latest from overlay, thanks to alexxy

(Portage version: 2.1.6.13/cvs/Linux x86_64)

10 files changed, 416 insertions, 6 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index d3c7dc40e17d..7bc7aa0be186 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,11 @@
 # 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 1.16 2009/03/03 02:50:01 darkside Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.17 2009/05/24 07:50:41 je_fro Exp $
+
+*pdb2pqr-1.4.0-r1 (24 May 2009)
+
+  24 May 2009; Jeff Gardner <je_fro@gentoo.org> +pdb2pqr-1.4.0-r1.ebuild:
+  Latest from overlay, thanks to alexxy.
 
   03 Mar 2009; Jeremy Olexa <darkside@gentoo.org> pdb2pqr-1.3.0.ebuild:
   amd64 stable, bug 245874
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch
new file mode 100644
index 000000000000..f837e90390e3
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch
@@ -0,0 +1,95 @@
+--- configure.ac	2009-04-02 16:53:56.000000000 +0200
++++ configure.ac.new	2009-04-22 11:41:28.000000000 +0200
+@@ -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])
+@@ -463,23 +431,8 @@
+     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  
+ 
+--- pdb2pka/NEWligand_topology.py	2007-10-12 21:52:40.000000000 +0200
++++ pdb2pka/NEWligand_topology.py.new	2009-04-22 17:01:11.000000000 +0200
+@@ -3,10 +3,7 @@
+ # PC 2005/09/23
+ # Get ligand topologies
+ #
+-try:
+-    import Numeric
+-except:
+-    import numpy as Numeric
++import numpy as Numeric
+     
+ from sets import Set
+ from ligandclean.trial_templates import *
+--- pdb2pka/ligand_topology.py	2008-06-13 16:15:38.000000000 +0200
++++ pdb2pka/ligand_topology.py.new	2009-04-22 17:02:59.000000000 +0200
+@@ -3,10 +3,7 @@
+ # PC 2005/09/23
+ # Get ligand topologies
+ #
+-try:
+-    import Numeric
+-except:
+-    import numpy as Numeric
++import numpy as Numeric
+     
+ from sets import Set
+ from ligandclean.trial_templates import *
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-gcc44.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-gcc44.patch
new file mode 100644
index 000000000000..09405ec7c3f3
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-gcc44.patch
@@ -0,0 +1,11 @@
+--- pdb2pka/pMC_mult.cpp.orig	2009-05-19 23:35:45.000000000 +0400
++++ pdb2pka/pMC_mult.cpp	2009-05-19 23:36:27.000000000 +0400
+@@ -7,7 +7,7 @@
+ //
+ //
+ //
+-
++#include <stdio.h>
+ #include <cstdlib>
+ 
+ void MC::reformat_arrays() {
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-install.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-install.patch
new file mode 100644
index 000000000000..4af9eda8e1b3
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-install.patch
@@ -0,0 +1,134 @@
+--- Makefile.am	2008-08-07 04:57:43.000000000 +0200
++++ Makefile.am.new	2009-04-22 13:45:22.000000000 +0200
+@@ -104,30 +104,11 @@
+ 	    mkdir $(CWD)/$$dir/tmp ; \
+ 	  fi ; \
+ 	  chmod 777 $(CWD)/$$dir/tmp ; \
+-	  echo "Adding server.html" ; \
+-	  cp $$c/html/server.html $(CWD)/$$dir/index.html ; \
+-	  echo "Adding python files" ; \
+-	  cp $$c/*.py* $(CWD)/$$dir/. ; \
++	  cp $$c/main*.py $(CWD)/$$dir/. ; \
+ 	  echo "Adding __init__.py" ; \
+ 	  cp $$c/__init__.py $(CWD)/$$dir/__init__.py ; \
+ 	  echo "Adding pdb2pqr.py" ; \
+ 	  cp $$c/pdb2pqr.py $(CWD)/$$dir/. ; \
+-	  echo "Adding pdb2pqr.cgi" ; \
+-	  cp $$c/pdb2pqr.cgi $(CWD)/$$dir/. ; \
+-	  echo "Adding pdb2pqr.css" ; \
+-	  cp $$c/apbs_cgi.cgi $(CWD)/$$dir/. ; \
