Version bump. This fixes bug #138534.

Package-Manager: portage-2.1.1_pre1-r5

5 files changed, 138 insertions, 10 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/Manifest b/sci-chemistry/pdb2pqr/Manifest
index 2541c429d40e..8e9e96bfca40 100644
--- a/sci-chemistry/pdb2pqr/Manifest
+++ b/sci-chemistry/pdb2pqr/Manifest
@@ -1,18 +1,36 @@
-MD5 52a8987cc7cd3a2794ff0dabb148659a ChangeLog 509
-RMD160 62b94b6de4f5b474b2eeb461d45688aaa11d2900 ChangeLog 509
-SHA256 fad7153ffcee41c7990cf25198e8318a7f9a04a2fa61c99000bb686fb5337a13 ChangeLog 509
-MD5 ab0a8a7c1095b9e755a10ed3f3640f6e files/digest-pdb2pqr-1.0.2 241
-RMD160 15e27b785c4ff5163da1ec819523ad3f2e37e75e files/digest-pdb2pqr-1.0.2 241
-SHA256 e6ab0164f55ac7850ae70b7fbea47161adfdd519cd21aaf888aad26266653240 files/digest-pdb2pqr-1.0.2 241
+AUX pdb2pqr-1.1.2-gcc4-gentoo.patch 1104 RMD160 87d7c92e4f24be4f205379acafdc9c41b8e99a9b SHA1 346ed354808f2d902a2d4076e9c41690a83995f5 SHA256 164ae1a21de69ea97f5439a15004d1441fc7d11cbd79cf1c5ab777363b1e3019
+MD5 2a1a14d26d040d99dd114fe930e3414a files/pdb2pqr-1.1.2-gcc4-gentoo.patch 1104
+RMD160 87d7c92e4f24be4f205379acafdc9c41b8e99a9b files/pdb2pqr-1.1.2-gcc4-gentoo.patch 1104
+SHA256 164ae1a21de69ea97f5439a15004d1441fc7d11cbd79cf1c5ab777363b1e3019 files/pdb2pqr-1.1.2-gcc4-gentoo.patch 1104
+AUX pdb2pqr-gcc4-gentoo.patch 627 RMD160 293cd6faa4c9d9a20ca8a708187652c79f106927 SHA1 bad480b23ad7d5e65b3e9c3e249538a180083609 SHA256 afcfb33b59d4feb18f35ebcafea3d759bcb8ba7211dca2b8694df2c9f179363f
 MD5 82af871442be1472152f5bf1274592e1 files/pdb2pqr-gcc4-gentoo.patch 627
 RMD160 293cd6faa4c9d9a20ca8a708187652c79f106927 files/pdb2pqr-gcc4-gentoo.patch 627
 SHA256 afcfb33b59d4feb18f35ebcafea3d759bcb8ba7211dca2b8694df2c9f179363f files/pdb2pqr-gcc4-gentoo.patch 627
+AUX pdb2pqr-propka-gentoo.patch 383 RMD160 aba20c68558d3131b9f04b4188c70e42611f013e SHA1 4bfd930bdfd719d22d8f8576949eb68dd35e0036 SHA256 5f75dfd2a72861b46685568ea6c55be0ed055ab5d72d231e328f7f482252101a
 MD5 3700078df26942f1b406cb767bfd9f97 files/pdb2pqr-propka-gentoo.patch 383
 RMD160 aba20c68558d3131b9f04b4188c70e42611f013e files/pdb2pqr-propka-gentoo.patch 383
 SHA256 5f75dfd2a72861b46685568ea6c55be0ed055ab5d72d231e328f7f482252101a files/pdb2pqr-propka-gentoo.patch 383
-MD5 8c623e53daafa025137077c6b65815bd metadata.xml 156
-RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 metadata.xml 156
-SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 metadata.xml 156
