Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv30444
Modified Files:
pymol-py.info
Added Files:
apbs.info apbs.patch pdb2pqr.info
Log Message:
new apbs and pdb2pqr for 10.7, pymol graphics update
--- NEW FILE: apbs.patch ---
diff -ruN apbs-1.3-source/configure apbs-1.3-source-orig/configure
--- apbs-1.3-source/configure 2010-10-21 08:17:07.000000000 -0700
+++ apbs-1.3-source-orig/configure 2010-11-23 20:07:40.000000000 -0800
@@ -22371,7 +22371,7 @@
SERVICEURL='http://kryptonite.nbcr.net/opal2/services/apbs_1.3'
PARALLELSERVICEURL='http://oolite.calit2.optiputer.net/opal2/services/apbs-parallel-1.3'
-SITEPKGS=${prefix}/lib/python${PY_VERSION}/site-packages
+SITEPKGS=@INSTALL_DIR@${prefix}/lib/python${PY_VERSION}/site-packages
# Check whether --with-maxmem was given.
diff -ruN apbs-1.3-source/contrib/opal/ZSI/Makefile.in
apbs-1.3-source-orig/contrib/opal/ZSI/Makefile.in
--- apbs-1.3-source/contrib/opal/ZSI/Makefile.in 2010-05-19
10:24:24.000000000 -0700
+++ apbs-1.3-source-orig/contrib/opal/ZSI/Makefile.in 2010-11-23
20:09:12.000000000 -0800
@@ -542,7 +542,7 @@
install-data-local:
-mkdir -p ${SITEPKGS}
- ${py_path} setup.py install --prefix=${prefix}
+ ${py_path} setup.py install --prefix=@INSTALL_DIR@${prefix}
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:
diff -ruN apbs-1.3-source/tools/python/Makefile.in
apbs-1.3-source-orig/tools/python/Makefile.in
--- apbs-1.3-source/tools/python/Makefile.in 2010-05-19 10:24:24.000000000
-0700
+++ apbs-1.3-source-orig/tools/python/Makefile.in 2010-11-23
20:11:08.000000000 -0800
@@ -52,7 +52,6 @@
${top_builddir}/bin/.libs/libapbsmainroutines.a \
${top_builddir}/src/aaa_lib/.libs/libapbs.a \
${top_builddir}/contrib/lib/libmaloc.a \
- ${top_builddir}/contrib/blas/.libs/libapbsblas.a \
$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
DEFAULT_INCLUDES = -I. -I$(top_builddir)/src/aaa_inc@am__isrc@
depcomp =
@@ -248,7 +247,7 @@
SUBDIRS = vgrid
_apbslib_so_SOURCES = apbslib.c
_apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
-_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a
${top_builddir}/src/aaa_lib/.libs/libapbs.a
${top_builddir}/contrib/lib/libmaloc.a
${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS) ${z_lib}
+_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a
${top_builddir}/src/aaa_lib/.libs/libapbs.a
${top_builddir}/contrib/lib/libmaloc.a $(PY_LDFLAGS) ${z_lib}
all: all-recursive
.SUFFIXES:
Index: pymol-py.info
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- pymol-py.info 26 Jul 2011 03:39:33 -0000 1.1
+++ pymol-py.info 1 Aug 2011 01:59:19 -0000 1.2
@@ -1,10 +1,10 @@
Info2: <<
Package: pymol-py%type_pkg[python]
Version: 1.4
-Revision: 7
+Revision: 8
Maintainer: W. G. Scott <[email protected]>
Type: python (2.6 2.7)
-# r3959
+# 3962.
#Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
Source: http://diablo.ucsc.edu/~wgscott/pymol/pymol-%v-src.tar.bz2
Source-MD5: c520de57b1b3ad7fbc891057a4e32c3e
@@ -83,7 +83,7 @@
DescPackaging: <<
The tarball used for this version was created in accordance to the BSD
license of pymol using the following instructions...
