ba91c8e780035c884e344c6c84c7bdbd606f3c9919a9aa803ff831d6f41bc905
 AUX apbs-1.2.1b-parallelbuild.patch 371 RMD160 22369e3923307f5cc17602a4cab0326131ac3b72 SHA1 d0b775bf826cc96a799bf1ef9273b79de64164d0 SHA256 907caa55463f5dd0bfc3bbc890c0f97f70bab782c3f76938b59b03e34a9e448c
 AUX apbs-1.2.1b-shared.patch 2508 RMD160 e122f33b7a64a70ebb17631e93085f982ff48074 SHA1 84d835d823e8fa82bc9aa7e274d63c59a4998a12 SHA256 9d35a22be4ea3cd1a0c821b25fbcaf0c44212a2004581e14a8245af4338d73f8
@@ -13,17 +13,20 @@ AUX apbs-1.3-contrib.patch 402 RMD160 18bdf5ef5940e8cb3b610acbc3c855105cb2dca7 S
 AUX apbs-1.3-link.patch 1578 RMD160 e103808470dd500d2077a27906ed4cc1f9ec3aee SHA1 1ea909005bb0ce6976978a93864e976146df381a SHA256 7261cb286599681669ce67b8c4cf376515db177ebece2aa555d730e1dd981284
 AUX apbs-1.3-mainroutines.patch 408 RMD160 00493750cfd8fe278fff4389e642277ca2566dd7 SHA1 3f80728313609d8cb12d582d842cd38cd9eeec79 SHA256 967a6682a71643e4a638e389dba188173a50f9efc1b9091d37dab4c676e5bfa1
 AUX apbs-1.3-openmp.patch 1843 RMD160 58030d378e217752c56b925e7e17ec4b4eb43e52 SHA1 d73cb3d1e061fd03b3785b29c093d8e0aabefc8a SHA256 e9810790f0ed06ce6948bc5b1eea496c23117139277fb04d8830bb064b370164
-AUX apbs-1.3-shared.patch 2880 RMD160 d517c11da5fe9f8c7df3f96199209eb9c3a0f11a SHA1 018012647d8722e1e3bd845b57efcf78f7e73ef2 SHA256 2faa9010d63c52a9cea73730220aca546748ceab2d16b0c273d142fd19990163
+AUX apbs-1.3-python.patch 985 RMD160 03562872ec1996a93c54bcfce16f4dbf15e7adf4 SHA1 1ea3b38334062c09f91b12edc54c5ed4de915e2e SHA256 fc0ba045bc0fb9b9913c5fa04e1d58f92c5c6df29c1586e7198f17d81d3876ec
+AUX apbs-1.3-shared.patch 2888 RMD160 89d7e36f6a361753a178111ce87d01616ccd9864 SHA1 f2178cf365e6c1930fc7a6c661c87064663db7c3 SHA256 f3965767dcdc17e4d97663d2febb7ede717d55736d4ba8554039dda5fd357c93
+AUX apbs-1.3-zlib.patch 1231 RMD160 a0278f6883bf045de59aae921072a756495587b9 SHA1 2635e07429e4ad110c347beeaf0cea1f1d279a85 SHA256 77e4752ccd3c466efcadb95c50004c2f62147e9f220d10a871ec7a72d30eb2be
 DIST apbs-1.2.1b-source.tar.gz 40647966 RMD160 4ba1f72a7f9adcf7b283dc18743488143025b398 SHA1 dc3e6933a987ff9fdf88db510db79b3dacb100d6 SHA256 7d088def1ed7689127eb64014ea44069b9d7bfc995941fe5800ff753d48c87be
 DIST apbs-1.3-source.tar.gz 48625351 RMD160 c075a747dc28f382f3a383a0944a1b20e0c8a9f1 SHA1 1494f36e35f2e4b1a18d4b22516fad4948c6391f SHA256 5fa5b597f7d5a3d9bb55429ec4fefc69e7d0f918d568c3c4a288088c0fde9ef2
 EBUILD apbs-1.2.1b-r4.ebuild 3541 RMD160 c45fce9c4a847495d0f77d15c5aa5867cbad8bc3 SHA1 53635842194acf3c9dc1eac5281bf92894c74635 SHA256 2d449cb42235431190e9ea848291c361ea4280fa7efbde2b06c34be90d043fe3
+EBUILD apbs-1.3-r1.ebuild 4467 RMD160 5dd014c235dc280292437977c705551d4a888b93 SHA1 b7849be2ce2c5f12f9b4fdcec7da57fe77e4787c SHA256 40f0e46ee61be4971a6187ca5b1e44180b7e1558fee9fec85f50a2804a2bb2f5
 EBUILD apbs-1.3.ebuild 4348 RMD160 0eff2ee05c338b5e13922f173f217a2141bd55b8 SHA1 1b289ca30b5d002a310a7a07d5686a8d116e193c SHA256 f11c1f948d4af526eb110ba9ab027c608ccf4af07899e51e7ae4479a572f0be7
