9 files changed, 136 insertions, 217 deletions
diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index fb5b45682d24..ea14f1c4dcc6 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/pdb2pqr
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.18 2009/09/24 23:43:11 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.19 2009/11/03 05:40:25 markusle Exp $
+
+*pdb2pqr-1.5.0 (03 Nov 2009)
+
+  03 Nov 2009; Markus Dittrich <markusle@gentoo.org> -pdb2pqr-1.1.2.ebuild,
+  -files/pdb2pqr-1.1.2-fpic-gentoo.patch, -files/pdb2pqr-gcc4-gentoo.patch,
+  -files/pdb2pqr-1.1.2-gcc4-gentoo.patch, -pdb2pqr-1.2.1.ebuild,
+  -files/pdb2pqr-propka-gentoo.patch, +pdb2pqr-1.5.0.ebuild:
+  Version bump and removed old ebuilds.
 
   24 Sep 2009; Markus Dittrich <markusle@gentoo.org>
   pdb2pqr-1.4.0-r1.ebuild, files/pdb2pqr-1.4.0-automagic.patch:
diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest
index 509764427807..0adde96b8588 100644
--- a/sci-chemistry/pdb2pqr/Manifest
+++ b/sci-chemistry/pdb2pqr/Manifest
@@ -1,20 +1,14 @@
-AUX pdb2pqr-1.1.2-fpic-gentoo.patch 668 RMD160 e076ebcfe1e0fd39ca7b2219b6d9938b6f4870c8 SHA1 38018f5494b21296dfabe02c61824d0af6d6ce36 SHA256 6455be2583ded00bea43f49789cde72cdd240858f187db6d59ed67c87163af45
-AUX pdb2pqr-1.1.2-gcc4-gentoo.patch 1104 RMD160 87d7c92e4f24be4f205379acafdc9c41b8e99a9b SHA1 346ed354808f2d902a2d4076e9c41690a83995f5 SHA256 164ae1a21de69ea97f5439a15004d1441fc7d11cbd79cf1c5ab777363b1e3019
 AUX pdb2pqr-1.3.0-gcc4.3.patch 349 RMD160 a7e241b288738faaee678609c61968dba990b9a3 SHA1 95e0dcb30e926f0bab2068bff550427a1a3a623e SHA256 4e65916b3370bc3c4690ca9424629a928f9753879939f0ebb881304331fab946
 AUX pdb2pqr-1.3.0-ldflags.patch 803 RMD160 ecc52d97bae89e1a961531eb5e4c87d456e87919 SHA1 ba777c53835045fd4538f3e1104a18d12df8d935 SHA256 8d2cf1f0d206e4162193877dd577ff0835f8e390d779ddfa4b73d30734dede77
 AUX pdb2pqr-1.4.0-automagic.patch 3526 RMD160 c4d662e68352d93f913fdc83b5c733a555a9bc17 SHA1 64598bff69e627a27ffa550ad5f3b38898a3a9cf SHA256 f145bc6222d56410035240e2d8be9fbbb0d70dabccad5c5efc5d4dacd602670a
 AUX pdb2pqr-1.4.0-gcc44.patch 229 RMD160 c5c1d51e6c695a3df8c04245a8d93168bef7a6b8 SHA1 5614b75a17b089624558026e51ba440479a5f658 SHA256 76a1bd592579d712bb6b22e6547edf1094d628e9d2b00b8d6ec89f8d9043c6df
 AUX pdb2pqr-1.4.0-install.patch 5372 RMD160 8d6c5f3c85ceea0562a767a3792228e6ff0eee96 SHA1 77a70693687be8d14eb3221ffc62a3daccc38f8e SHA256 e93025a88b5d6fff6e1fb45471471aef006d3074ece0b9cd9ff781736a2f1643
 AUX pdb2pqr-1.4.0-ldflags.patch 1293 RMD160 47c2e4b484cf0936176683342afa6e89bb0b0712 SHA1 6c9088bbbf87a91c28fe6fdd39b3db097143f103 SHA256 cfab690b3c128b2c65e217893b546d6e56ffb2ffd7110872f352d6243f56f726
-AUX pdb2pqr-gcc4-gentoo.patch 627 RMD160 293cd6faa4c9d9a20ca8a708187652c79f106927 SHA1 bad480b23ad7d5e65b3e9c3e249538a180083609 SHA256 afcfb33b59d4feb18f35ebcafea3d759bcb8ba7211dca2b8694df2c9f179363f
