Version bump. This fixes bug #138534.

(Portage version: 2.1.1_pre1-r5)

4 files changed, 111 insertions, 1 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index 01374be787c7..88d92922601a 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/pdb2pqr
 # Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.2 2006/03/21 17:09:34 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.3 2006/07/01 16:57:48 markusle Exp $
+
+*pdb2pqr-1.1.2 (01 Jul 2006)
+
+  01 Jul 2006; Markus Dittrich <markusle@gentoo.org>
+  +files/pdb2pqr-1.1.2-gcc4-gentoo.patch, +pdb2pqr-1.1.2.ebuild:
+  Version bump. Thanks much to je_fro <je_fro@yahoo.com> for
+  his ebuild. This fixes bug #138534.
 
 *pdb2pqr-1.0.2 (21 Mar 2006)
 
diff --git a/sci-chemistry/pdb2pqr/files/digest-pdb2pqr-1.1.2 b/sci-chemistry/pdb2pqr/files/digest-pdb2pqr-1.1.2
new file mode 100644
index 000000000000..21eb97a75969
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/digest-pdb2pqr-1.1.2
@@ -0,0 +1,3 @@
+MD5 40386de56577ba6842076483327bc341 pdb2pqr-1.1.2.tar.gz 653600
+RMD160 40510384a6b03213d6c857a270d508d4bbefa884 pdb2pqr-1.1.2.tar.gz 653600
+SHA256 ea45ec40b420044e5c7a11744a5db867c544b93d25a8bccf27ebac43cd7d6f94 pdb2pqr-1.1.2.tar.gz 653600
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.1.2-gcc4-gentoo.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.1.2-gcc4-gentoo.patch
new file mode 100644
index 000000000000..6c59bf8b4d71
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.1.2-gcc4-gentoo.patch
@@ -0,0 +1,20 @@
+--- pdb2pqr-1.1.2/propka/configure	2006-06-23 09:16:25.000000000 -0500
++++ pdb2pqr-1.1.2-patched/propka/configure	2006-06-28 05:40:50.000000000 -0500
+@@ -2819,7 +2819,7 @@
+ ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ ac_compiler_gnu=$ac_cv_f77_compiler_gnu
+ if test -n "$ac_tool_prefix"; then
+-  for ac_prog in g77 f77 xlf frt pgf77 fl32 af77 fort77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 lf95 g95
++  for ac_prog in g77 f77 gfortran xlf frt pgf77 fl32 af77 fort77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 lf95 g95
+   do
+     # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+ set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+@@ -2861,7 +2861,7 @@
+ fi
+ if test -z "$F77"; then
+   ac_ct_F77=$F77
+-  for ac_prog in g77 f77 xlf frt pgf77 fl32 af77 fort77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 lf95 g95
++  for ac_prog in g77 f77 gfortran xlf frt pgf77 fl32 af77 fort77 f90 xlf90 pgf90 epcf90 f95 fort xlf95 lf95 g95
+ do
+   # Extract the first word of "$ac_prog", so it can be a program name with args.
+ set dummy $ac_prog; ac_word=$2
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.1.2.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.1.2.ebuild
new file mode 100644
index 000000000000..d837b876ac4c
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.1.2.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.1.2.ebuild,v 1.1 2006/07/01 16:57:48 markusle Exp $
+
+inherit eutils fortran multilib flag-o-matic distutils
+
+DESCRIPTION="pdb2pqr is an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations"
+LICENSE="GPL-2"
+HOMEPAGE="http://pdb2pqr.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND="dev-lang/python"
+
+FORTRAN="g77 gfortran"
+
+src_unpack() {
+	unpack "${A}"
+	cd "${S}"
+
+	epatch "${FILESDIR}"/${P}-gcc4-gentoo.patch
+
+	# need to add -fPIC to CFLAGS and FFLAGS to avoid TEXTRELS 
+	# in _propkalib.so
+	append-flags -fPIC
+	FFLAGS="${FFLAGS} -fPIC"
+}
+
+src_compile() {
+	econf || die "econf failed"
+	emake || die "emake failed"
+}
+
+src_install() {
+	python_version
+	INPATH="/usr/$(get_libdir)/python${PYVER}/site-packages/${PN}"
+
+	insinto "${INPATH}"
+	doins __init__.py || \
+		die "Setting up the pdb2pqr site-package failed."
+
+	exeinto "${INPATH}"
+	doexe ${PN}.py || die "Installing pdb2pqr failed."
+
+	exeinto "${INPATH}"/propka
+	doexe propka/_propkalib.so || \
+		die "Failed to install propka."
+
+	exeinto "${INPATH}"/extensions
+	doexe extensions/* || \
+		die "Failed to install extensions."
+
+	insinto "${INPATH}"/propka
+	doins propka/propkalib.py propka/__init__.py || \
+		die "Failed to install propka."
+
+	insinto "${INPATH}"/src
+	doins src/* || die "Installing of python scripts failed."
+
+	insinto "${INPATH}"/dat
+	doins dat/* || die "Installing data failed."
+
+	# generate pdb2pqr wrapper 
+	cat >> "${T}"/${PN} << EOF
+#!/bin/sh
+${python} ${INPATH}/${PN}.py \$*
+EOF
+
+	exeinto /usr/bin
+	doexe ${T}/${PN} || die "Failed to install pdb2pqr wrapper."
+
+
+	dodoc ChangeLog NEWS README AUTHORS || \
+		die "Failed to install docs"
+	dohtml -r doc/* || die "Failed to install html docs."
+}
+