-MISC ChangeLog 7426 RMD160 f4bd004063e8711ecac32df22cf84281a0170bad SHA1 5b097131bd37fa96d7048a4ea3911f1f3e3b9c8e SHA256 0ead744fbf3222c22e53668fc8a3b8ce0f8a606f8ff8a93211bfc327eeca5e50
+MISC ChangeLog 7707 RMD160 0257174392c01d2f6c15e8d445dc5ed6b25d431f SHA1 b9c7b0d309bccb307fe322ff75e4c6daa59a440e SHA256 598836d861e82eed16717c643114a7f9fdf52ef44559db117e5eaa57aafad9e2
 MISC metadata.xml 988 RMD160 5f6563d920eeb90db740cba47956926ab837ceb7 SHA1 228ebe33a325ee98da4b692a43e64ccf3ae84495 SHA256 8c6a731f821905e3ae8fce77b651d07d1a7b35db129091938e5b01df6004764a
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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/Manifest b/sci-chemistry/pdb2pqr/Manifest
index 3f7e5bb48992..9632fe7b4d5b 100644
--- a/sci-chemistry/pdb2pqr/Manifest
+++ b/sci-chemistry/pdb2pqr/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX 1.7.0-install.patch 5165 RMD160 6937f62cd4035c40d3575455f1faed6114b1bfd2 SHA1 304cdd46d76745e29a8bd00f4bdbd63dbe4b135c SHA256 965c0bf8077eebc733c60d4e80d05167ce31d7188b01ca43c0fb5c0b27ede22b
 AUX pdb2pqr-1.4.0-automagic.patch 3526 RMD160 c4d662e68352d93f913fdc83b5c733a555a9bc17 SHA1 64598bff69e627a27ffa550ad5f3b38898a3a9cf SHA256 f145bc6222d56410035240e2d8be9fbbb0d70dabccad5c5efc5d4dacd602670a
 AUX pdb2pqr-1.4.0-install.patch 5372 RMD160 8d6c5f3c85ceea0562a767a3792228e6ff0eee96 SHA1 77a70693687be8d14eb3221ffc62a3daccc38f8e SHA256 e93025a88b5d6fff6e1fb45471471aef006d3074ece0b9cd9ff781736a2f1643
@@ -5,6 +8,14 @@ AUX pdb2pqr-1.4.0-ldflags.patch 1293 RMD160 47c2e4b484cf0936176683342afa6e89bb0b
 DIST pdb2pqr-1.5.tar.gz 5747178 RMD160 543545513811bae058e23cfe1f24e02eaa094b87 SHA1 5249064cf4ebfb2291a382121ecea4d457e65e6a SHA256 2a83433b50a57aa0a05102c425cd7b4bb6750487327195ab719992f4186281c5
 DIST pdb2pqr-1.7.tar.gz 6906538 RMD160 606fd8451c52e642a08d5f6c7cdcd51659ea57bc SHA1 23a0a0a5ed54b55269b60b4c4161d914cb30ecca SHA256 8d27f2df430c40b99cde7952d0e96e72e433871a289d39c970b5eefe34345757
 EBUILD pdb2pqr-1.5.0-r2.ebuild 3447 RMD160 487656d0509a17551de50605f4580be46ca39a14 SHA1 19c1ca1a25511be39edfbe9314f881e79faa97cf SHA256 11d120ec76745e2c5a33adbccfeb3357b54cecb175d9dd6a0110533199973276
+EBUILD pdb2pqr-1.7.0-r1.ebuild 4192 RMD160 eb6391b4752e0805eeed7498315a30455ff68689 SHA1 e1f342bd635e68015ae1fa03b701c930f409ac16 SHA256 601e2db397bc422b6b6bb7212a92046ec2696b53a78ab7d30caec387f6cd1690
 EBUILD pdb2pqr-1.7.0.ebuild 3439 RMD160 bb93f2c05697d80fa179df088b280d016ec3fef9 SHA1 8ba85c3a02c810f6526ab125f76a5b366573135e SHA256 0b46dc54389b243d74f657206e3ddb588432bf5de760329c4ac6d6746e0b7496
-MISC ChangeLog 4643 RMD160 cafa081a9338c804523b371081836e47ee75f5fd SHA1 d1b0702655a249dc6d308db96da4aa62a685d6bd SHA256 4034e7e25f3c8cb7f500e6ea73318d9f62a350abf7c6df474fd7a0c800823789
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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"
+}