+-	  echo "Adding apbs_cgi.cgi" ; \
+-	  cp $$c/jmol.cgi $(CWD)/$$dir/. ; \
+-	  echo "Adding jmol.cgi" ; \
+-	  cp $$c/visualize.cgi $(CWD)/$$dir/. ; \
+-	  echo "Adding visualize.cgi" ; \
+-	  cp $$c/querystatus.cgi $(CWD)/$$dir/. ; \
+-	  echo "Adding querystatus.cgi" ; \
+-	  cp $$c/Jmol.js $(CWD)/$$dir/. ; \
+-	  echo "Adding Jmol.js" ; \
+-	  cp $$c/JmolApplet.jar $(CWD)/$$dir/. ; \
+-	  echo "Adding JmolApplet.jar" ; \
+-	  cp $$c/pdb2pqr.css $(CWD)/$$dir/. ; \
+ 	  if ! test -d $(CWD)/$$dir/dat  ; then \
+ 	    mkdir $(CWD)/$$dir/dat ; \
+ 	  fi ; \
+@@ -135,44 +115,11 @@
+ 	  cp $$c/dat/*.xml $(CWD)/$$dir/dat/. ; \
+ 	  cp $$c/dat/*.DAT $(CWD)/$$dir/dat/. ; \
+ 	  cp $$c/dat/*.names $(CWD)/$$dir/dat/. ; \
+-	  if ! test -d $(CWD)/$$dir/doc  ; then \
+-	    mkdir $(CWD)/$$dir/doc ; \
+-	  fi ; \
+-	  echo "Adding doc/" ; \
+-	  cp $$c/doc/*.html $(CWD)/$$dir/doc/. ; \
+-	  cp $$c/doc/*.sh $(CWD)/$$dir/doc/. ; \
+-	  if ! test -d $(CWD)/$$dir/doc/images  ; then \
+-	    mkdir $(CWD)/$$dir/doc/images ; \
+-	  fi ; \
+-	  cp $$c/doc/images/*.png $(CWD)/$$dir/doc/images/. ; \
+-	  if ! test -d $(CWD)/$$dir/doc/pydoc ; then \
+-	    mkdir $(CWD)/$$dir/doc/pydoc ; \
+-	  fi ; \
+-	  cp $$c/doc/pydoc/*.html $(CWD)/$$dir/doc/pydoc/. ; \
+-	  if ! test -d $(CWD)/$$dir/examples ; then \
+-	    mkdir $(CWD)/$$dir/examples ; \
+-	  fi ; \
+-	  echo "Adding examples/" ; \
+-	  cp $$c/examples/*.html $(CWD)/$$dir/examples/. ; \
+-	  if ! test -d $(CWD)/$$dir/examples/1a1p ; then \
+-	    mkdir $(CWD)/$$dir/examples/1a1p ; \
+-	  fi ; \
+-	  cp $$c/examples/1a1p/*.pdb $(CWD)/$$dir/examples/1a1p/. ; \
+-	  cp $$c/examples/1a1p/README $(CWD)/$$dir/examples/1a1p/. ; \
+-	  if ! test -d $(CWD)/$$dir/examples/ligands ; then \
+-	    mkdir $(CWD)/$$dir/examples/ligands ; \
+-	  fi ; \
+-	  cp $$c/examples/ligands/*.mol* $(CWD)/$$dir/examples/ligands/. ; \
+-	  if ! test -d $(CWD)/$$dir/extensions ; then \
+-	    mkdir $(CWD)/$$dir/extensions ; \
+-	  fi ; \
+ 	  echo "Adding extensions" ; \
++	  if ! test -d $(CWD)/$$dir/extensions ; then \
++	    mkdir $(CWD)/$$dir/extensions ; \
++	  fi ; \
+ 	  cp $$c/extensions/*.py $(CWD)/$$dir/extensions/. ; \
+-	  if ! test -d $(CWD)/$$dir/html  ; then \
+-	    mkdir $(CWD)/$$dir/html ; \
+-	  fi ; \
+-	  cp $$c/html/master-index.html $(CWD)/$$dir/html/. ; \
+-	  cp $$c/html/server.html $(CWD)/$$dir/html/server.html ; \
+ 	  if ! test -d $(CWD)/$$dir/src ; then \
+ 	    mkdir $(CWD)/$$dir/src ; \
+ 	  fi ; \
+--- Makefile.am	2009-04-22 13:48:23.000000000 +0200
++++ Makefile.am.new	2009-04-22 13:49:52.000000000 +0200
+@@ -168,49 +168,6 @@
+ 	  echo PDB2PQR has been installed in $(CWD)/$$dir ; \
+ 	  echo ; \
+ 	  cd $(CWD)/$$dir ; \
+-	  cd $$c; \
+-	  rm lastfieldfile prefixfile dir1file fieldfile ; \
+-	  echo $(URL) > url_file ; \
+-	  awk -F"/" '{print $$(NF-1)}' url_file > url_file_2 ; \
+-	  last_url=`cat url_file_2` ; \
+-	  echo $(PREFIX) > p_file ; \
+-	  awk -F"/" '{print $$(NF-1)}' p_file > p_file_2 ; \
+-	  last_p=`cat p_file_2` ; \
+-	  rm -f url_file* p_file* ; \
+-	  if test `whoami` = "root" ; then \
+-            webviewable="true" ; \
+-	    echo ${prefix} > prefix_file_tmp ; \
+-            first=`awk -F"/" '{ print $$2 }' prefix_file_tmp` ; \
+-	    second=`awk -F"/" '{ print $$3 }' prefix_file_tmp` ; \
+-	    third=`awk -F"/" '{ print $$4 }' prefix_file_tmp` ; \
