Package: coot Version: 0.8.0 Revision: 3 SourceDirectory: %n-0.8 Distribution: 10.6 GCC: 4.0 Source: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/%n-0.8.tar.gz Source-MD5: b9fb5e12978b7b633f4c9621fad5beae Source2: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/reference-structures.tar.gz Source2-MD5: 257ab90d44f1c877ada96720dbb87c13 ############################################################################### Description: Crystallographic molecular graphics DescDetail: << This version contains "pre-release" features and will be updated upon request. . Coot stands for Crystallograhic Object Oriented Toolkit. It is a toolkit and interactive molecular graphical display and manipulation program designed for macromolecular crystallography. Coot uses professional (and free) widgets (with the gui builder glade), mmdb2, clipper, OpenGL, together with a new approach to map contouring and importing/creation and other (modelling) operations. The mmdb2, clipper, ssm and mccp4 libraries are provided in fink packages that replace the now obsolete ccp4-onlylibs-dev fink package. On-line documentation is available from the coot website accessed via the help menu, or manually, via the web-site, (see below) and is updated regularly. . To have an Aqua-like Coot gtk+2 environment, issue the following command: echo "include \"%p/share/themes/Glossy_P/gtk-2.0/gtkrc\"">~/.gtkrc-2.0 or simply create a file called ~/.gtkrc-2.0 and put this line in it: include \"%p/share/themes/Glossy_P/gtk-2.0/gtkrc\" . Install povray and raster3d fink packages to use the F8 key for producing ray-traced images. You may have to re-map the Spaces.app keybinding. . Coot now works with Zalman LCD hardware stereo and old-fashioned CRT hardware stereo on OS X. << ############################################################################### Recommends: povray, ccp4, raster3d Replaces: coot-pre BuildDepends: << fink (>= 0.24.12) , boost1.53.python27 (>= 1.53.0-1) , clipper-dev (>= 2:2.1-2) , libccp4-dev (>= 1:6.4.0-2) , mmdb2-dev (>= 2.0.1-1) , ssm-dev (>= 1.4.0-6) , 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) , freeglut , giflib , glib2-dev (>= 2.22.0-1) , glitz , goocanvas (>= 0.15-2) , gmp5 , gsl , gtk+2 (>= 2.18.0-1) , gtk+2-dev (>= 2.18.0-1) , gtkglext1 , guile18 , guile18-dev , guile18-lib , guile18-gui , guile18-gtk-dev , guile18-gtk , libart2 (>= 2.3.16-2) , libcurl4 , libgettext8-dev , libglade2 (>= 2.6.2-1) , libgnomecanvas2-dev (>= 2.20.0) , libjpeg9 , libpng16 , libtool2 , libxml2 , openldap24-dev , pango1-xft2-ft219-dev (>= 1.24.5-4) , pixman (>= 0.16.0-1) , pkgconfig (>= 0.23) , pygtk2-gtk-py27-dev , pygobject2-py27-dev , python27 , rdkit-dev (>= 1:2013.09.2-102) , rdkit (>= 1:2013.09.2-102) , swig , x11-dev << # ccp4srs-dev (>= 1.0-1) , # Depends: << %N-shlibs (= %v-%r) , boost1.53.python27-shlibs (>= 1.53.0-1) , clipper-shlibs (>= 2:2.1-2) , libccp4-shlibs (>= 1:6.4.0-2) , libccp4-lib (>= 1:6.4.0-2) , mmdb2-shlibs (>= 2.0.1-1) , ssm-shlibs (>= 1.4.0-6) , atk1-shlibs (>= 1.28.0-1) , fftw-shlibs | fftw-mpi-shlibs , freeglut-shlibs , gcc49-shlibs (>= 4.9.0-1000) , giflib-shlibs , glib2-shlibs (>= 2.22.0-1) , goocanvas-shlibs (>= 0.15-2) , gmp5-shlibs , gnome-themes-glossy-p , gsl-shlibs , gtk+2-shlibs (>= 2.18.0-1) , gtkglext1-shlibs , guile18 , guile18-lib , guile18-shlibs , guile18-gui , guile18-gtk-shlibs , guile18-gtk , libart2-shlibs , libcurl4-shlibs , libgettext8-shlibs , libgnomecanvas2-shlibs (>= 2.20.0) , libjpeg9-shlibs , libpng16-shlibs , librsvg2-gtk (>= 2.20.0-1) , libtiff5-shlibs , libtool2-shlibs , librsvg2-gtk (>= 2.20.0-1) , libxml2-shlibs , openldap24-shlibs , pango1-xft2-ft219-shlibs (>= 1.24.5-4) , pygtk2-gtk-py27 , python27 , raster3d (>= 3.0-2-3) , rdkit-shlibs (>= 1:2013.09.2-102) , rdkit (>= 1:2013.09.2-102) , refmac (>=5.7.0032-1) , refmac (>=5.7.0032-1) | ccp4-setup , x11 << # ccp4srs-shlibs (>= 1.0-1) , # ############################################################################### BuildDependsOnly: false