1 files changed, 95 insertions, 0 deletions
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 *