Initial import (fixes bug #124791).

(Portage version: 2.1_pre6-r4)

7 files changed, 122 insertions, 0 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
new file mode 100644
index 000000000000..12dcf567413b
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -0,0 +1,11 @@
+# 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 1.1 2006/03/21 17:07:14 markusle Exp $
+
+*pdb2pqr-1.0.2 (21 Mar 2006)
+
+  21 Mar 2006; Markus Dittrich <markusle@gentoo.org>
+  +files/pdb2pqr-gcc4-gentoo.patch, +pdb2pqr-propka-gentoo.patch, +metadata.xml, +pdb2pqr-1.0.2.ebuild:
+  Initial import (fixes bug #124791). Many thanks to je_fro 
+  <je_fro@yahoo.com> for his ebuild.
+
diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest
new file mode 100644
index 000000000000..a1f75ad04e58
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/Manifest
@@ -0,0 +1,18 @@
+MD5 63e17ee36fece87aa557b1b3b735b5a5 ChangeLog 408
+RMD160 a6fe688f2b94c3059fc9295a40cead6397ceb268 ChangeLog 408
+SHA256 ba229f50966562c414ba539753c3fbe653980bd237eaa7df91156a1850603322 ChangeLog 408
+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 82af871442be1472152f5bf1274592e1 files/pdb2pqr-gcc4-gentoo.patch 627
+RMD160 293cd6faa4c9d9a20ca8a708187652c79f106927 files/pdb2pqr-gcc4-gentoo.patch 627
+SHA256 afcfb33b59d4feb18f35ebcafea3d759bcb8ba7211dca2b8694df2c9f179363f files/pdb2pqr-gcc4-gentoo.patch 627
+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
+MD5 00cfdca9321dc55e07731e9d3fc15c62 pdb2pqr-1.0.2.ebuild 1539
+RMD160 af04a8d4d0143cb1283cdeeab1c713d77aa8ed8b pdb2pqr-1.0.2.ebuild 1539
+SHA256 3873897ef662701996326949512f6cbfa44fe5ead032b08c1d4729b1df802bb7 pdb2pqr-1.0.2.ebuild 1539
diff --git a/sci-chemistry/pdb2pqr/files/digest-pdb2pqr-1.0.2 b/sci-chemistry/pdb2pqr/files/digest-pdb2pqr-1.0.2
new file mode 100644
index 000000000000..a909e4fb8b23
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/digest-pdb2pqr-1.0.2
@@ -0,0 +1,3 @@
+MD5 4294713d22ae34079fcd4f652f2c793a pdb2pqr-1.0.2.tar.gz 582352
+RMD160 ef3a743eff3533ccb3a72c90721362a217f6e038 pdb2pqr-1.0.2.tar.gz 582352
+SHA256 081eba71c84d2a0437503bf7aa909de9f2ff311acef5f214af2f906b90c1d23a pdb2pqr-1.0.2.tar.gz 582352
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-gcc4-gentoo.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-gcc4-gentoo.patch
new file mode 100644
index 000000000000..a909cf6d70b1
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-gcc4-gentoo.patch
@@ -0,0 +1,12 @@
+diff -Naur pdb2pqr-1.0.2/propka/configure pdb2pqr-1.0.2-new/propka/configure
+--- pdb2pqr-1.0.2/propka/configure	2005-12-16 09:50:58.000000000 -0600
++++ pdb2pqr-1.0.2-new/propka/configure	2006-03-21 09:18:26.000000000 -0600
+@@ -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/files/pdb2pqr-propka-gentoo.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-propka-gentoo.patch
new file mode 100644
index 000000000000..c57b8e210d6e
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-propka-gentoo.patch
@@ -0,0 +1,12 @@
+diff -Naur pdb2pqr-1.0.2/pdb2pqr.py pdb2pqr-1.0.2-new/pdb2pqr.py
+--- pdb2pqr-1.0.2/pdb2pqr.py	2005-12-16 09:50:57.000000000 -0600
++++ pdb2pqr-1.0.2-new/pdb2pqr.py	2006-03-21 10:09:52.000000000 -0600
+@@ -37,6 +37,8 @@
+ from src.protein import *
+ from src.server import *
+ from StringIO import *
++from propka import propkalib
++from propka.propkalib import *
+ 
+ def usage(rc):
+     """
diff --git a/sci-chemistry/pdb2pqr/metadata.xml b/sci-chemistry/pdb2pqr/metadata.xml
new file mode 100644
index 000000000000..b229aec85b8f
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.0.2.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.0.2.ebuild
new file mode 100644
index 000000000000..4f6d3b4d0431
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.0.2.ebuild
@@ -0,0 +1,61 @@
+# 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-1.0.2.ebuild,v 1.1 2006/03/21 17:07:14 markusle Exp $
+
+inherit eutils fortran python multilib
+
+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="http://umn.dl.sourceforge.net/sourceforge/${PN}/${P}.tar.gz"
+
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND="dev-lang/python"
+
+FORTRAN="g77 gfortran"
+
+src_unpack() {
+	unpack "${A}"
+	cd "${S}"
+
+	epatch "${FILESDIR}"/${PN}-gcc4-gentoo.patch
+	epatch "${FILESDIR}"/${PN}-propka-gentoo.patch
+}
+
+src_install() {
+	python_version
+	INPATH="/usr/$(get_libdir)/python${PYVER}/site-packages/${PN}"
+
+	insinto "${INPATH}"
+	doins __init__.py constants.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."
+
+	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 "${INPATH}"/dat
+	doins dat/* || die "Installing data failed."
+
+	into /usr/bin
+	dosym "${INPATH}"/${PN}.py /usr/bin/${PN} \
+		|| die "Failed to install symlink into /usr/bin."
+
+	dodoc ChangeLog NEWS README AUTHORS || \
+		die "Failed to install docs"
+	dohtml doc/* || die "Failed to install html docs."
+}
+