Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv31318
Modified Files:
coot.info
Added Files:
rdkit.info
Log Message:
rdkit added as new dependency for coot
--- NEW FILE: rdkit.info ---
Package: rdkit
Version: 2012.12.1
Revision: 1
Distribution: 10.6, 10.7, 10.8
GCC: 4.0
BuildDependsOnly: false
Source: mirror:sourceforge:rdkit/RDKit_2012_12_1.tgz
Source-MD5: 36596b18ff71c70b04d25c43810c2b01
Source2: mirror:sourceforge:boost/boost_1_53_0.tar.bz2
Source2-MD5: a00d22605d5dbcfb4c9936a9b35bc4c2
Description: Cheminformatics and machine-learning software
DescDetail: <<
A collection of cheminformatics and machine-learning software written in C++
and Python. Core algorithms and data structures are written in C++. Wrappers
are provided to use the toolkit from either Python or Java. Additionally, the
RDKit distribution includes a PostgreSQL-based cartridge that allows molecules
to be stored in a relational database and retrieved via substructure and
similarity searches.
<<
BuildConflicts: boost1.35.nopython, boost1.35.python26, boost1.35.python27,
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake
Depends: %N-shlibs, python27-shlibs, numpy-py27, sqlite3-shlibs
BuildDepends: python27, numpy-py27, sqlite3-dev, cmake
CompileScript: <<
#!/bin/sh -efv
#
# First build a more current boost libboost_python library and we will put it
in the rdkit
# library subdirectory to avoid confusion
#
RDKIT_ROOT="$PWD"
cd ../boost_1_53_0
BOOSTROOT="$PWD"
./bootstrap.sh --with-libraries="python,regex" --with-python-root=%p
--with-python=%p/bin/python2.7 --prefix="$PWD"
#
./b2 install --prefix="$BOOSTROOT"
cd lib
# Despite the above it links to the system python, so fix that and give it a
proper instal name id
install_name_tool -change
/System/Library/Frameworks/Python.framework/Versions/2.7/Python
%p/lib/python2.7/config/libpython2.7.dylib libboost_python.dylib
install_name_tool -id %p/lib/rdkit/libboost_python.dylib libboost_python.dylib
#
#
install_name_tool -change
/System/Library/Frameworks/Python.framework/Versions/2.7/Python
%p/lib/python2.7/config/libpython2.7.dylib libboost_regex.dylib
install_name_tool -id %p/lib/rdkit/libboost_regex.dylib libboost_regex.dylib
#
#
# Now for rdkit itself
#
cd "$RDKIT_ROOT"
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=%p -DCMAKE_INSTALL_NAME_DIR=%p/lib/%n
-DCMAKE_PREFIX_PATH=%p -DBOOST_ROOT="$BOOSTROOT" -DBoost_NO_SYSTEM_PATHS=ON
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7
..
# NUMPROC="$(sysctl -n hw.ncpu)"
# make -j $NUMPROC install
make install
#
# We only require the boost_python library and boost_regex library
cp "$BOOSTROOT"/lib/libboost_python.dylib
"$RDKIT_ROOT"/lib/libboost_python.dylib
cp "$BOOSTROOT"/lib/libboost_regex.dylib
"$RDKIT_ROOT"/lib/libboost_regex.dylib
cp -R "$BOOSTROOT"/boost "$RDKIT_ROOT"/Code/.
<<
InstallScript: <<
#!/bin/sh -efv
mkdir -p %i/lib/python2.7/site-packages
cp -R rdkit %i/lib/python2.7/site-packages/.
