diff options
Diffstat (limited to 'science/coot')
| -rw-r--r-- | science/coot/Makefile | 58 | ||||
| -rw-r--r-- | science/coot/distinfo | 7 | ||||
| -rw-r--r-- | science/coot/files/patch-src_cc-interface-image.hh | 9 | ||||
| -rw-r--r-- | science/coot/files/patch-src_rama__plot.cc | 11 | ||||
| -rw-r--r-- | science/coot/pkg-descr | 9 | ||||
| -rw-r--r-- | science/coot/pkg-plist | 14492 |
6 files changed, 0 insertions, 14586 deletions
diff --git a/science/coot/Makefile b/science/coot/Makefile deleted file mode 100644 index ed7cda066262..000000000000 --- a/science/coot/Makefile +++ /dev/null @@ -1,58 +0,0 @@ -# $FreeBSD$ - -PORTNAME= coot -DISTVERSION= 0.8.9.2 -PORTREVISION= 3 -CATEGORIES= science -MASTER_SITES= https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/${PORTNAME}/source/releases/ \ - https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/${PORTNAME}/dependencies/:data -DISTFILES= ${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX} refmac-monomer-library${EXTRACT_SUFX}:data reference-structures${EXTRACT_SUFX}:data -DIST_SUBDIR= ${PORTNAME} - -MAINTAINER= yuri@FreeBSD.org -COMMENT= Crystallographic Object-Oriented Toolkit - -BROKEN= unfetchable -DEPRECATED= Broken, uses EOLed python27 -EXPIRATION_DATE= 2020-02-19 - -LICENSE= LGPL3 -LICENSE_FILE= ${WRKSRC}/COPYING - -BUILD_DEPENDS= fftw>0:math/fftw -LIB_DEPENDS= libccp4c.so:science/libccp4 \ - libclipper-core.so:science/clipper \ - libcurl.so:ftp/curl \ - libfontconfig.so:x11-fonts/fontconfig \ - libfreetype.so:print/freetype2 \ - libgoocanvas.so:graphics/goocanvas \ - libgtkglext-x11-1.0.so:x11-toolkits/gtkglext \ - libgsl.so:math/gsl \ - libmmdb2.so:science/mmdb2 \ - libpng.so:graphics/png \ - libsfftw.so:math/fftw-float \ - libssm.so:science/libssm -RUN_DEPENDS= bash:shells/bash - -USES= compiler:c++11-lang desktop-file-utils fortran gettext-runtime \ - gl gmake gnome libtool localbase:ldflags pkgconfig python:2.7 \ - shebangfix sqlite xorg -SHEBANG_FILES= src/coot.in -GNU_CONFIGURE= yes -CONFIGURE_ARGS= --enable-shared --disable-static --with-goocanvas-prefix=${LOCALBASE} -USE_GNOME= atk cairo gdkpixbuf2 glib20 gtk20 libartlgpl2 libgnomecanvas pango pangox-compat -USE_GL= gl glu glut -USE_XORG= ice sm x11 xmu xt -INSTALL_TARGET= install-strip -USE_LDCONFIG= yes -INSTALLS_ICONS= yes - -MAKE_ENV= PYTHON=${PYTHON_CMD} -CXXFLAGS+= -I${PYTHON_INCLUDEDIR} -DANALYSE_REFINEMENT_TIMING - -post-install: - @${MKDIR} ${STAGEDIR}${DATADIR}/lib/data - @cd ${WRKDIR} && ${COPYTREE_SHARE} monomers ${STAGEDIR}${DATADIR}/lib/data/ - @cd ${WRKDIR} && ${COPYTREE_SHARE} reference-structures ${STAGEDIR}${DATADIR}/ - -.include <bsd.port.mk> diff --git a/science/coot/distinfo b/science/coot/distinfo deleted file mode 100644 index 770660202e67..000000000000 --- a/science/coot/distinfo +++ /dev/null @@ -1,7 +0,0 @@ -TIMESTAMP = 1554259683 -SHA256 (coot/coot-0.8.9.2.tar.gz) = f24ed258e43ea31452b54c62649c071aa15f356d077dce0dab94eb04f27a6625 -SIZE (coot/coot-0.8.9.2.tar.gz) = 19635513 -SHA256 (coot/refmac-monomer-library.tar.gz) = 03562eec612103a48bd114cfe0d171943e88f94b84610d16d542cda138e5f36b -SIZE (coot/refmac-monomer-library.tar.gz) = 37439851 -SHA256 (coot/reference-structures.tar.gz) = 44db38506f0f90c097d4855ad81a82a36b49cd1e3ffe7d6ee4728b15109e281a -SIZE (coot/reference-structures.tar.gz) = 6728787 diff --git a/science/coot/files/patch-src_cc-interface-image.hh b/science/coot/files/patch-src_cc-interface-image.hh deleted file mode 100644 index 9d3be41be529..000000000000 --- a/science/coot/files/patch-src_cc-interface-image.hh +++ /dev/null @@ -1,9 +0,0 @@ ---- src/cc-interface-image.hh.orig 2018-06-08 16:50:29 UTC -+++ src/cc-interface-image.hh -@@ -1,5 +1,6 @@ - - #ifdef USE_PYTHON -+#include <Python.h> - - // make a png given the info in text_info_dict - // fields: text, font, size, colour, slant, weight diff --git a/science/coot/files/patch-src_rama__plot.cc b/science/coot/files/patch-src_rama__plot.cc deleted file mode 100644 index d9238804822f..000000000000 --- a/science/coot/files/patch-src_rama__plot.cc +++ /dev/null @@ -1,11 +0,0 @@ ---- src/rama_plot.cc.orig 2018-07-08 02:28:57 UTC -+++ src/rama_plot.cc -@@ -39,6 +39,8 @@ - #include <iostream> - #include <algorithm> - -+#include <sys/stat.h> -+ - #include <gdk/gdkkeysyms.h> // for keyboarding. - - #include "utils/coot-utils.hh" // int to string diff --git a/science/coot/pkg-descr b/science/coot/pkg-descr deleted file mode 100644 index 805efdc1ccf9..000000000000 --- a/science/coot/pkg-descr +++ /dev/null @@ -1,9 +0,0 @@ -Coot is for macromolecular model building, model completion and validation, -particularly suitable for protein modelling using X-ray data. - -Coot displays maps and models and allows model manipulations such as -idealization, real space refinement, manual rotation/translation, rigid-body -fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, -skeletonization, non-crystallographic symmetry and more. - -WWW: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ diff --git a/science/coot/pkg-plist b/science/coot/pkg-plist deleted file mode 100644 index 9b2362532a9b..000000000000 --- a/science/coot/pkg-plist +++ /dev/null @@ -1,14492 +0,0 @@ -bin/coot -bin/coot-available-comp-id -bin/coot-bfactan -bin/coot-compare-dictionaries -bin/coot-density-score-by-residue -bin/coot-fix-nomenclature-errors -bin/coot-make-shelx-restraints -bin/coot-mini-rsr -bin/dynarama -bin/findligand -bin/findwaters -bin/lidia -include/coot/analysis/bfkurt.hh -include/coot/analysis/mogul-interface.hh -include/coot/analysis/stats.hh -include/coot/angles/AngleInfo.h -include/coot/angles/ncube.h -include/coot/angles/wrapped-ncube.h -include/coot/build/CalphaBuild.hh -include/coot/ccp4mg-utils/cartesian.h -include/coot/ccp4mg-utils/geomutil.h -include/coot/ccp4mg-utils/matrix.h -include/coot/ccp4mg-utils/mgtree.h -include/coot/ccp4mg-utils/ppmutil.h -include/coot/ccp4mg-utils/quat.h -include/coot/compat/coot-getopt.h -include/coot/compat/coot-sysdep.h -include/coot/compat/getopt_int.h -include/coot/compat/sleep-fixups.h -include/coot/coords/Bond_lines.h -include/coot/coords/Bond_lines_ext.h -include/coot/coords/Cartesian.h -include/coot/coords/coot-close.hh -include/coot/coords/cos-sin.h -include/coot/coords/loop-path.hh -include/coot/coords/mmdb-crystal.h -include/coot/coords/mmdb-extras.h -include/coot/coords/mmdb.h -include/coot/coords/phenix-geo.hh -include/coot/coords/ramachandran-container.hh -include/coot/coords/utils.h -include/coot/coot-utils/atom-overlaps.hh -include/coot/coot-utils/bonded-pairs.hh -include/coot/coot-utils/coot-coord-extras.hh -include/coot/coot-utils/coot-coord-utils.hh -include/coot/coot-utils/coot-density-stats.hh -include/coot/coot-utils/coot-h-bonds.hh -include/coot/coot-utils/coot-hole.hh -include/coot/coot-utils/coot-least-squares.hh -include/coot/coot-utils/coot-lsq-types.h -include/coot/coot-utils/coot-map-heavy.hh -include/coot/coot-utils/coot-map-utils.hh -include/coot/coot-utils/coot-rama.hh -include/coot/coot-utils/coot-shelx.hh -include/coot/coot-utils/coot-trim.hh -include/coot/coot-utils/elastic.hh -include/coot/coot-utils/emma.hh -include/coot/coot-utils/glyco-torsions.hh -include/coot/coot-utils/helix-analysis.hh -include/coot/coot-utils/lsq-improve.hh -include/coot/coot-utils/peak-search.hh -include/coot/coot-utils/plane-utils.hh -include/coot/coot-utils/read-sm-cif.hh -include/coot/coot-utils/reduce.hh -include/coot/coot-utils/secondary-structure-headers.hh -include/coot/coot-utils/tree.hh -include/coot/coot-utils/xmap-stats.hh -include/coot/crunch-model.hh -include/coot/db-main/db-main.hh -include/coot/db-main/db-strands.hh -include/coot/density-contour/CIsoSurface.h -include/coot/density-contour/Vectors.h -include/coot/density-contour/density-contour-triangles.hh -include/coot/geometry/chem_mods.hh -include/coot/geometry/dict-mismatches.hh -include/coot/geometry/dict-utils.hh -include/coot/geometry/energy-lib.hh -include/coot/geometry/hb-types.hh -include/coot/geometry/lbg-graph.hh -include/coot/geometry/main-chain.hh -include/coot/geometry/match-results.hh -include/coot/geometry/mol-utils-2.hh -include/coot/geometry/protein-geometry.hh -include/coot/geometry/read-sbase.hh -include/coot/geometry/residue-and-atom-specs.hh -include/coot/geometry/srs-interface.hh -include/coot/high-res/coot-atom-graph.hh -include/coot/high-res/coot-node-info.hh -include/coot/high-res/high-res.hh -include/coot/high-res/sequence-assignment.hh -include/coot/ideal/extra-restraints.hh -include/coot/ideal/lograma.h -include/coot/ideal/model-bond-deltas.hh -include/coot/ideal/parallel-planes.hh -include/coot/ideal/pepflip.hh -include/coot/ideal/phi-psi.hh -include/coot/ideal/regularize-minimol.hh -include/coot/ideal/simple-restraint.hh -include/coot/ideal/test-indexing.hh -include/coot/ideal/torsion-bonds.hh -include/coot/ideal/zo-rama.hh -include/coot/lbg/alerts.hh -include/coot/lbg/graphics-c-interface-functions.hh -include/coot/lbg/lbg-drag-and-drop.hh -include/coot/lbg/lbg.hh -include/coot/lbg/qed-interface.hh -include/coot/lbg/solvent-exposure-difference.hh -include/coot/lbg/topological-equivalence.hh -include/coot/lbg/w-atom.hh -include/coot/lbg/w-bond.hh -include/coot/lbg/wmolecule.hh -include/coot/lidia-core/bond-record-container-t.hh -include/coot/lidia-core/bond-table-record-t.hh -include/coot/lidia-core/chemical-feature-clusters.hh -include/coot/lidia-core/cod-atom-type-t.hh -include/coot/lidia-core/cod-atom-types.hh -include/coot/lidia-core/cod-types.hh -include/coot/lidia-core/lbg-molfile.hh -include/coot/lidia-core/lbg-shared.hh -include/coot/lidia-core/lig-build.hh -include/coot/lidia-core/neighbour-sorter.hh -include/coot/lidia-core/primes.hh -include/coot/lidia-core/rdkit-interface.hh -include/coot/lidia-core/third-neighbour-info-t.hh -include/coot/lidia-core/use-rdkit.hh -include/coot/ligand/backrub-rotamer.hh -include/coot/ligand/base-pairing.hh -include/coot/ligand/chi-angles.hh -include/coot/ligand/dipole.hh -include/coot/ligand/dunbrack.hh -include/coot/ligand/fast-ss-search.hh -include/coot/ligand/helix-placement.hh -include/coot/ligand/ideal-rna.hh -include/coot/ligand/ligand-score-card.hh -include/coot/ligand/ligand.hh -include/coot/ligand/ligands-db.hh -include/coot/ligand/map-point-cluster.hh -include/coot/ligand/monomer-utils.hh -include/coot/ligand/multi-peptide.hh -include/coot/ligand/primitive-chi-angles.hh -include/coot/ligand/residue_by_phi_psi.hh -include/coot/ligand/richardson-rotamer.hh -include/coot/ligand/rigid-body.hh -include/coot/ligand/rotamer.hh -include/coot/ligand/scored-coord.hh -include/coot/ligand/scored-molecule.hh -include/coot/ligand/torsion-general.hh -include/coot/ligand/trace.hh -include/coot/ligand/wligand.hh -include/coot/mini-mol/atom-quads.hh -include/coot/mini-mol/mini-mol-utils.hh -include/coot/mini-mol/mini-mol.hh -include/coot/pli/flev-annotations.hh -include/coot/pli/pi-stacking.hh -include/coot/pli/protein-ligand-interactions.hh -include/coot/pli/specs.hh -include/coot/protein_db/protein_db.h -include/coot/protein_db/protein_db_utils.h -include/coot/protein_db/rna_db.h -include/coot/skeleton/BuildCas.h -include/coot/skeleton/dm-utils.h -include/coot/skeleton/graphical_skel.h -include/coot/tw/coot-tw.hh -include/coot/utils/coot-fasta.hh -include/coot/utils/coot-utils.hh -include/coot/utils/ctpl_stl.h -include/coot/utils/dodec.hh -include/coot/utils/pir-alignment.hh -include/coot/utils/win-compat.hh -lib/libccp4mg-utils.so -lib/libccp4mg-utils.so.0 -lib/libccp4mg-utils.so.0.0.0 -lib/libcoot-AngleInfo.so -lib/libcoot-AngleInfo.so.0 -lib/libcoot-AngleInfo.so.0.0.0 -lib/libcoot-analysis.so -lib/libcoot-analysis.so.0 -lib/libcoot-analysis.so.0.0.0 -lib/libcoot-cabuild.so -lib/libcoot-cabuild.so.0 -lib/libcoot-cabuild.so.0.0.0 -lib/libcoot-compat.so -lib/libcoot-compat.so.0 -lib/libcoot-compat.so.0.0.0 -lib/libcoot-coord-extras.so -lib/libcoot-coord-extras.so.0 -lib/libcoot-coord-extras.so.0.0.0 -lib/libcoot-coord-utils.so -lib/libcoot-coord-utils.so.0 -lib/libcoot-coord-utils.so.0.0.0 -lib/libcoot-coords.so -lib/libcoot-coords.so.0 -lib/libcoot-coords.so.0.0.0 -lib/libcoot-db-main.so -lib/libcoot-db-main.so.0 -lib/libcoot-db-main.so.0.0.0 -lib/libcoot-electrostatics.so -lib/libcoot-electrostatics.so.0 -lib/libcoot-electrostatics.so.0.0.0 -lib/libcoot-geometry.so -lib/libcoot-geometry.so.0 -lib/libcoot-geometry.so.0.0.0 -lib/libcoot-goograph.so -lib/libcoot-goograph.so.0 -lib/libcoot-goograph.so.0.0.0 -lib/libcoot-gtkgraph.so -lib/libcoot-gtkgraph.so.0 -lib/libcoot-gtkgraph.so.0.0.0 -lib/libcoot-high-res.so -lib/libcoot-high-res.so.0 -lib/libcoot-high-res.so.0.0.0 -lib/libcoot-ideal.so -lib/libcoot-ideal.so.0 -lib/libcoot-ideal.so.0.0.0 -lib/libcoot-isosurface.so -lib/libcoot-isosurface.so.0 -lib/libcoot-isosurface.so.0.0.0 -lib/libcoot-lidia-core.so -lib/libcoot-lidia-core.so.0 -lib/libcoot-lidia-core.so.0.0.0 -lib/libcoot-lidia.so -lib/libcoot-lidia.so.0 -lib/libcoot-lidia.so.0.0.0 -lib/libcoot-ligand.so -lib/libcoot-ligand.so.0 -lib/libcoot-ligand.so.0.0.0 -lib/libcoot-map-heavy.so -lib/libcoot-map-heavy.so.0 -lib/libcoot-map-heavy.so.0.0.0 -lib/libcoot-map-utils.so -lib/libcoot-map-utils.so.0 -lib/libcoot-map-utils.so.0.0.0 -lib/libcoot-mini-mol.so -lib/libcoot-mini-mol.so.0 -lib/libcoot-mini-mol.so.0.0.0 -lib/libcoot-pli.so -lib/libcoot-pli.so.0 -lib/libcoot-pli.so.0.0.0 -lib/libcoot-protein-db.so -lib/libcoot-protein-db.so.0 -lib/libcoot-protein-db.so.0.0.0 -lib/libcoot-shelx.so -lib/libcoot-shelx.so.0 -lib/libcoot-shelx.so.0.0.0 -lib/libcoot-skeleton.so -lib/libcoot-skeleton.so.0 -lib/libcoot-skeleton.so.0.0.0 -lib/libcoot-surface.so -lib/libcoot-surface.so.0 -lib/libcoot-surface.so.0.0.0 -lib/libcoot-tw.so -lib/libcoot-tw.so.0 -lib/libcoot-tw.so.0.0.0 -lib/libcoot-utils.so -lib/libcoot-utils.so.0 -lib/libcoot-utils.so.0.0.0 -lib/libcootaneer.so -lib/libcootaneer.so.0 -lib/libcootaneer.so.0.0.0 -lib/libcootilus.so -lib/libcootilus.so.0 -lib/libcootilus.so.0.0.0 -%%PYTHON_SITELIBDIR%%/coot/3d_generator_import.py -%%PYTHON_SITELIBDIR%%/coot/3d_generator_import.pyc -%%PYTHON_SITELIBDIR%%/coot/3d_generator_import.pyo -%%PYTHON_SITELIBDIR%%/coot/acedrg_link.py -%%PYTHON_SITELIBDIR%%/coot/acedrg_link.pyc -%%PYTHON_SITELIBDIR%%/coot/acedrg_link.pyo -%%PYTHON_SITELIBDIR%%/coot/add_linked_cho.py -%%PYTHON_SITELIBDIR%%/coot/add_linked_cho.pyc -%%PYTHON_SITELIBDIR%%/coot/add_linked_cho.pyo -%%PYTHON_SITELIBDIR%%/coot/americanisms.py -%%PYTHON_SITELIBDIR%%/coot/americanisms.pyc -%%PYTHON_SITELIBDIR%%/coot/americanisms.pyo -%%PYTHON_SITELIBDIR%%/coot/background_demo.py -%%PYTHON_SITELIBDIR%%/coot/background_demo.pyc -%%PYTHON_SITELIBDIR%%/coot/background_demo.pyo -%%PYTHON_SITELIBDIR%%/coot/bones_reader.py -%%PYTHON_SITELIBDIR%%/coot/bones_reader.pyc -%%PYTHON_SITELIBDIR%%/coot/bones_reader.pyo -%%PYTHON_SITELIBDIR%%/coot/brute_lsqman.py -%%PYTHON_SITELIBDIR%%/coot/brute_lsqman.pyc -%%PYTHON_SITELIBDIR%%/coot/brute_lsqman.pyo -%%PYTHON_SITELIBDIR%%/coot/check_for_updates.py -%%PYTHON_SITELIBDIR%%/coot/check_for_updates.pyc -%%PYTHON_SITELIBDIR%%/coot/check_for_updates.pyo -%%PYTHON_SITELIBDIR%%/coot/chemical_feature_clusters.py -%%PYTHON_SITELIBDIR%%/coot/chemical_feature_clusters.pyc -%%PYTHON_SITELIBDIR%%/coot/chemical_feature_clusters.pyo -%%PYTHON_SITELIBDIR%%/coot/cho_restraints_from_models.py -%%PYTHON_SITELIBDIR%%/coot/cho_restraints_from_models.pyc -%%PYTHON_SITELIBDIR%%/coot/cho_restraints_from_models.pyo -%%PYTHON_SITELIBDIR%%/coot/clear_backup.py -%%PYTHON_SITELIBDIR%%/coot/clear_backup.pyc -%%PYTHON_SITELIBDIR%%/coot/clear_backup.pyo -%%PYTHON_SITELIBDIR%%/coot/cns2coot.py -%%PYTHON_SITELIBDIR%%/coot/cns2coot.pyc -%%PYTHON_SITELIBDIR%%/coot/cns2coot.pyo -%%PYTHON_SITELIBDIR%%/coot/contact_score_isolated_ligand.py -%%PYTHON_SITELIBDIR%%/coot/contact_score_isolated_ligand.pyc -%%PYTHON_SITELIBDIR%%/coot/contact_score_isolated_ligand.pyo -%%PYTHON_SITELIBDIR%%/coot/coot_gui.py -%%PYTHON_SITELIBDIR%%/coot/coot_gui.pyc -%%PYTHON_SITELIBDIR%%/coot/coot_gui.pyo -%%PYTHON_SITELIBDIR%%/coot/coot_load_modules.py -%%PYTHON_SITELIBDIR%%/coot/coot_load_modules.pyc -%%PYTHON_SITELIBDIR%%/coot/coot_load_modules.pyo -%%PYTHON_SITELIBDIR%%/coot/coot_lsq.py 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