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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 *
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