-AUX pdb2pqr-propka-gentoo.patch 383 RMD160 aba20c68558d3131b9f04b4188c70e42611f013e SHA1 4bfd930bdfd719d22d8f8576949eb68dd35e0036 SHA256 5f75dfd2a72861b46685568ea6c55be0ed055ab5d72d231e328f7f482252101a
-DIST pdb2pqr-1.1.2.tar.gz 653600 RMD160 40510384a6b03213d6c857a270d508d4bbefa884 SHA1 89ae9b50e64fc3bbd2a868af01da708fb3f45395 SHA256 ea45ec40b420044e5c7a11744a5db867c544b93d25a8bccf27ebac43cd7d6f94
-DIST pdb2pqr-1.2.1.tar.gz 2090993 RMD160 647aa616703208f81396917b805be1daf3adf180 SHA1 8ff7423fe42dbd86db62227c8d729dfc9a3ee7dd SHA256 d05d6ae084c689f3873b8ab68fb7285863d57125ecbe8def14de879430d753d7
 DIST pdb2pqr-1.3.0.tar.gz 2641989 RMD160 469b38457a10e93ce96c7ea4e580cb4656ba3218 SHA1 e2095a7130ff6114d15466b009cc8ed335d8ffd1 SHA256 7e8a733aacdb76ec8f920b6827ebbc86712044a10c50363535978bc22b7fd413
 DIST pdb2pqr-1.4.0.tar.gz 5471743 RMD160 4d5596da5f9bdb2c657e7d0d88d91d20d00569e2 SHA1 967f3f2f2ab532e7a0abeb253bac95185bca1602 SHA256 19bfa106e7b41537594ab627c8c670c03c3445e9efb69d878528355825080fd5
-EBUILD pdb2pqr-1.1.2.ebuild 1887 RMD160 0f9fa1296696d9e6a1588830673ba8ae068ab1fd SHA1 ed35a726600197eec5e5b985a602d34c652ba301 SHA256 cd5fb2648e1c104fb3cec78df44ae7a554d7ac9a656995b99bd4267fa824145c
-EBUILD pdb2pqr-1.2.1.ebuild 1736 RMD160 3087df9d6f47e99d51f9dbb8014a442803d40182 SHA1 1b7b8f2cc68b0eca72469145769cecc69b79e7d2 SHA256 10cb0ef51344bc4eb29f5855e99c461befb532451f80fafaf0630532414b131a
+DIST pdb2pqr-1.5.tar.gz 5747178 RMD160 543545513811bae058e23cfe1f24e02eaa094b87 SHA1 5249064cf4ebfb2291a382121ecea4d457e65e6a SHA256 2a83433b50a57aa0a05102c425cd7b4bb6750487327195ab719992f4186281c5
 EBUILD pdb2pqr-1.3.0.ebuild 1981 RMD160 d9e8eb2f45aa12cd478e4e27e99ddf66aa202c5a SHA1 39de5c8e05de1827ab618959f73b256fd915fe8d SHA256 831d3e176306826bd44146f489030186beba521d00d7a87864ebb13272edfd17
 EBUILD pdb2pqr-1.4.0-r1.ebuild 2771 RMD160 95b243244ebf8167bb3d1d3a233f52985046345a SHA1 5ee56fc36c834c8a11d5b06d5d57404c9c844435 SHA256 3dc0ffb3b9e414f15b6aaee11e03309ec40558ad001a0bd2225465a5da028a26
-MISC ChangeLog 2845 RMD160 fd9429385a718717868a3d716995d9fdf0a8245d SHA1 a8259e42ebca0c2dc8a4b02c787bd714323cf959 SHA256 020824489012e158f79112789673d5c3020dca01eb798d3b7586d81b3a783cbb
+EBUILD pdb2pqr-1.5.0.ebuild 3000 RMD160 689ae4c01f4c258899a1fdf3fe87d515513957ea SHA1 8fef56d1a8f1a6c6b1dd0c10b0a0f4c085f7b76d SHA256 6d2743f05a5370be804df774e315eb5d89fcce4016f10453ad89bc75c4270874
+MISC ChangeLog 3194 RMD160 a0f98e51028a5f56e2bb315594e0d32dc4c58bdf SHA1 d13a3bc79fb94e7717e2ed7bbc2983cde81c03fa SHA256 f0b6b3e272274f708daff7ff28130c16f9b3419d4d09d6552b4d79528f21a565
 MISC metadata.xml 239 RMD160 c9646b9b2171a8eeac8517b70efe2d2f8b6aa0f0 SHA1 48e78f37fbb221dc94978bf1ea4a9ba874a52464 SHA256 5dd1bfe10b60a7f631b103e6755e771471fea0334312522ef256db4ddb6923c2
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.1.2-fpic-gentoo.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.1.2-fpic-gentoo.patch
deleted file mode 100644
index 254041a7b586..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.1.2-fpic-gentoo.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- pdb2pqr-1.1.2/propka/Makefile.in	2006-06-23 10:16:25.000000000 -0400
