Package: coot # BOOST1.68 PINNED # Needs gnome -pyXX suite, we only have 27 so need matching boost. Version: 0.8.9.1 Revision: 3 SourceDirectory: %n-%v GCC: 4.0 Source: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/%n-%v.tar.gz # Source: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/pre-releases/%n-%v-revision-%r.tar.gz Source-Checksum: SHA256(51b6faef11177a8ab682fbe28448f935ae1252ad53b4efa31339ff658a63ff94) Source2: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/reference-structures.tar.gz Source2-Checksum: SHA256(44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a) Description: Crystallographic molecular graphics DescDetail: << . 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. . This package actually requires a flat namespace build, according to the primary author. << DescPackaging: << coot stack uses fftw-2, not fftw3 https://www.mail-archive.com/coot@jiscmail.ac.uk/msg00336.html << ############################################################################### Recommends: povray, ccp4, raster3d Replaces: coot-pre BuildDepends: << atk1 (>= 1.32.0-1) , automake1.15 , boost1.68-python27 (>= 1.68.0-1) , cairo (>= 1.12.14-1) , ccp4srs-dev (>= 1.0-1) , clipper-dev (>= 2:2.1.20160708-3) , expat1 , fink-buildenv-modules (>= 0.1.3-1) , fink-package-precedence , fontconfig2-dev (>= 2.10.0-1) , freeglut2 , freetype219 (>= 2.10.2-1) , glib2-dev (>= 2.22.0-1) , goocanvas (>= 0.15-2) , gtk+2 (>= 2.18.0-1) , gtk+2-dev (>= 2.18.0-1) , gtkglext1 (>= 1.2.0-4) , libart2 (>= 2.3.16-2) , libccp4-dev (>= 1:6.4.0-5) , libcurl4 , libgettext8-dev , libglade2 (>= 2.6.2-1) , libgnomecanvas2-dev (>= 2.20.0) , libgsl25-dev , libpng16 , libtool2 (>= 2.4.2-4) , mmdb2-dev (>= 2.0.1-1) , pango1-xft2-ft219-dev (>= 1.24.5-4) , pkgconfig (>= 0.23) , pygobject2-py27-dev , pygtk2-gtk-py27-dev , python27 , rdkit (>= 1:2017.09.3-1) , rdkit-dev (>= 1:2017.09.3-1) , sqlite3 , ssm-dev (>= 1.4.0-6) , swig , x11-dev << # Depends: << %N-shlibs (= %v-%r) , atk1-shlibs (>= 1.32.0-1) , boost1.68-python27-shlibs (>= 1.68.0-1) , cairo-shlibs (>= 1.12.14-1) , ccp4srs-shlibs (>= 1.0-1) , clipper-shlibs (>= 2:2.1.20160708-3) , fftw-shlibs | fftw-mpi-shlibs , fontconfig2-shlibs (>= 2.10.0-1) , freeglut2-shlibs , freetype219-shlibs (>= 2.10.2-1) , glib2-shlibs (>= 2.22.0-1) , gnome-themes-glossy-p , goocanvas-shlibs (>= 0.15-2) , gtk+2-shlibs (>= 2.18.0-1) , gtkglext1-shlibs (>= 1.2.0-4) , libart2-shlibs , libccp4-lib (>= 1:6.4.0-5) , libccp4-shlibs (>= 1:6.4.0-5) , libcurl4-shlibs , libgettext8-shlibs , libglade2-shlibs (>= 2.6.2-1) , libgnomecanvas2-shlibs (>= 2.20.0) , libgsl25-shlibs , libpng16-shlibs , librsvg2-gtk (>= 2.20.0-1) , libtool2-shlibs (>= 2.4.2-4) , mmdb2-shlibs (>= 2.0.1-1) , pango1-xft2-ft219-shlibs (>= 1.24.5-4) , probe (>= 2.12.071128-1) , pygtk2-gtk-py27 , python27 , rdkit (>= 1:2017.09.3-1) , rdkit-shlibs (>= 1:2017.09.3-1) , reduce (>= 3.14.080821-1) , refmac (>= 5.8-5) , ssm-shlibs (>= 1.4.0-6) , x11 << # ############################################################################### BuildDependsOnly: false NoSetCPPFLAGS: true NoSetLDFLAGS: true PatchFile: %n.patch PatchFile-MD5: dd8d983e053eaa9abb80a5c353c0540e PatchScript: << %{default_script} perl -pi -e 's|CXX\=\"libtool --mode\=link \$CXX\"|#CXX|g' configure perl -pi -e 's|define coot-png-display-program \"display\"|define coot-png-display-program \"open\"|g' scheme/raster3d.scm perl -ni -e 'print unless /^current_exe_dir/../^export PATH=/' pyrogen/pyrogen.in perl -pi -e "s|python -m pyrogen|%p/bin/python2.7 -m pyrogen|g" pyrogen/pyrogen.in perl -pi -e "s|if \(residues_mol_and_res_vec.first \> 0\) |if \(residues_mol_and_res_vec.first \!