latest from overlay, thanks to alexxy

Package-Manager: portage-2.1.6.13/cvs/Linux x86_64

11 files changed, 427 insertions, 11 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/Manifest b/sci-chemistry/pdb2pqr/Manifest
index c6efd6d801bf..8110fb396a86 100644
--- a/sci-chemistry/pdb2pqr/Manifest
+++ b/sci-chemistry/pdb2pqr/Manifest
@@ -2,13 +2,19 @@ AUX pdb2pqr-1.1.2-fpic-gentoo.patch 668 RMD160 e076ebcfe1e0fd39ca7b2219b6d9938b6
 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 2962 RMD160 aa3dbdde3174c3035b8bea7a8ceb79733fc1a175 SHA1 22da361d832f9260d3cec1468535e28647357b6d SHA256 1a2dbd1b75be1b578d424506a6ff0365d2105bf57d36afe6a91751482da1b9bf
+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
-EBUILD pdb2pqr-1.1.2.ebuild 1867 RMD160 4ecdcd3b1781d114e153436182fccb9c079c1ba6 SHA1 8c23726868d38e65263de452f9577909e024a924 SHA256 5bbbd124a678e6db4cc75ecfb812cc347c7f3aa0e7777be3291813a054216340
-EBUILD pdb2pqr-1.2.1.ebuild 1717 RMD160 a47593b7d6a5a206ed34544719ccc603f9cf5196 SHA1 db42c2869b3bb57f68a51a8efed5871db71a9079 SHA256 8c97db05b9e2bb337d4d8f19eb74119b1bf0edf9882089493ccefd2727ac4c7a
-EBUILD pdb2pqr-1.3.0.ebuild 1962 RMD160 e9a1e7ef16e365bdef0d4960d1f9ea85e9cc1346 SHA1 7abd9d7ab587f5b0cc3d38690176b8947835386a SHA256 aa6ec3345d843385fb206172e1a89b90132956ea9b73d1a0e14d866161667441
-MISC ChangeLog 2462 RMD160 82c2854f0e4c53f8983977a781d69403f4461d30 SHA1 9d5b146522016bca605c8570db5873ee613f189e SHA256 0d8d897f3efb8ecaf2a8f401deec9cdb942f1333f290bfc95d7f26c8cb64cd19
-MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
+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
+EBUILD pdb2pqr-1.3.0.ebuild 1981 RMD160 d9e8eb2f45aa12cd478e4e27e99ddf66aa202c5a SHA1 39de5c8e05de1827ab618959f73b256fd915fe8d SHA256 831d3e176306826bd44146f489030186beba521d00d7a87864ebb13272edfd17
+EBUILD pdb2pqr-1.4.0-r1.ebuild 2989 RMD160 2d561fd8b9ce8e7d98eb2352975706cde529eed1 SHA1 8f159be0741d11d2f2d4864c779d998fae128d39 SHA256 d2d3d7cd26fc1c2014fc78ee31390aa6eb46ea369de0b2214abdb6a57bb334ea
+MISC ChangeLog 2609 RMD160 fdc89855c085a3d6a054add537e1fedecfca848d SHA1 2944baae9647808c9e995a2a66dacc425275c7f5 SHA256 a4c849fda59361558c83bdf34e669760016d8ed828b461b92923eb10930c8a9c
+MISC metadata.xml 239 RMD160 c9646b9b2171a8eeac8517b70efe2d2f8b6aa0f0 SHA1 48e78f37fbb221dc94978bf1ea4a9ba874a52464 SHA256 5dd1bfe10b60a7f631b103e6755e771471fea0334312522ef256db4ddb6923c2
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."
+
+
+}