mkdir -p %i/lib
cp -R lib %i/lib/%n
mkdir -p %i/include
cp -R Code %i/include/%n
<<
SplitOff: <<
Package: %N-shlibs
Description: rdkit dynamic libraries
Files:<<
lib/%N/*.1.dylib
lib/%N/libboost_python.dylib
lib/%N/libboost_regex.dylib
<<
Shlibs: <<
%p/lib/%N/libboost_python.dylib 0.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libboost_regex.dylib 0.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libAlignment.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libCatalogs.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libChemReactions.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libChemTransforms.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libChemicalFeatures.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libDataStructs.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libDepictor.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libDescriptors.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libDistGeomHelpers.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libDistGeometry.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libEigenSolvers.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libFileParsers.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libFingerprints.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libForceField.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libForceFieldHelpers.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libFragCatalog.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libGraphMol.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libMolAlign.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libMolCatalog.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libMolChemicalFeatures.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libMolTransforms.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libOptimizer.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libPartialCharges.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libRDBoost.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libRDGeneral.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libRDGeometryLib.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libShapeHelpers.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libSimDivPickers.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libSmilesParse.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libSubgraphs.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libSubstructMatch.1.dylib 1.0.0 %n (>=
2012.12.1-1)
%p/lib/%N/libhc.1.dylib 1.0.0 %n (>=
2012.12.1-1)
<<
DocFiles: license.txt README
License: BSD
<<
SplitOff2: <<
Package: %N-dev
BuildDependsOnly: true
Description: rdkit static libraries and headers
Files:<<
lib/%N/*.a
include/%N/*
<<
DocFiles: license.txt README
License: BSD
<<
License: BSD
Maintainer: W. G. Scott <wgsc...@users.sourceforge.net>
Homepage: http://www.rdkit.org
Index: coot.info
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -d -r1.18 -r1.19
--- coot.info 29 Jan 2013 07:24:53 -0000 1.18
+++ coot.info 11 Feb 2013 22:08:49 -0000 1.19
@@ -1,14 +1,17 @@
Package: coot
Version: 0.7.1-pre
-Revision: 4552
+Revision: 4562
SourceDirectory: %n-%v
+Distribution: 10.6, 10.7, 10.8
GCC: 4.0
Source:
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: dc42bb2504ff3281f14f1dc7694c5107
+Source-MD5: 82d653d6e97bb940b024833314a3ccfc
Source2:
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.38.tar.gz
Source2-MD5: 174a5fc5e5be03cb432c61e8da4283df
Source3:
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
Source3-MD5: 257ab90d44f1c877ada96720dbb87c13
+#Source4:
http://coot.googlecode.com/svn-history/r4544/trunk/lidia-core/cod-types.hh
+#Source4-MD5: 333ee49b341b9ee534b3e6f72cff7064
###############################################################################
Description: Crystallographic molecular graphics
DescDetail: <<
@@ -39,14 +42,14 @@
fink (>= 0.24.12) ,
clipper-dev (>= 1:2.1-31) ,
gpp4-dev (>= 1.2.0-31) ,
- mmdb-dev (>= 1.23.2-31) ,
+ mmdb-dev (>= 1.23.2-31) ,
ssm-dev (>= 0.1-31) ,
atk1 (>= 1.28.0-1) ,
cairo (>= 1.8.8-3) ,
expat1 ,
fftw | fftw-mpi ,
fontconfig2-dev (>= 2.8.0-4) ,
- freetype219 (>= 2.3.12-1) ,
+ freetype219 (>= 2.3.12-1) ,
freeglut ,
giflib ,
glib2-dev (>= 2.22.0-1) ,
@@ -63,6 +66,7 @@
guile18-gtk-dev (>= 2.0-10) ,
libart2 (>= 2.3.16-2) ,
libcurl4 ,
+ libgettext8-dev ,
libglade2 (>= 2.6.2-1) ,
libgnomecanvas2-dev (>= 2.20.0) ,
libjpeg8 ,