\= 0\) |g" src/graphics-info-modelling.cc << ############################################################################### ConfigureParams: << --libexecdir=%i/bin \ --with-fftw-prefix=%p \ --with-enhanced-ligand-tools \ --with-goocanvas-prefix=%p \ --with-gsl-prefix=%p \ --with-gsl-exec-prefix=%p \ --with-pygtk=%p \ --with-python=%p \ --with-boost=%p \ --with-sqlite3 \ --disable-static \ --x-includes=$X11_BASE_DIR/include \ --x-libraries=$X11_BASE_DIR/lib << ############################################################################### CompileScript: << #!/bin/bash -efv # autoreconf -fi # Run-time errors occur when we do this. I am working on it. export GUILE=%p/bin/guile-1.8 export PATH=%p/var/lib/fink/path-prefix-libcxx:%p/share/guile/1.8/scripts/binoverride:%p/bin:$PWD/bin:$PATH export X11_BASE_DIR=/opt/X11 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:${PKG_CONFIG_PATH} FLIBS="-L%p/lib -L%p/lib/rdkit" \ CPPFLAGS="-I%b/ccp4mg-utils -I%p/include/rdkit -I%b/lidia-core -I%p/include/libglade-2.0/glade -I%p/include/libglade-2.0 -I%p/include/python2.7 -I%p/include/mmdb2 -I%p/include/ssm -I%p/include/ccp4 -I%p/include/clipper -I%p/include -I$X11_BASE_DIR/include -I%p/opt/boost-1_68/include" \ LDFLAGS="-Wl,-dylib_file,%p/lib/python2.7/site-packages/libboost_python27-1_68.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 -L$X11_BASE_DIR/lib -L%p/opt/boost-1_68/lib -L/usr/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries" \ DYLD_LIBRARY_PATH="" \ RDKIT_CXXFLAGS=-I%p/include/rdkit \ RDKIT_LIBS="-L%p/lib/rdkit -lRDKitMolChemicalFeatures -lRDKitDescriptors -lRDKitSubgraphs -lRDKitPartialCharges \ -lRDKitForceFieldHelpers -lRDKitForceField -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDistGeomHelpers \ -lRDKitDistGeometry -lRDKitAlignment -lRDKitEigenSolvers -lRDKitDepictor -lRDKitFileParsers \ -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDataStructs -lRDKitRDGeneral -lboost_python27" \ PYTHON=%p/bin/python2.7 PYTHON_CONFIG=%p/bin/python2.7-config ./configure %c # NUMPROC="$(sysctl -n hw.ncpu)" # NUMPROC="1" make -j $NUMPROC # fink-package-precedence --prohibit-bdep=%N . << ############################################################################### InstallScript: << #!/bin/zsh -efv export GUILE=%p/bin/guile-1.8 export PATH=$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 # mkdir -p %i/share/ccp4 ln -s %p/share/refmac/data/monomers %i/share/ccp4/. # 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 # Fix incorrect paths in wrapper scripts perl -pi -e 's|libexec|bin|g' %i/bin/coot-density-score-by-residue %i/bin/coot-mini-rsr %i/bin/findligand %i/bin/findwaters perl -pi -e 's|bin/density-score-by-residue-bin|bin/coot-density-score-by-residue-bin|g' %i/bin/coot-density-score-by-residue perl -pi -e 's|bin/findligands-bin|bin/findligand-bin|g' %i/bin/findligand # Clean up the rest of the mess. /bin/rm -rf %i/include %i/**/.libs %i/lib/*.la %i/share/coot/etc/**/*.la %i/share/coot/etc/scheme # Remove compiled objects with reference to build directory cd %i/lib/python2.7/site-packages/coot touch junk.pyo junk.pyc rcrane/junk.pyo rcrane/junk.pyc ../lidia/junk.pyo ../lidia/junk.pyc rm -rf *.pyo *.pyc rcrane/*.pyo rcrane/*.pyc ../coot.pyc ../coot.pyo ../lidia/*.pyo ../lidia/*.pyc << ############################################################################### 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 Depends: << atk1-shlibs (>= 1.32.0-1) , boost1.68-python27-shlibs (>= 1.68.0-1) , cairo-shlibs (>= 1.12.14-1) , clipper-shlibs (>= 2:2.1.20160708-3) , fftw-shlibs| fftw-mpi-shlibs , fontconfig2-shlibs (>= 2.10.0-1) , freeglut2-shlibs , freetype219-shlibs (>= 2.10.2-1) , glib2-shlibs (>= 2.22.0-1) , goocanvas-shlibs (>= 0.15-2) , gtk+2-shlibs (>= 2.18.0-1) , libccp4-shlibs (>= 1:6.4.0-5) , libgsl25-shlibs , libpng16-shlibs , mmdb2-shlibs (>= 2.0.1-1) , pango1-xft2-ft219-shlibs (>= 1.24.5-4) , python27 , rdkit-shlibs (>= 1:2017.09.3-1) , sqlite3-shlibs , x11 << Files: << lib/libccp4mg-*.0*.dylib lib/libcoot-*.0*.dylib lib/libcootaneer.0*.dylib lib/libcootilus.0*.dylib lib/libcoot_py_restraints.0*.dylib << Shlibs: << %p/lib/libccp4mg-utils.