NoSetCPPFLAGS: true NoSetLDFLAGS: true PatchScript: << #sed 's|@FINKPREFIX@|%p|g' <%{PatchFile} | patch -p1 perl -pi -e 's|CXX\=\"libtool --mode\=link \$CXX\"|#CXX|g' configure perl -pi -e 's|test \! \"x\$pythonexists\" \= \"xyes|test \"x\$pythonexists\" \= \"xyes|g' configure perl -pi -e 's|define coot-png-display-program \"display\"|define coot-png-display-program \"open\"|g' scheme/raster3d.scm << ############################################################################### ConfigureParams: << --libexecdir=%i/bin \ --with-clipper-prefix=%p \ --with-enhanced-ligand-tools \ --with-glut-prefix=%p \ --with-goocanvas-prefix=%p \ --with-gsl-exec-prefix=%p \ --with-gsl-prefix=%p \ --with-guile \ --with-guile-gtk-prefix=%p \ --with-guile-gtk \ --with-pygtk=%p \ --with-python=%p \ --with-ssmlib-prefix=%p << # --with-database \ # --with-ccp4srs-prefix=%p \ ############################################################################### CompileScript: << #!/bin/bash -efv alias python=%p/bin/python2.7 export PYTHON=%p/bin/python2.7 export python=%p/bin/python2.7 export GUILE=%p/bin/guile-1.8 OSXVERSION=$(sw_vers -productVersion |perl -p -e 's|10.||g') if (( $OSXVERSION < 6. )); then export PATH=%p/share/guile/1.8/scripts/binoverride:%p/bin:$PWD/bin:$PATH else export PATH=%p/var/lib/fink/path-prefix-10.6:%p/share/guile/1.8/scripts/binoverride:%p/bin:$PWD/bin:$PATH fi export SED=/usr/bin/sed export GDK_USE_XFT='1' export COOT_REFMAC_LIB_DIR=%p/share/coot/lib export PKG_CONFIG_PATH=%p/lib/glib-2.0/pkgconfig-strict:%p/lib/fontconfig2/lib/pkgconfig:${PKG_CONFIG_PATH} 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%b/ccp4mg-utils -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/mmdb2 -I%p/include/ssm -I%p/include/ccp4 -I%p/include/clipper -I%p/include -I/usr/X11R6/include" \ LDFLAGS="-Wl,-dylib_file,%p/lib/libboost_python.dylib:%p/lib/python2.7/site-packages/libboost_python-1_53.dylib:%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/python2.7 -L%p/lib -L/usr/lib -flat_namespace -L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries" \ DYLD_LIBRARY_PATH="" \ RDKIT_CXXFLAGS=-I$rdkit_prefix/include/rdkit \ RDKIT_LIBS="\"-L%p/lib/rdkit $rdkit_libs\"" \ PYTHON_LDFLAGS="-L%p/lib -L%p/lib/python2.7 -lpython2.7" \ PYTHON_LIBS="-L%p/lib -L%p/lib/python2.7 -lpython2.7 -ldl -lutil" \ PYTHON_EXTRA_LIBS="-L%p/lib -L%p/lib/python2.7 -lpython2.7 -ldl -lutil" \ PYTHON_EXEC_PREFIX="%p/bin" \ PYTHON_PREFIX="%p/bin" \ PYTHON=%p/bin/python2.7 ./configure %c # # Force coot to link to single-precision fftw libraries. The double-precision libraries # cause coot to crash. find . -name "Makefile" -exec perl -pi -e 's|lrfftw |lsrfftw |g' '{}' \; find . -name "Makefile" -exec perl -pi -e 's|lfftw |lsfftw |g' '{}' \; perl -pi -e 's|include |include |g' surface/CXXFFTSolventMap.h # OSXVERSION=$(sw_vers -productVersion |perl -p -e 's|10.||g') if (( $OSXVERSION < 5. )); then # Fix libtool compatibility issues sed -e '/verstring=/s/\${wl}//g' < libtool > libtool.fixed mv libtool.fixed libtool fi # #NUMPROC="$(sysctl -n hw.ncpu)" NUMPROC="1" PYTHON=%p/bin/python2.7 make -j $NUMPROC << ############################################################################### InstallScript: << #!/bin/zsh -efv alias python=%p/bin/python2.7 export PYTHON=%p/bin/python2.7 export python=%p/bin/python2.7 export GUILE=%p/bin/guile-1.8 export PATH=$PWD/bin:%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH export SED=/usr/bin/sed export COOT_REFMAC_LIB_DIR=%p/share/coot/lib # NUMPROC="$(sysctl -n hw.ncpu)" #NUMPROC="1" make -j $NUMPROC install prefix=%i # # Clean up the 120 MB mess, which zsh makes so much fun: /bin/rm -f **/*.o # Add ancillary files to %i/share/coot: # mkdir -p %i/share/coot/etc mkdir -p %i/share/coot/python mkdir -p %i/bin # # 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-bin 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/python2.7/config/libpython2.7.dylib %i/bin/coot-bin fi # Reference structures should be in %i/share/coot/reference-structures cp -R ../reference-structures %i/share/coot/. cp -R * %i/share/coot/etc/. cp src/coot.py %i/share/coot/python/. # The original wrapper creates problems. Get rid of it. # Replace with a new wrapper to set the required PYTHONPATH variable # and a few others as follows: /bin/rm -f %i/bin/coot echo '#!