pdb2pqr stable port information

Package: pdb2pqr
Version: 1.7
Revision: 1
UseMaxBuildJobs: false
Source: mirror:sourceforge:%n/%n-%v.tar.gz
Source-MD5: 058622cb2ca6ca12af04d4f11b272951
SourceDirectory: %n-%v
Depends: python27, gcc46-shlibs
BuildDepends: python, python27, gcc46
BuildConflicts: g77, g95, fort77
Description: Converts pdb files to pqr
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
CompileScript: <<
#!/bin/bash -efv
#PATH=%p/bin:%p/sbin:${PATH} ; export PATH
#source %p/bin/init.sh
#
if [[ "%m" != "x86_64" ]]; then
export CCPFLAGS="-m32"
export LDFLAGS="-m32"
perl -pi -e 's|-Wl,-framework -Wl,Python -bundle|%p/lib/python2.7/config/libpython2.7.dylib -m32 -bundle|g' ./configure
perl -pi -e 's|-Wl,-framework -Wl,Python -bundle|%p/lib/python2.7/config/libpython2.7.dylib -m32 -bundle|g' ./propka/configure
else
perl -pi -e 's|-Wl,-framework -Wl,Python -bundle|%p/lib/python2.7/config/libpython2.7.dylib -bundle|g' ./configure
perl -pi -e 's|-Wl,-framework -Wl,Python -bundle|%p/lib/python2.7/config/libpython2.7.dylib -bundle|g' ./propka/configure
fi
perl -pi -e 's|fort xlf95 lf95 g95|gfortran|g' ./propka/configure
perl -pi -e 's|/usr/bin/python|%p/bin/python2.7|g' ./pdb2pka/pka.py
perl -pi -e 's|/usr/bin/python|%p/bin/python2.7|g' ./src/psize.py
rm -fr contrib
./configure --with-max-atoms="1000000" --without-url --with-python=%p/bin/python2.7 --with-f77=gfortran
if [[ "%m" != "x86_64" ]]; then
perl -pi -e 's|-DPACKAGE|-m32 -DPACKAGE|g' Makefile pdb2pka/substruct/Makefile tests/Makefile tests/test/Makefile pdb2pka/Makefile propka/Makefile tests/adv-test/Makefile
fi
make
rm -f pdb2pka/pMC_mult.o pdb2pka/substruct/Algorithms.o propka/propkac.o tests/adv-test/test.o
rm -r pdb2pka/pMC_mult_wrap.o propka/propka.o propka/propkalib.o tests/test/test.o
<<
InstallScript: <<
#!/bin/zsh -efv
source %p/bin/init.sh
PATH=%p/bin:%p/sbin:${PATH} ; export PATH

mkdir -p %i/share/pdb2pqr
cp -R * %i/share/pdb2pqr
#
mkdir -p %i/bin
echo "#!/bin/zsh -f" >| %i/bin/pdb2pqr
echo "%p/share/pdb2pqr/pdb2pqr.py \"\$@\" " >>| %i/bin/pdb2pqr
chmod a+x %i/bin/pdb2pqr
#
echo "#!/bin/zsh -f" >| %i/bin/propka
echo "%p/share/pdb2pqr/propka/propka \"\$@\" " >>| %i/bin/propka
chmod a+x %i/bin/propka
<<
Homepage: http://pdb2pqr.sourceforge.net/
DescDetail: <<
PDB2PQR is a Python software package that automates many of the common tasks
of preparing structures for continuum electrostatics calculations, providing
a platform-independent utility for converting protein files in PDB format to
PQR format. These tasks include: Adding a limited number of missing heavy
atoms to biomolecular structures Determining side-chain pKas Placing missing
hydrogens Optimizing the protein for favorable hydrogen bonding Assigning
charge and radius parameters from a variety of force fields PDB2PQR was
ported to Python by Todd Dolinsky while working with Nathan Baker at
Washington University in St. Louis. The PDB2PQR code is based on C++ design
and algorithms by Jens Erik Nielsen. PDB2PQR was originally designed to
facilitate structure preparation for APBS. PDB2PQR uses PropKa to determine
protein pKa values. PropKa is developed by the Jensen Research Group at the
University of Iowa. More information about PropKa can be found at
http://propka.chem.uiowa.edu.
<<
License: GPL
Maintainer: W. G. Scott