sci-chemistry/pdb2pqr: Version Bump

Package-Manager: portage-2.2.14/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 178 insertions, 16 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index 6b70f1fa377b..d475c25007f7 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pdb2pqr
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.40 2014/10/24 12:06:42 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.41 2014/10/27 17:03:21 jlec Exp $
+
+*pdb2pqr-1.9.0 (27 Oct 2014)
+
+  27 Oct 2014; Justin Lecher <jlec@gentoo.org> +pdb2pqr-1.9.0.ebuild,
+  +files/pdb2pqr-1.9.0-flags.patch:
+  Version Bump
 
 *pdb2pqr-1.8.0-r1 (24 Oct 2014)
 
diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest
index 0212ac1826ff..56420792667f 100644
--- a/sci-chemistry/pdb2pqr/Manifest
+++ b/sci-chemistry/pdb2pqr/Manifest
@@ -7,31 +7,34 @@ AUX pdb2pqr-1.4.0-install.patch 5372 SHA256 e93025a88b5d6fff6e1fb45471471aef006d
 AUX pdb2pqr-1.4.0-ldflags.patch 1293 SHA256 cfab690b3c128b2c65e217893b546d6e56ffb2ffd7110872f352d6243f56f726 SHA512 4edf74ae59b5ca99e2c492103d16769f300293df07f833d78d8e7d24d85c10531ac7907c5444b65507952f4622608459952ae57835f52af8b0f7e09637f1fcf5 WHIRLPOOL 359a84ecaa55cadfa7cf1bb3c116105c486f1fa737d74b6f2ba2f399147dfcd15d088682c75efee7a69394a3f7adf7dc0c978c060ad64c105b3e96a0b75f49d5
 AUX pdb2pqr-1.8.0-automagic.patch 2544 SHA256 135cfe03fc38a7bef028452010dedab3cc90c1f554cef1139b1d9836824520e9 SHA512 65dc03368909a9378ecda6c8357e9119bd76311b5fd6dc0ce00ff7d5b948190ad9f07ac3626dad04915928558f911f4deea5f44725e6cf029ca26dcb2e54b76c WHIRLPOOL 8462f3288722bcaca651845242b3354f365a9686a6400d3fae9c8ca69e3fa55d9282a62bdc2a3374eb468fbfae2611f8fa700ddecc404943c2a08080fad34b06
 AUX pdb2pqr-1.8.0-ldflags.patch 1098 SHA256 b9ab2740e062b130c4b61d385b762d4ce54ec3d6a040f37b8b501b4f107890b8 SHA512 0bd250efd74c70096011ed6f9f6fd2f22a987bbe0355f5ba33ad4675141d1d7b02e9eaa90bc1c7328454da2225183a56dae6acbaae97a929b2455430ca55ab4e WHIRLPOOL 75b4110d4259454551256c3a647b1981aa4ee040f73baf8f3e5ce1f0a4b01b54cdf2879030265dde4c7dbc0a5c60bd400a0d498f00446c88125d147c291ef107
+AUX pdb2pqr-1.9.0-flags.patch 1392 SHA256 478b86cf3871e39b9d231a10474abbcade07eceb32db2a83c0e68bbd2c1f5f32 SHA512 deed0aef88dc43515745204f2b4209bd6b42702d9004d48797d642b8f497229424bd0bb92017982cec54c448ea35de563bd42017cd5dc042840acae8495d135b WHIRLPOOL 7280c677dbfeb309c6c66d495c857a581fbac80801f9241c20ff17a2c6f4e051929f675807ec30f8dce1fd5337937c76e857b955570f2c1f134855a2b7c0ec2c
 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
-MISC ChangeLog 6550 SHA256 8f4756212aae809b24de13d6d162323faa8f7049c5e65c64e211a4e99789a2b9 SHA512 8eb5feb80a501fb143ec309809ef2f6f1e9c2ce40f5e67e87a59af3102328326bba62c12de254c87feef04f0f31f29761d38ff58b75f5f14123368d87b4fd49b WHIRLPOOL 9dbb00d7bc21ccd5f255bc22e578e25340990f434288ec5b4c5c782dd3462f479bfb5153e77810ae885e6664717a50d6177917ce868ed1695a85f4bf0e68749b
+EBUILD pdb2pqr-1.9.0.ebuild 2885 SHA256 3cc1b5fb2d0fa57fe4f22b508780c70a491c58214c85010d5af6ebce7de7cce7 SHA512 28004d4566cf7bd9e71333b8daa99b4059c21e4f5de6deeaece9f8c049949d58bfad08bee4c62212097a42aeaaba393d3b54d7074f15b69ed85050ab0396686c WHIRLPOOL 2c34524521ad4a2efca448c84957eaa59b35f7f56903aceb5c829e35d1703870c8bd5e98eee29e6531bab02193e5f64fdbbb6880050e4c63b6ade82ab6c0394b
+MISC ChangeLog 6702 SHA256 ad7303307bf7a5594083d664c87c6f7e543109dcd819be76dba12111a82c0ad4 SHA512 2773c3ff206ddcd7c424ade15a6b63293b6a3daf32f578981eca71f7c3cbf307f342f45493094395e0967db8b7a2a6886760462f06658183fd9c0785a0f45e5a WHIRLPOOL cabfd1e3a56200659205025c0fdcf69bcdd03036bc236674e7cd680b620867ae44ee4b2f7e160c28dd7cd5b4246076dd078aad5a57192bb559f719206645fe2a
 MISC metadata.xml 312 SHA256 8429f63a843f77336614a26f2dea0611353036db4a73026665c69fe09269f109 SHA512 50808ebe11a46f56e2a1fe043274e3dc04e681044dc68762df143cf94df9f2e95c8f5eee201be100479d363dde91ea1f6b7e8138b238f143c4743659b9643e4c WHIRLPOOL 735e2ebaee7b1d623695e6b3b60fe92b16be8264bf6d8a4f2b7b24c43ae49048ded02af0fa8a2e58e8f9ac4374831d708438168835f1908403f5c31f27cb9423
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diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch
new file mode 100644
index 000000000000..fac32b233e6b
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.9.0-flags.patch
@@ -0,0 +1,45 @@
+ pdb2pka/SConscript           | 9 ++++++++-
+ pdb2pka/substruct/SConscript | 6 ++++++
+ 2 files changed, 14 insertions(+), 1 deletion(-)
+
+diff --git a/pdb2pka/SConscript b/pdb2pka/SConscript
+index 583cdc5..6c30011 100644
+--- a/pdb2pka/SConscript
++++ b/pdb2pka/SConscript
+@@ -1,4 +1,11 @@
+ Import('env')