+-	    rm -f prefix_file_tmp ; \
+-	    if test $$first != var || test $$second != www || test $$third != html ; then  \
+-	      webviewable=false ; \
+-	    fi ; \
+-	    if test "$$last_url" != "$$last_p" || test "$$webviewable" = "false" ; then \
+-	      echo Need to make symbolic link between $(PREFIX) and /var/www/html/"$$last_url" ; \
+-	      if test -d "/var/www/html/$$last_url" ; then \
+-	        echo "***" Warning! Directory /var/www/html/"$$last_url" already exists. ; \
+-		echo Do you want to overwrite this? \(Y/N\); \
+-		read choice ; \
+-	        while (test $$choice != "Y" && test $$choice != "y" && test $$choice != "N" && test $$choice != "n")  \
+-	          do  \
+-	          echo You have entered $$choice. Please enter Y or N: ; \
+-	          read choice ; \
+-	        done ; \
+-	        if test $$choice = "N" || test $$choice = "n" ; then  \
+-	          echo Please run configure again and specify a different --prefix ; \
+-	          exit 0 ; \
+-	        fi ; \
+-	  	rm -rf /var/www/html/"$$last_url" ; \
+-	      fi ; \
+-	      ln -s $(PREFIX) /var/www/html/"$$last_url" ; \
+-	      echo "Symbolic link created." ; \
+-	    fi ; \
+-	  else  \
+-	    echo Ask your system administrator to make a symbolic link in /var/www/html by executing the following command; \
+-	    echo ln -s $(PREFIX) /var/www/html/"$$last_url" ; \
+-	  fi ; \
+ 	fi
+ 
+ 
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-ldflags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-ldflags.patch
new file mode 100644
index 000000000000..ea5dc85ba07d
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-ldflags.patch
@@ -0,0 +1,33 @@
+--- pdb2pka/Makefile.am	2008-04-24 21:44:28.000000000 +0200
++++ pdb2pka/Makefile.am.new	2009-04-22 17:26:24.000000000 +0200
+@@ -16,7 +16,7 @@
+ 
+ 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:
+--- pdb2pka/substruct/Makefile.am	2008-04-24 19:54:39.000000000 +0200
++++ pdb2pka/substruct/Makefile.am.new	2009-04-22 17:26:57.000000000 +0200
+@@ -15,7 +15,7 @@
+ 
+ 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
+--- propka/Makefile.in	2007-10-12 00:26:48.000000000 +0200
++++ propka/Makefile.in.new	2009-04-22 17:41:21.000000000 +0200
+@@ -99,7 +99,7 @@
+ noinst_PROGRAMS = _propkalib.so propka
+ _propkalib_so_SOURCES = propkalib.c propka.f propkac.c
+ _propkalib_so_LINK = $(F77)
+-_propkalib_so_LDFLAGS = -o $@ $(PY_SHARED)
++_propkalib_so_LDFLAGS = $(LDFLAGS) -o $@ $(PY_SHARED)
+ _propkalib_so_LDADD = $(PY_LDFLAGS)
+ propka_SOURCES = propka.f
+ 
diff --git a/sci-chemistry/pdb2pqr/metadata.xml b/sci-chemistry/pdb2pqr/metadata.xml
index 9ac9ffdb3a41..8a6b36d4b5ce 100644
--- a/sci-chemistry/pdb2pqr/metadata.xml
+++ b/sci-chemistry/pdb2pqr/metadata.xml
@@ -2,4 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 <herd>sci-chemistry</herd>
+<use>
+        <flag name='opal'>Add web interafce via opal</flag>
+</use>
 </pkgmetadata>
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.1.2.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.1.2.ebuild
index 5160f4085d9f..24ef55bdcf14 100644
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.1.2.ebuild
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.1.2.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# 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 1.9 2008/10/11 11:23:45 markusle Exp $
+# $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
 