-+++ pdb2pqr-1.1.2-new/propka/Makefile.in	2006-07-01 14:15:29.000000000 -0400
-@@ -210,13 +210,13 @@
- 	-rm -f *.tab.c
- 
- .c.o:
--	$(COMPILE) -c `test -f '$<' || echo '$(srcdir)/'`$<
-+	$(COMPILE) -fPIC -c `test -f '$<' || echo '$(srcdir)/'`$<
- 
- .c.obj:
- 	$(COMPILE) -c `if test -f '$<'; then $(CYGPATH_W) '$<'; else $(CYGPATH_W) '$(srcdir)/$<'`
- 
- .f.o:
--	$(F77COMPILE) -c -o $@ `test -f '$<' || echo '$(srcdir)/'`$<
-+	$(F77COMPILE) -fPIC -c -o $@ `test -f '$<' || echo '$(srcdir)/'`$<
- 
- .f.obj:
- 	$(F77COMPILE) -c -o $@ `if test -f '$<'; then $(CYGPATH_W) '$<'; else $(CYGPATH_W) '$(srcdir)/$<'`
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.1.2-gcc4-gentoo.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.1.2-gcc4-gentoo.patch
deleted file mode 100644
index 6c59bf8b4d71..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.1.2-gcc4-gentoo.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- pdb2pqr-1.1.2/propka/configure	2006-06-23 09:16:25.000000000 -0500
-+++ pdb2pqr-1.1.2-patched/propka/configure	2006-06-28 05:40:50.000000000 -0500
-@@ -2819,7 +2819,7 @@
- ac_link='$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=$2
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-gcc4-gentoo.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-gcc4-gentoo.patch
deleted file mode 100644
index a909cf6d70b1..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-gcc4-gentoo.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naur pdb2pqr-1.0.2/propka/configure pdb2pqr-1.0.2-new/propka/configure
---- pdb2pqr-1.0.2/propka/configure	2005-12-16 09:50:58.000000000 -0600
-+++ pdb2pqr-1.0.2-new/propka/configure	2006-03-21 09:18:26.000000000 -0600
-@@ -2861,7 +2861,7 @@
- fi
- if test -z "$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
deleted file mode 100644
index c57b8e210d6e..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-propka-gentoo.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-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/pdb2pqr-1.1.2.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.1.2.ebuild
deleted file mode 100644
index 24ef55bdcf14..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.1.2.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2009 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 1.10 2009/05/24 07:50:41 je_fro Exp $
-
-inherit eutils fortran multilib flag-o-matic distutils
-
-DESCRIPTION="pdb2pqr is an automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-LICENSE="GPL-2"
-HOMEPAGE="http://pdb2pqr.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND="dev-lang/python
-		dev-python/numpy"
-
-RDEPEND="${DEPEND}"
-
-FORTRAN="g77 gfortran"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	epatch "${FILESDIR}"/${P}-gcc4-gentoo.patch
-	epatch "${FILESDIR}"/${P}-fpic-gentoo.patch
-}
-
-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."