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-analysis.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-AngleInfo.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-cabuild.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-compat.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-coord-extras.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-coord-utils.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-coords.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-db-main.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-geometry.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-goograph.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-gtkgraph.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-high-res.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-ideal.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-isosurface.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-lidia-core.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-lidia.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-ligand.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-map-heavy.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-map-utils.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-mini-mol.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-protein-db.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-shelx.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-skeleton.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-surface.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-tw.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-utils.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcootaneer.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcootilus.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot_py_restraints.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-electrostatics.0.dylib 1.0.0 %n (>= 0.8.8-1) %p/lib/libcoot-pli.0.dylib 1.0.0 %n (>= 0.8.8-1) << DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO << ############################################################################### # SplitOff2: << Package: %N-dev Depends: %N (= %v-%r) Replaces: coot-pre-dev BuildDependsOnly: True Files: << << DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO << ############################################################################### PostInstScript: << # This changes the paths for the python compiled objects to those of the # final install point rather than the build or debian root directory. mv %p/lib/python2.7/site-packages/coot/extensions.py %p/lib/python2.7/site-packages/coot/coot_extensions.py perl -pi -e 's|"extensions.py"|"coot_extensions.py"|g' %p/lib/python2.7/site-packages/coot/coot_load_modules.py touch %p/lib/python2.7/site-packages/coot/junk.pyc %p/lib/python2.7/site-packages/coot/rcrane/junk.pyc /bin/rm -f %p/lib/python2.7/site-packages/coot/*.pyc %p/lib/python2.7/site-packages/coot/rcrane/*.pyc %p/bin/python2.7 -m compileall %p/lib/python2.7/site-packages/coot/. # << PreRmScript: << /bin/rm -f %p/lib/python2.7/site-packages/coot/*.pyc /bin/rm -f %p/lib/python2.7/site-packages/coot/rcrane/*.pyc /bin/rm -f %p/lib/python2.7/site-packages/coot/coot_extensions.py <<