Drop old, fixes bug #478592

Signed-off-by: Justin Lecher <jlec@gentoo.org>
(Portage version: 2.2.20/cvs/Linux x86_64, signed Manifest commit with key E9402A79B03529A2!)

8 files changed, 7 insertions, 668 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index a1a3589acb8a..2231d93962da 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pdb2pqr
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.50 2015/08/07 10:36:03 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.51 2015/08/07 11:03:57 jlec Exp $
+
+  07 Aug 2015; Justin Lecher <jlec@gentoo.org> -files/1.7.0-install.patch,
+  -files/pdb2pqr-1.4.0-automagic.patch, -files/pdb2pqr-1.4.0-install.patch,
+  -files/pdb2pqr-1.4.0-ldflags.patch, -files/pdb2pqr-1.8.0-automagic.patch,
+  -files/pdb2pqr-1.8.0-ldflags.patch, -pdb2pqr-1.5.0-r2.ebuild:
+  Drop old, fixes bug #478592
 
   07 Aug 2015; Agostino Sarubbo <ago@gentoo.org> pdb2pqr-1.9.0-r1.ebuild:
   Stable for x86, wrt bug #534696
diff --git a/sci-chemistry/pdb2pqr/files/1.7.0-install.patch b/sci-chemistry/pdb2pqr/files/1.7.0-install.patch
deleted file mode 100644
index 77ee077937dc..000000000000
--- a/sci-chemistry/pdb2pqr/files/1.7.0-install.patch
+++ /dev/null
@@ -1,131 +0,0 @@
-diff --git a/Makefile.am b/Makefile.am
-index d5d020d..550d52a 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -113,24 +113,11 @@ install:
- 	    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 $$c/visualize.cgi $(CWD)/$$dir/. ; \
--	  echo "Adding visualize.cgi" ; \
--	  cp $$c/querystatus.cgi $(CWD)/$$dir/. ; \
--	  echo "Adding querystatus.cgi" ; \
--	  cp $$c/pdb2pqr.css $(CWD)/$$dir/. ; \
- 	  if ! test -d $(CWD)/$$dir/dat  ; then \
- 	    mkdir $(CWD)/$$dir/dat ; \
- 	  fi ; \
-@@ -138,49 +125,12 @@ install:
- 	  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/. ; \
-+	  echo "Adding extensions" ; \
- 	  if ! test -d $(CWD)/$$dir/extensions ; then \
- 	    mkdir $(CWD)/$$dir/extensions ; \
- 	  fi ; \
- 	  echo "Adding extensions" ; \
- 	  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)/$$dir/jmol ; then \
--	    mkdir $(CWD)/$$dir/jmol ; \
--	  fi ; \
--	  echo "Adding jmol/" ; \
--	  cp -rf $$c/jmol/*.* $(CWD)/$$dir/jmol/. ; \
- 	  if ! test -d $(CWD)/$$dir/src ; then \
- 	    mkdir $(CWD)/$$dir/src ; \
- 	  fi ; \
-@@ -229,49 +179,6 @@ install:
- 	  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-automagic.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch
deleted file mode 100644
index addb76b9b4e6..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-automagic.patch
+++ /dev/null
@@ -1,105 +0,0 @@
-diff -Naur pdb2pqr-1.4.0/configure.ac pdb2pqr-1.4.0.new/configure.ac
---- pdb2pqr-1.4.0/configure.ac	2009-04-02 10:53:56.000000000 -0400
-+++ pdb2pqr-1.4.0.new/configure.ac	2009-09-24 19:36:47.000000000 -0400
-@@ -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 $PY_NUMERIC"
--    else
--      AC_MSG_RESULT([no])
--    fi
--  fi
- 
-   # If failed, test for numpy
-   AC_MSG_CHECKING([whether you defined numpy])
-@@ -457,29 +425,14 @@
-   HAVE_PDB2PQR_OPAL=1
- fi
- 
--if test "$PDB2PQR_OPAL_URL" != ""; then 
-+if test "$PDB2PQR_OPAL_URL" != "no"; then 
-   HAVE_PDB2PQR_OPAL=1
-   if test -d $PY_PREFIX/lib/python$PY_VERSION/site-packages/ZSI ; then
-     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  
- 
-diff -Naur pdb2pqr-1.4.0/pdb2pka/NEWligand_topology.py pdb2pqr-1.4.0.new/pdb2pka/NEWligand_topology.py
---- pdb2pqr-1.4.0/pdb2pka/NEWligand_topology.py	2007-10-12 15:52:40.000000000 -0400
-+++ pdb2pqr-1.4.0.new/pdb2pka/NEWligand_topology.py	2009-09-24 19:36:07.000000000 -0400
-@@ -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 -Naur pdb2pqr-1.4.0/pdb2pka/ligand_topology.py pdb2pqr-1.4.0.new/pdb2pka/ligand_topology.py
---- pdb2pqr-1.4.0/pdb2pka/ligand_topology.py	2008-06-13 10:15:38.000000000 -0400
-+++ pdb2pqr-1.4.0.new/pdb2pka/ligand_topology.py	2009-09-24 19:36:07.000000000 -0400
-@@ -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-install.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-install.patch
deleted file mode 100644
index 4af9eda8e1b3..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-install.patch
+++ /dev/null
@@ -1,134 +0,0 @@
---- 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
deleted file mode 100644
index ea5dc85ba07d..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.4.0-ldflags.patch
+++ /dev/null
@@ -1,33 +0,0 @@
---- 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 = $(PY_LDFLAGS)
- propka_SOURCES = propka.f
- 
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch
deleted file mode 100644
index c218fe6a816e..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch
+++ /dev/null
@@ -1,75 +0,0 @@
-diff -Naur pdb2pqr-1.4.0/configure.ac pdb2pqr-1.4.0.new/configure.ac
---- pdb2pqr-1.4.0/configure.ac	2009-04-02 10:53:56.000000000 -0400
-+++ pdb2pqr-1.4.0.new/configure.ac	2009-09-24 19:36:47.000000000 -0400
-@@ -255,38 +255,6 @@
- 
-   # Test for Numeric install
-   AC_MSG_CHECKING([whether you defined Numeric or Numpy])
--  if (test -n "${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 $PY_NUMERIC"
--    else
--      AC_MSG_RESULT([no])
--    fi
--  fi
- 
-   # If failed, test for numpy
-   AC_MSG_CHECKING([whether you defined numpy])
-@@ -457,29 +425,14 @@
-   HAVE_PDB2PQR_OPAL=1
- fi
- 
--if test "$PDB2PQR_OPAL_URL" != ""; then 
-+if test "$PDB2PQR_OPAL_URL" != "no"; then 
-   HAVE_PDB2PQR_OPAL=1
-   if test -d $PY_PREFIX/lib/python$PY_VERSION/site-packages/ZSI ; then
-     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  
- 
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch
deleted file mode 100644
index 5a7e04419ce6..000000000000
--- a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- pdb2pka/Makefile.am           | 2 +-
- pdb2pka/substruct/Makefile.am | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/pdb2pka/Makefile.am b/pdb2pka/Makefile.am
-index 75f6ffd..e40a2f6 100644
---- a/pdb2pka/Makefile.am
-+++ b/pdb2pka/Makefile.am
-@@ -16,7 +16,7 @@ SUBDIRS          = substruct
- 
- 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:
-diff --git a/pdb2pka/substruct/Makefile.am b/pdb2pka/substruct/Makefile.am
-index b1638a0..ae95e94 100644
---- a/pdb2pka/substruct/Makefile.am
-+++ b/pdb2pka/substruct/Makefile.am
-@@ -15,7 +15,7 @@ CLEANFILES       = Algorithms.so
- 
- 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
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r2.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r2.ebuild
deleted file mode 100644
index baacac906039..000000000000
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.5.0-r2.ebuild
+++ /dev/null
@@ -1,159 +0,0 @@
-# Copyright 1999-2012 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-r2.ebuild,v 1.11 2012/10/19 10:10:18 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-SUPPORT_PYTHON_ABIS="1"
-PYTHON_EXPORT_PHASE_FUNCTIONS="1"
-RESTRICT_PYTHON_ABIS="2.4 3.*"
-
-inherit autotools eutils fortran-2 flag-o-matic python toolchain-funcs 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}/${MY_P}.tar.gz"
-
-SLOT="0"
-IUSE="doc examples opal"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="
-	dev-python/numpy
-	sci-chemistry/openbabel
-	opal? ( dev-python/zsi )"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	python_pkg_setup
-}
-
-src_prepare() {
-	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"
-	python_src_prepare
-	preparation() {
-		eautoreconf
-	}
-	python_execute_function -s preparation
-}
-
-src_configure() {
-	# we need to compile the *.so as pic
-	append-flags -fPIC
-	FFLAGS="${FFLAGS} -fPIC"
-
-	configuration() {
-		# Avoid automagic to numeric
-		NUMPY="${EPREFIX}/$(python_get_sitedir)" \
-			F77="$(tc-getFC)" \
-			econf \
-			$(use_with opal)
-	}
-	python_execute_function -s configuration
-}
-
-src_compile() {
-	compilation() {
-		emake || die
-	}
-	python_execute_function -s compilation
-}
-
-src_test() {
-	testing() {
-		emake -j1 test \
-			|| die "tests failed"
-	}
-	python_execute_function -s testing
-}
-
-src_install() {
-	installation() {
-		dodir $(python_get_sitedir)/${PN}
-		emake -j1 DESTDIR="${ED}$(python_get_sitedir)/${PN}" \
-			PREFIX=""  install || die "install failed"
-
-		INPATH="$(python_get_sitedir)/${PN}"
-
-		# generate pdb2pqr wrapper
-		cat >> "${T}"/${PN}-$(python_get_version) <<-EOF
-			#!/bin/sh
-			$(PYTHON) ${EPREFIX}/${INPATH}/${PN}.py \$*
-		EOF
-
-		dobin "${T}"/${PN}-$(python_get_version) || die "Failed to install pdb2pqr wrapper."
-
-		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."
-	}
-	python_execute_function -s installation
-
-	dosym ${PN}-$(python_get_version -f) /usr/bin/${PN}
-
-	if use doc; then
-		cd doc
-		sh genpydoc.sh \
-			|| die "genpydoc failed"
-		dohtml -r *.html images pydoc \
-			|| die "failed to install html docs"
-		cd -
-	fi
-
-	if use examples; then
-		insinto /usr/share/${PN}/
-		doins -r examples || die "Failed to install examples."
-	fi
-
-	dodoc ChangeLog NEWS README AUTHORS || \
-		die "Failed to install docs"
-}
-
-pkg_postinst() {
-	python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
-	python_mod_cleanup ${PN}
-}