-}
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.2.1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.2.1.ebuild
deleted file mode 100644
index a0e7ef896c5a..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.2.1.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.2.1.ebuild,v 1.5 2009/05/24 07:50:41 je_fro Exp $
-
-inherit eutils fortran multilib flag-o-matic distutils
-
-DESCRIPTION="pdb2pqr is an automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
-LICENSE="GPL-2"
-HOMEPAGE="http://pdb2pqr.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="dev-lang/python"
-
-RDEPEND="${DEPEND}"
-
-FORTRAN="g77 gfortran"
-
-src_compile() {
-	econf || die "econf failed"
-	emake || die "emake failed"
-}
-
-src_install() {
-	python_version
-	INPATH="/usr/$(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."
-}
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0.ebuild
new file mode 100644
index 000000000000..898517a899cd
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0.ebuild
@@ -0,0 +1,124 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0.ebuild,v 1.1 2009/11/03 05:40:25 markusle Exp $
+
+inherit eutils fortran multilib flag-o-matic distutils python versionator
+
+MY_PV=$(get_version_component_range 1-2)
+MY_P="${PN}-${MY_PV}"
+
+DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
+LICENSE="BSD"
+HOMEPAGE="http://pdb2pqr.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
+
+SLOT="0"
+IUSE="doc examples opal"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="dev-lang/python
+	dev-python/numpy
+	opal? ( dev-python/zsi )"
+RDEPEND="${DEPEND}"
+
+FORTRAN="g77 gfortran"
+
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${PN}-1.4.0-ldflags.patch
+	epatch "${FILESDIR}"/${PN}-1.4.0-automagic.patch
+	epatch "${FILESDIR}"/${PN}-1.4.0-install.patch
+	sed '50,200s:CWD:DESTDIR:g' -i Makefile.am \
+		|| die "Failed to fix Makefile.am"
+	eautoreconf
+}
+
+src_compile() {
+	# we need to compile the *.so as pic
+	append-flags -fPIC
+	FFLAGS="${FFLAGS} -fPIC"
+
+	# Avoid automagic to numeric
+	NUMPY="$(python_get_sitedir)" \
+		F77="${FORTRANC}" \
+		econf \
+		$(use_with opal) || \
+		die "econf failed"
+	emake || die "emake failed"
+}
+
+src_test() {
+	emake -j1 test && \
+		F77="${FORTRANC}" emake -j1 adv-test \
+		|| die "tests failed"
+}
+
+src_install() {
+	dodir $(python_get_sitedir)/${PN}
+	emake -j1 DESTDIR="${D}$(python_get_sitedir)/${PN}" \
+		PREFIX=""  install || die "install failed"
+
+	if use doc; then
+		cd doc
+		sh genpydoc.sh \
+			|| die "genpydoc failed"
+		dohtml -r *.html images pydoc \
+			|| die "failed to install html docs"
+		cd -
+	fi
+
+	if use examples; then
+		insinto /usr/share/${PN}/
+		doins -r examples || die "Failed to install examples."
+	fi
+
+	INPATH="$(python_get_sitedir)/${PN}"
+
+	# 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"
+
+	insinto "${INPATH}"
+	doins __init__.py || \
+		die "Setting up the pdb2pqr site-package failed."
+
+	exeinto "${INPATH}"
+	doexe ${PN}.py || die "Installing pdb2pqr failed."
+
+	insinto "${INPATH}"/dat
+	doins dat/* || die "Installing data failed."
+
+	exeinto "${INPATH}"/extensions
+	doexe extensions/* || \
+		die "Failed to install extensions."
+
+	insinto "${INPATH}"/src
+	doins src/*.py || die "Installing of python scripts 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 "${INPATH}"/pdb2pka
+	doins pdb2pka/*.{py,so,DAT,h} || \
+		die "Failed to install pdb2pka."
+
+	insinto "${INPATH}"/pdb2pka/
+	doins pdb2pka/*.{py,so,DAT,h} || \
+		die "Failed to install pdb2pka."
+}