sci-chemistry/pdb2pqr: Version Bump

(Portage version: 2.2.14/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

5 files changed, 236 insertions, 7 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index 5bbf9582a6ba..c90d76e18459 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/pdb2pqr
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.37 2012/10/19 10:10:18 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.38 2014/10/24 10:54:05 jlec Exp $
+
+*pdb2pqr-1.8.0 (24 Oct 2014)
+
+  24 Oct 2014; Justin Lecher <jlec@gentoo.org> +pdb2pqr-1.8.0.ebuild,
+  +files/pdb2pqr-1.8.0-automagic.patch, +files/pdb2pqr-1.8.0-ldflags.patch,
+  metadata.xml:
+  Version Bump
 
   19 Oct 2012; Justin Lecher <jlec@gentoo.org> pdb2pqr-1.5.0-r2.ebuild,
   pdb2pqr-1.7.0.ebuild, pdb2pqr-1.7.0-r2.ebuild:
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch
new file mode 100644
index 000000000000..c218fe6a816e
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch
@@ -0,0 +1,75 @@
+diff -Naur pdb2pqr-1.4.0/configure.ac pdb2pqr-1.4.0.new/configure.ac
+--- pdb2pqr-1.4.0/configure.ac	2009-04-02 10:53:56.000000000 -0400
++++ pdb2pqr-1.4.0.new/configure.ac	2009-09-24 19:36:47.000000000 -0400
+@@ -255,38 +255,6 @@
+ 
+   # Test for Numeric install
+   AC_MSG_CHECKING([whether you defined Numeric or Numpy])
+-  if (test -n "${NUMERIC}") ; then
+-    AC_MSG_RESULT([yes])
+-    NUMERIC_INC=`find ${NUMERIC} -iname "arrayobject.h" | tail -n1`
+-    if test "$NUMERIC_INC" = ""; then
+-      AC_MSG_ERROR([Please check your NUMERIC path.  arrayobject.h cannot be found in ${NUMERIC}])
+-    fi
+-    NUMERIC_INC=`dirname ${NUMERIC_INC}`
+-    NUMERIC_LIB=`find ${NUMERIC} -iname "Numeric.pth" | tail -n1`
+-    if test "${NUMERIC_LIB}" = ""; then
+-      AC_MSG_ERROR([Please check your NUMERIC path.  Numeric.pth cannot be found in ${NUMERIC}])
+-    fi
+-    NUMERIC_NAME=`cat ${NUMERIC_LIB}`
+-    NUMERIC_LIB=`dirname ${NUMERIC_LIB}`
+-    NUMERIC_LIB=${NUMERIC_LIB}/${NUMERIC_NAME}
+-    if test "${PACKAGE_PATH}" = ""; then
+-      PACKAGE_PATH=${NUMERIC_LIB}
+-    else
+-      PACKAGE_PATH="${PACKAGE_PATH}:${NUMERIC_LIB}"
+-    fi
+-    PY_NUMERIC="-I${NUMERIC_INC} "
+-    PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC"
+-  else
+-    AC_MSG_RESULT([no])	
+-    AC_MSG_CHECKING([for Numeric include files])
+-    if test -f $PY_PREFIX/include/python$PY_VERSION/Numeric/arrayobject.h; then
+-      PY_NUMERIC="-I$PY_PREFIX/include/python$PY_VERSION/Numeric"   
+-      AC_MSG_RESULT([$PY_NUMERIC])
+-      PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC"
+-    else
+-      AC_MSG_RESULT([no])
+-    fi
+-  fi
+ 
+   # If failed, test for numpy
+   AC_MSG_CHECKING([whether you defined numpy])
+@@ -457,29 +425,14 @@
+   HAVE_PDB2PQR_OPAL=1
+ fi
+ 
+-if test "$PDB2PQR_OPAL_URL" != ""; then 
++if test "$PDB2PQR_OPAL_URL" != "no"; then 
+   HAVE_PDB2PQR_OPAL=1
+   if test -d $PY_PREFIX/lib/python$PY_VERSION/site-packages/ZSI ; then
+     echo ZSI is installed
+   else
+     #  need to install ZSI
+-    echo Installing ZSI.  This might take a while...
+-    cd contrib/ZSI-2.1-a1 
+-    if test `whoami` = "root"; then
+-      $py_path setup.py install
+-    else
+-      zsi_install="true"
+-      mkdir -p ${prefix}lib/python$PY_VERSION/site-packages
+-      export PYTHONPATH=${prefix}lib/python$PY_VERSION/site-packages
+-      $py_path setup.py install --prefix=${prefix}