/bin/sh -f ' > %i/bin/coot echo 'export GUILE_WARN_DEPRECATED="no"' >> %i/bin/coot echo "export LC_NUMERIC=C" >> %i/bin/coot echo "export COOT_REFMAC_LIB_DIR=%p/share/refmac" >> %i/bin/coot echo "export COOT_PYTHON_DIR=%p/lib/python2.7/site-packages/coot" >> %i/bin/coot echo 'export COOT_SBASE_DIR="%p/share/ccp4"' >> %i/bin/coot echo 'export CLIBD="%p/share/ccp4"' >> %i/bin/coot echo "export PYTHONPATH=%p/lib/python2.7/site-packages:%p/lib/python2.7/site-packages/gtk-2.0:%p/lib/python2.7/site-packages/coot:%p/share/coot/python" >> %i/bin/coot echo "%p/bin/coot-bin \"\$@\" " >> %i/bin/coot chmod a+x %i/bin/coot # Clean up the rest of the mess. /bin/rm -rf %i/include %i/**/.libs %i/lib/*.la %i/share/coot/etc/**/*.la << ############################################################################### DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO License: GPL Maintainer: W. G. Scott Homepage: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/ ############################################################################### # SplitOff: << Package: %N-shlibs Replaces: coot-pre-shlibs Files: << lib/libccp4mg-*.0*.dylib lib/libcoot-*.0*.dylib lib/libcootaneer.0*.dylib lib/libcootilus.0*.dylib lib/libcoot_py_restraints.0*.dylib lib/libpyrogen_boost.0.*dylib << Shlibs: << %p/lib/libccp4mg-surface.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libccp4mg-utils.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-analysis.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-AngleInfo.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-cabuild.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-compat.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-coord-extras.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-coord-utils.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-coords.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-db-main.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-geometry.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-goograph.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-gtkgraph.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-high-res.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-ideal.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-isosurface.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-lidia-core.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-lidia.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-ligand.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-map-heavy.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-map-utils.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-mini-mol.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-protein-db.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-shelx.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-skeleton.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-surface.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-tw.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot-utils.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcootaneer.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcootilus.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libcoot_py_restraints.0.dylib 1.0.0 %n (>= 0.8-1) %p/lib/libpyrogen_boost.0.dylib 1.0.0 %n (>= 0.8-1) << DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO << # ############################################################################### # SplitOff2: << Package: %N-dev Depends: %N (= %v-%r) Replaces: coot-pre-dev BuildDependsOnly: True Files: << lib/*.a << DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO << ###############################################################################