+DIST pdb2pqr-1.0.2.tar.gz 582352 RMD160 ef3a743eff3533ccb3a72c90721362a217f6e038 SHA256 081eba71c84d2a0437503bf7aa909de9f2ff311acef5f214af2f906b90c1d23a
+DIST pdb2pqr-1.1.2.tar.gz 653600 RMD160 40510384a6b03213d6c857a270d508d4bbefa884 SHA1 89ae9b50e64fc3bbd2a868af01da708fb3f45395 SHA256 ea45ec40b420044e5c7a11744a5db867c544b93d25a8bccf27ebac43cd7d6f94
+EBUILD pdb2pqr-1.0.2.ebuild 1645 RMD160 ebecb11e695825c9d8e82d9d833dbe8ee51e2643 SHA1 858f0b02221798201bc2109444321c63398945b9 SHA256 5d9cafa88d8aa70d119223f5858c31bad7e5e1285869c1b632e5a81b9f7e6005
 MD5 08a7a0573e1ce75bfc1fb14570a8f6b5 pdb2pqr-1.0.2.ebuild 1645
 RMD160 ebecb11e695825c9d8e82d9d833dbe8ee51e2643 pdb2pqr-1.0.2.ebuild 1645
 SHA256 5d9cafa88d8aa70d119223f5858c31bad7e5e1285869c1b632e5a81b9f7e6005 pdb2pqr-1.0.2.ebuild 1645
+EBUILD pdb2pqr-1.1.2.ebuild 1956 RMD160 c127cb07c261b0328ea8ada0bfe4eda9b6cac1d3 SHA1 19f165f07e0656d4296d9463368bd054aebbb48e SHA256 bc87af44beca7ac63ca9f826d9598931b9231285d89fcd850929e9915d61c43e
+MD5 9b574c64bb402af344c0ab93dd189027 pdb2pqr-1.1.2.ebuild 1956
+RMD160 c127cb07c261b0328ea8ada0bfe4eda9b6cac1d3 pdb2pqr-1.1.2.ebuild 1956
+SHA256 bc87af44beca7ac63ca9f826d9598931b9231285d89fcd850929e9915d61c43e pdb2pqr-1.1.2.ebuild 1956
+MISC ChangeLog 757 RMD160 7ace584321574638107dcc686e174787d122002a SHA1 b045c21fe13d14871edcc9ebd668b79f77f3066b SHA256 8a665a02ef98842e2303e245ed01e77e1bdfd7f5a29f709d4afcefb1daf7e6d7
+MD5 82af991181a05b0611d66670ff555733 ChangeLog 757
+RMD160 7ace584321574638107dcc686e174787d122002a ChangeLog 757
+SHA256 8a665a02ef98842e2303e245ed01e77e1bdfd7f5a29f709d4afcefb1daf7e6d7 ChangeLog 757
+MISC metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 SHA1 da2b240a255820145b7c83a5c48e45b96b7e9ee6 SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900
+MD5 8c623e53daafa025137077c6b65815bd metadata.xml 156
+RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 metadata.xml 156
+SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 metadata.xml 156
+MD5 ab0a8a7c1095b9e755a10ed3f3640f6e files/digest-pdb2pqr-1.0.2 241
+RMD160 15e27b785c4ff5163da1ec819523ad3f2e37e75e files/digest-pdb2pqr-1.0.2 241
+SHA256 e6ab0164f55ac7850ae70b7fbea47161adfdd519cd21aaf888aad26266653240 files/digest-pdb2pqr-1.0.2 241
+MD5 81f7d39024c32ceff1cda274993ace06 files/digest-pdb2pqr-1.1.2 241
+RMD160 043e9c03c065830075fec6a4b561282371f0eb9c files/digest-pdb2pqr-1.1.2 241
+SHA256 362b2c4e1ec25dd3971cef2e00039728697329cecef2432a7e19bd6b2bd6ba62 files/digest-pdb2pqr-1.1.2 241
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."
+}
+