@@ -76,6 +80,8 @@
pygtk2-gtk-py27-dev ,
pygobject2-py27-dev ,
python27 ,
+ rdkit-dev ,
+ rdkit ,
swig ,
x11-dev
<<
@@ -83,7 +89,7 @@
Depends: <<
clipper-shlibs (>= 1:2.1-31) ,
gpp4-shlibs (>= 1.2.0-31) ,
- mmdb-shlibs (>= 1.23.2-31) ,
+ mmdb-shlibs (>= 1.23.2-31) ,
ssm-shlibs (>= 0.1-31) ,
atk1-shlibs (>= 1.28.0-1) ,
coot-shlibs (= %v-%r) ,
@@ -106,6 +112,7 @@
guile18-shlibs ,
libart2-shlibs ,
libcurl4-shlibs ,
+ libgettext8-shlibs ,
libgnomecanvas2-shlibs (>= 2.20.0),
libjpeg8-shlibs ,
libpng15-shlibs ,
@@ -118,6 +125,7 @@
pango1-xft2-ft219-shlibs (>= 1.24.5-4) ,
pygtk2-gtk-py27 ,
python27 ,
+ rdkit ,
x11
<<
#
@@ -131,6 +139,7 @@
sed 's|@PREFIX@|%p|g' <%{PatchFile} | patch -p1
perl -pi -e 's|ccp4c=ccp4c|ccp4c=gpp4|g' configure
perl -pi -e 's|CXX\=\"libtool --mode\=link \$CXX\"|#CXX|g' configure
+#cp ../cod-types.hh lidia-core/cod-types.hh
<<
###############################################################################
ConfigureParams: <<
@@ -138,7 +147,7 @@
--with-fftw=%p --with-gnomecanvas-prefix=%p --with-gtk2 --with-glut-prefix=%p
\
--with-guile-gtk --with-guile-gtk-prefix=%p --with-gl-prefix=/usr/X11R6
\
--with-gtkgl-prefix=%p --with-glib-prefix=%p --with-goocanvas-prefix=%p
\
---with-gsl-prefix=%p --with-guile --with-python=%p --with-pygtk=%p
+--with-gsl-prefix=%p --with-guile --with-python=%p --with-pygtk=%p
--with-enterprise-tools
<<
###############################################################################
CompileScript: <<
@@ -156,11 +165,15 @@
export GDK_USE_XFT='1'
export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
export
PKG_CONFIG_PATH=%p/lib/glib-2.0/pkgconfig-strict:%p/lib/fontconfig2/lib/pkgconfig:${PKG_CONFIG_PATH}
- FLIBS="-L%p/lib" \
- CPPFLAGS="-I%b/lidia-core -I%p/include/libglade-2.0/glade
-I%p/include/libglade-2.0 -I%p/include/python2.7 -I%p/include/mmdb
-I%p/include/ssm -I%p/include/gpp4/ccp4 -I%p/include/clipper -I%p/include
-I/usr/X11R6/include" \
+rdkit_libs='-lMolChemicalFeatures -lDescriptors -lSubgraphs -lPartialCharges
-lForceFieldHelpers -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers
-lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lFileParsers
-lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral
-lboost_python ' \
+ rdkit_prefix=%p \
+ FLIBS="-L%p/lib -L%p/lib/rdkit" \
+ CPPFLAGS="-I%p/include/rdkit -I%b/lidia-core -I%p/include/libglade-2.0/glade
-I%p/include/libglade-2.0 -I%p/include/python2.7 -I%p/include/mmdb
-I%p/include/ssm -I%p/include/gpp4/ccp4 -I%p/include/clipper -I%p/include
-I/usr/X11R6/include" \
LDFLAGS="-Wl,-dylib_file,%p/lib/python2.7/config/libpython2.7.dylib:%p/lib/libsfftw.2.0.7.dylib:%p/lib/libsrfftw.2.0.7.dylib:%p/lib/pango-ft219/lib/libpango-1.0.dylib:%p/lib/pango-ft219/lib/libpangocairo-1.0.dylib:%p/lib/pango-ft219/lib/libpangoft2-1.0.dylib:%p/lib/pango-ft219/lib/libpangox-1.0.dylib:%p/lib/pango-ft219/lib/libpangoxft-1.0.dylib
-L%p/lib -L/usr/lib -flat_namespace
-L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries" \
DYLD_LIBRARY_PATH="" \
- ./configure %c
+ RDKIT_CXXFLAGS=-I$rdkit_prefix/include/rdkit \
+ RDKIT_LIBS="\"-L%p/lib/rdkit $rdkit_libs\"" \
+ PYTHON=%p/bin/python2.7 ./configure %c
#
# Force coot to link to single-precision fftw libraries. The double-precision
libraries
# cause coot to crash.
@@ -175,8 +188,9 @@
fi
perl -pi -e 's|lidia_LDFLAGS = -Wl,--export-dynamic||g' lbg/Makefile
#
-NUMPROC="$(sysctl -n hw.ncpu)"
-make -j $NUMPROC
+# NUMPROC="$(sysctl -n hw.ncpu)"
+ NUMPROC="1"
+ PYTHON=%p/bin/python2.7 make -j $NUMPROC
<<
###############################################################################
InstallScript: <<
@@ -202,14 +216,14 @@
mkdir -p %i/bin
#
-if [[ $(sw_vers -productVersion) < 10.8 ]]; then
- true
-else
-# Fix a new bug that appears with 10.8.
+# Fix a bug with system python linking
+
if [[ -f
/System/Library/Frameworks/Python.framework/Versions/2.7/Python ]];then
install_name_tool -change
/System/Library/Frameworks/Python.framework/Versions/2.7/Python
%p/lib/python2.7/config/libpython2.7.dylib %i/bin/coot-real
+ elif [[ -f /System/Library/Frameworks/Python.framework/Versions/2.6/Python
]];then
+ install_name_tool -change
/System/Library/Frameworks/Python.framework/Versions/2.6/Python
%p/lib/python2.6/config/libpython2.6.dylib %i/bin/coot-real
fi
-fi
+
# This installs the refmac monomer library
mkdir -p %i/share/coot/lib/data
cp -R ../monomers %i/share/coot/lib/data/monomers
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