- svn -r3959 co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol
pymol-1.4
+ svn -r3962 co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol
pymol-1.4
tar --exclude=.svn -jcvf pymol-1.4-src.tar.bz2 pymol-1.4
Added eMovie.py plug-in manually. Commented out line that opens the window
for eMovie by
default every time pymol is started as this is annoying behavior. eMovie is
activated via
--- NEW FILE: pdb2pqr.info ---
Package: pdb2pqr
Version: 1.7
Revision: 1
Source: mirror:sourceforge:%n/%n-%v.tar.gz
Source-MD5: 058622cb2ca6ca12af04d4f11b272951
SourceDirectory: %n-%v
Depends: python27, gcc46-shlibs
BuildDepends: python, python27, gcc46
BuildConflicts: g77, g95, fort77
Description: Converts pdb files to pqr
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
CompileScript: <<
#!/bin/bash -efv
#PATH=%p/bin:%p/sbin:${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 <[email protected]>
--- NEW FILE: apbs.info ---
Package: apbs
Version: 1.3.0
Revision: 2
Source:
http://downloads.sourceforge.net/project/%n/%n/%n-%v/%n-1.3-source.tar.gz
Source-MD5: f99a505365f07f6853979cfe2ef23365
Depends: readline5-shlibs, gcc46-shlibs, python27
BuildDepends: gcc46, python27, fink (>= 0.24.12)
BuildConflicts: g77, g95, fort77
Conflicts: maloc, maloc-mpi-lammpi, maloc-mpi-openmpi
Replaces: maloc, maloc-mpi-lammpi, maloc-mpi-openmpi
ConfigureParams: --disable-openmp --build=%m-apple-darwin`uname -r|cut -f1 -d.`
--host=%m-apple-darwin`uname -r|cut -f1 -d.`
SetCFLAGS: -O3
Description: Adaptive Poisson-Boltzmann Solver
PatchFile: %n.patch
PatchFile-MD5: 2662144e3e3508a944902c0a5e29eaf1
PatchScript: <<
sed 's|@INSTALL_DIR@|%d|g' < %{PatchFile} | patch -p1
<<
CompileScript: <<
#!/bin/bash -efv
PATH=%p/bin:%p/sbin:${PATH} ; export PATH
source %p/bin/init.sh
perl -pi -e 's|PY_SHARED="-shared"|PY_SHARED="-bundle"|g' configure
BLAS_DIR='/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A'
py_path=%p/bin/python2.7 F77=gfortran ./configure %c --enable-python
--with-python=%p/bin/python2.7 \
--disable-openmp --with-blas="-L${BLAS_DIR} -lblas -Wl,-framework -Wl,vecLib
-Wl,-undefined -Wl,dynamic_lookup" FFLAGS="-O3"
perl -pi -e 's|\${prefix}/share|%i/share/%n|g' Makefile
perl -pi -e 's|\$\(DESTDIR\)\$\(libdir\)|share/apbs/lib|g'
contrib/blas/Makefile
make
<<
InstallScript: <<
#!/bin/zsh -efv
rm -Rf **/CVS # fink validate complains if this junk is left behind.
perl -pi -e 's|/usr/bin/env python|%p/bin/python|g' examples/**/*.py
perl -pi -e 's|/usr/bin/env python|%p/bin/python|g' tools/**/*.py
rm -f **/*.o
#
# make install DESTDIR=%d
# install it ourselves:
mkdir -p %i/bin
/bin/cp bin/apbs bin/ApbsClient.py %i/bin/.
echo '#!%p/bin/python2.7' >| %i/bin/wsdl2py
echo "from ZSI.generate.commands import wsdl2py" >> %i/bin/wsdl2py
echo "wsdl2py()" >> %i/bin/wsdl2py
chmod a+x %i/bin/wsdl2py
#
mkdir -p %i/share/%n
/bin/cp -r examples %i/share/%n/.
/bin/cp -r tools %i/share/%n/.
/bin/cp -r doc %i/share/%n/.
#
mkdir -p %i/share/doc
ln -s %p/share/%n/doc %i/share/doc/%n
#
mkdir -p %i/lib/python2.7/site-packages/ZSI
/bin/cp -r contrib/opal/ZSI/ZSI/*
%i/lib/python2.7/site-packages/ZSI/.
#
mkdir -p %i/include/apbs
/bin/cp **/*.h %i/include/apbs/.
#
mkdir -p %i/lib
/bin/rm -rf contrib
/bin/cp **/.*/*.a %i/lib/.
/bin/cp **/*.la %i/lib/.
ranlib %i/lib/*.a
#
<<
PreRmScript: <<
/usr/bin/find %p/lib/python2.7/site-packages/ZSI -name '*.pyo' -delete
<<
PostInstScript: <<
%p/bin/python2.7 -O %p/lib/python2.7/compileall.py -q
%p/lib/python2.7/site-packages/ZSI
<<
################################################################################
SplitOff: <<
Package: %N-dev
BuildDependsOnly: true
Description: apbs headers, static libraries and libtool files
Files:<<
include/apbs
lib/*.a
lib/*.la
<<
<<
################################################################################
Homepage: http://apbs.sourceforge.net/
RunTimeVars: <<
APBS_PSIZE:%p/share/%n/tools/manip
<<
DescDetail: <<
APBS is a software package for the numerical solution of the
Poisson-Boltzmann equation, a popular continuum model for describing
electrostatic interactions between molecular solutes over a wide range
of length scales. The Fink pymol package is pre-configured to permit
apbs to be used as a plug-in.
.
The software is released under the GPL, but the author requests that you
register your use with him to aid him in obtaining funding to continue to
develop the code. Most electrostatics software is payware, so please help
him continue to support this free software. You can do so at this URL:
http://agave.wustl.edu/apbs/download/
<<
License: GPL
Maintainer: W. G. Scott <[email protected]>
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