+-      if test -d ${prefix}ZSI ; then
+-        echo ZSI is installed
+-      else
+-        cp -r ./build/lib/ZSI ${prefix}ZSI
+-      fi
+-      PYTHONPATH=""
+-    fi 
+-    cd ../..
++    echo Missing ZSI
++    exit 1
+   fi
+ fi  
+ 
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch
new file mode 100644
index 000000000000..5a7e04419ce6
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch
@@ -0,0 +1,30 @@
+ pdb2pka/Makefile.am           | 2 +-
+ pdb2pka/substruct/Makefile.am | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/pdb2pka/Makefile.am b/pdb2pka/Makefile.am
+index 75f6ffd..e40a2f6 100644
+--- a/pdb2pka/Makefile.am
++++ b/pdb2pka/Makefile.am
+@@ -16,7 +16,7 @@ SUBDIRS          = substruct
+ 
+ noinst_PROGRAMS         = _pMC_mult.so
+ _pMC_mult_so_SOURCES     = pMC_mult.cpp pMC_mult_wrap.cpp  
+-_pMC_mult_so_LINK        = $(CXX) -o $@ $(PY_SHARED)
++_pMC_mult_so_LINK        = $(CXX) $(LDFLAGS) -o $@ $(PY_SHARED)
+ _pMC_mult_so_LDADD       = $(PY_LDFLAGS)
+ 
+ #all:
+diff --git a/pdb2pka/substruct/Makefile.am b/pdb2pka/substruct/Makefile.am
+index b1638a0..ae95e94 100644
+--- a/pdb2pka/substruct/Makefile.am
++++ b/pdb2pka/substruct/Makefile.am
+@@ -15,7 +15,7 @@ CLEANFILES       = Algorithms.so
+ 
+ noinst_PROGRAMS          = Algorithms.so
+ Algorithms_so_SOURCES     = Algorithms.cpp  
+-Algorithms_so_LINK        = $(CXX) -o $@ $(PY_SHARED)
++Algorithms_so_LINK        = $(CXX) $(LDFLAGS) -o $@ $(PY_SHARED)
+ Algorithms_so_LDADD       = $(PY_LDFLAGS)
+ 
+ distclean-local: clean-local
diff --git a/sci-chemistry/pdb2pqr/metadata.xml b/sci-chemistry/pdb2pqr/metadata.xml
index 678d75f1cf5a..efc939161a8f 100644
--- a/sci-chemistry/pdb2pqr/metadata.xml
+++ b/sci-chemistry/pdb2pqr/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-chemistry</herd>
-	<use>
-		<flag name="opal">Add web interface via opal</flag>
-		<flag name="pdb2pka">Install experimental pdb2pka interface</flag>
-	</use>
+  <herd>sci-chemistry</herd>
+  <use>
+    <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-1.8.0.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.8.0.ebuild
new file mode 100644
index 000000000000..39f2cbef012f
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.8.0.ebuild
@@ -0,0 +1,117 @@
+# 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.ebuild,v 1.1 2014/10/24 10:54:05 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit autotools eutils fortran-2 flag-o-matic python-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}/${MY_P}.tar.gz"
+
+SLOT="0"
+IUSE="doc examples opal +pdb2pka"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="
+	dev-python/numpy
+	sci-chemistry/openbabel
+	opal? ( dev-python/zsi )
+	pdb2pka? ( sci-chemistry/apbs[python,-mpi] )"
+DEPEND="${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 ${MAXATOMS} during calculations"
+	fi
+	fortran-2_pkg_setup
+	python_export_best
+}
+
+src_prepare() {
+	rm -rf contrib/* || die
+	epatch \
+		"${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} \
+		$(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)/${PN}"
+
+	python_newscript "${ED}"/$(python_get_sitedir)/${PN}/${PN}.py ${PN}
+	python_newscript "${ED}"/$(python_get_sitedir)/${PN}/pdb2pka/pka.py pdb2pka
+
+	for lib in _apbs.so apbslib.py{,c,o}; do
+		dosym ../../apbs/${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
+}
+
+pkg_postinst() {
+	python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup ${PN}
+}