++import os

++

++env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())

++env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())

++env['CXX'] = os.environ['CXX']

++env['LINK'] = os.environ['CXX']

++

+ 

+ if env['REBUILD_SWIG']:

+     pyc = env.LoadableModule('_pMC_mult', ['pMC_mult.cpp', 'pMC_mult.i'])

+@@ -9,4 +16,4 @@ Default(pyc)
+     

+ algorithms_module = SConscript('substruct/SConscript')

+ 

+-Return('pyc algorithms_module')
+\ No newline at end of file
++Return('pyc algorithms_module')

+diff --git a/pdb2pka/substruct/SConscript b/pdb2pka/substruct/SConscript
+index 7dbcdb0..56fb577 100644
+--- a/pdb2pka/substruct/SConscript
++++ b/pdb2pka/substruct/SConscript
+@@ -1,7 +1,13 @@
+ import distutils

+ import numpy

++import os

+ Import('env')

+ 

++env['CCFLAGS'].extend(os.environ['CXXFLAGS'].split())

++env['LINKFLAGS'].extend(os.environ['LDFLAGS'].split())

++env['CXX'] = os.environ['CXX']

++env['LINK'] = os.environ['CXX']

++

+ env.Append(CPPPATH=[distutils.sysconfig.get_python_inc(), numpy.get_include()])

+ 

+ algorithms_pyc = env.LoadableModule('Algorithms', ['Algorithms.cpp'])

diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0.ebuild
new file mode 100644
index 000000000000..360ae3fbd21e
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.9.0.ebuild
@@ -0,0 +1,108 @@
+# 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 1.1 2014/10/27 17:03:21 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools 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[${PYTHON_USEDEP}]
+	sci-chemistry/openbabel[python]
+	opal? ( dev-python/zsi[${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
+}