@@ -16,6 +16,8 @@ KEYWORDS="amd64 x86"
 DEPEND="dev-lang/python
 		dev-python/numpy"
 
+RDEPEND="${DEPEND}"
+
 FORTRAN="g77 gfortran"
 
 src_unpack() {
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.2.1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.2.1.ebuild
index fade32bc1c9a..a0e7ef896c5a 100644
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.2.1.ebuild
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.2.1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# 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 1.4 2008/02/06 15:14:10 markusle Exp $
+# $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
 
@@ -15,6 +15,8 @@ KEYWORDS="~amd64 ~x86"
 
 DEPEND="dev-lang/python"
 
+RDEPEND="${DEPEND}"
+
 FORTRAN="g77 gfortran"
 
 src_compile() {
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.3.0.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.3.0.ebuild
index d14e56d26c54..941c66d0bd8e 100644
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.3.0.ebuild
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.3.0.ebuild
@@ -1,6 +1,6 @@
 # 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-1.3.0.ebuild,v 1.5 2009/03/03 02:50:01 darkside Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.3.0.ebuild,v 1.6 2009/05/24 07:50:41 je_fro Exp $
 
 inherit eutils fortran multilib flag-o-matic distutils
 
@@ -16,6 +16,8 @@ KEYWORDS="amd64 x86"
 DEPEND="dev-lang/python
 		dev-python/numpy"
 
+RDEPEND="${DEPEND}"
+
 FORTRAN="g77 gfortran"
 
 src_unpack() {
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild
new file mode 100644
index 000000000000..c48acdc23faf
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.4.0-r1.ebuild
@@ -0,0 +1,123 @@
+# 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-1.4.0-r1.ebuild,v 1.1 2009/05/24 07:50:41 je_fro Exp $
+
+inherit eutils fortran multilib flag-o-matic distutils python
+
+DESCRIPTION="An automated pipeline for performing Poisson-Boltzmann electrostatics calculations"
+LICENSE="BSD"
+HOMEPAGE="http://pdb2pqr.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${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"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${P}-ldflags.patch
+	epatch "${FILESDIR}"/${P}-automagic.patch
+	epatch "${FILESDIR}"/${P}-install.patch
+	epatch "${FILESDIR}"/${P}-gcc44.patch
+
+	sed '50,200s:CWD:DESTDIR:g' -i 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"
+#die
+#		$(use_with opal)="http://ws.nbcr.net/opal/services/pdb2pqr_1.4.0" || \
+	emake || die "emake failed"
+}
+
+src_test() {
+	emake -j1 test && \
+		F77="${FORTRANC}" emake -j1 adv-test || \
+		die "test failed"
+}
+
+src_install() {
+#	emake -j1 PREFIX="${D}"/$(python_get_sitedir)/${PN} install || die
+	dodir $(python_get_sitedir)/${PN}
+#	emake -j1 DESTDIR="${D}"/$(python_get_sitedir)/${PN}  install || die
+	emake -j1 DESTDIR="${D}$(python_get_sitedir)/${PN}" PREFIX=""  install || die
+
+	if use doc; then
+		cd doc
+		sh genpydoc.sh || die
+		dohtml -r *.html images pydoc || die
+		cd -
+	fi
+
+	if use examples; then
+		insinto /usr/share/${PN}/
+		doins -r examples || die
+	fi
+
+	INPATH="$(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."
+
+
+}