diff options
| author | yuri <yuri@FreeBSD.org> | 2018-07-08 12:45:25 +0800 |
|---|---|---|
| committer | yuri <yuri@FreeBSD.org> | 2018-07-08 12:45:25 +0800 |
| commit | 4ecbd26ba680b686b137cdd642cf0659059cebc3 (patch) | |
| tree | 3e85fa7845c78a9ccfe8497a468b0bc8fc918855 /science | |
| parent | faf3799f6b29cf2cd391b97245a27572ca2d0891 (diff) | |
| download | freebsd-ports-gnome-4ecbd26ba680b686b137cdd642cf0659059cebc3.tar.gz freebsd-ports-gnome-4ecbd26ba680b686b137cdd642cf0659059cebc3.tar.zst freebsd-ports-gnome-4ecbd26ba680b686b137cdd642cf0659059cebc3.zip | |
New port: science/coot: Crystallographic Object-Oriented Toolkit
Diffstat (limited to 'science')
| -rw-r--r-- | science/Makefile | 1 | ||||
| -rw-r--r-- | science/coot/Makefile | 50 | ||||
| -rw-r--r-- | science/coot/distinfo | 7 | ||||
| -rw-r--r-- | science/coot/files/patch-src_cc-interface-image.hh | 8 | ||||
| -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 | 14466 |
7 files changed, 14552 insertions, 0 deletions
diff --git a/science/Makefile b/science/Makefile index 7d64c0b2c579..5ec46488dad8 100644 --- a/science/Makefile +++ b/science/Makefile @@ -46,6 +46,7 @@ SUBDIR += clhep SUBDIR += clipper SUBDIR += colt + SUBDIR += coot SUBDIR += crf++ SUBDIR += dcl SUBDIR += devisor diff --git a/science/coot/Makefile b/science/coot/Makefile new file mode 100644 index 000000000000..a71b8fd55289 --- /dev/null +++ b/science/coot/Makefile @@ -0,0 +1,50 @@ +# $FreeBSD$ + +PORTNAME= coot +DISTVERSION= 0.8.9.1 +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 + +LICENSE= LGPL3 +LICENSE_FILE= ${WRKSRC}/COPYING + +LIB_DEPENDS= libccp4c.so:science/libccp4 \ + libclipper-core.so:science/clipper \ + libcurl.so:ftp/curl \ + libfontconfig.so:x11-fonts/fontconfig \ + libfreetype.so:print/freetype2 \ + libgtkglext-x11-1.0.so:x11-toolkits/gtkglext \ + libgsl.so:math/gsl \ + libmmdb2.so:science/mmdb2 \ + libpng16.so:graphics/png \ + libsfftw.so:math/fftw-float \ + libssm.so:science/libssm +RUN_DEPENDS= bash:shells/bash + +USES= desktop-file-utils fortran gettext-runtime gmake libtool localbase:ldflags pkgconfig python:2.7 shebangfix sqlite +SHEBANG_FILES= src/coot.in +GNU_CONFIGURE= yes +CONFIGURE_ARGS= --with-python +CONFIGURE_ARGS= --enable-shared --disable-static +USE_GNOME= atk cairo gdkpixbuf2 glib20 gtk20 libartlgpl2 libgnomecanvas pango pangox-compat +USE_GL= gl glu glut +USE_XORG= ice sm x11 xmu xt +INSTALL_TARGET= install-strip +USE_LDCONFIG= yes +INSTALLS_ICONS= yes + +MAKE_ENV= PYTHON=${PYTHON_CMD} +CXXFLAGS+= -I${PYTHON_INCLUDEDIR} + +post-install: + @${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 new file mode 100644 index 000000000000..dc4e1a0a163f --- /dev/null +++ b/science/coot/distinfo @@ -0,0 +1,7 @@ +TIMESTAMP = 1531013796 +SHA256 (coot/coot-0.8.9.1.tar.gz) = 51b6faef11177a8ab682fbe28448f935ae1252ad53b4efa31339ff658a63ff94 +SIZE (coot/coot-0.8.9.1.tar.gz) = 19360553 +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 new file mode 100644 index 000000000000..93799f768b1d --- /dev/null +++ b/science/coot/files/patch-src_cc-interface-image.hh @@ -0,0 +1,8 @@ +--- src/cc-interface-image.hh.orig 2018-07-08 02:10:49 UTC ++++ src/cc-interface-image.hh +@@ -1,4 +1,5 @@ + ++#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 new file mode 100644 index 000000000000..d9238804822f --- /dev/null +++ b/science/coot/files/patch-src_rama__plot.cc @@ -0,0 +1,11 @@ +--- 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 new file mode 100644 index 000000000000..805efdc1ccf9 --- /dev/null +++ b/science/coot/pkg-descr @@ -0,0 +1,9 @@ +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 new file mode 100644 index 000000000000..112d61dc27bb --- /dev/null +++ b/science/coot/pkg-plist @@ -0,0 +1,14466 @@ +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/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/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/regularize-minimol.hh +include/coot/ideal/simple-restraint.hh +include/coot/ideal/test-indexing.hh +include/coot/ideal/torsion-bonds.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.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/coot/acedrg_link.py +%%PYTHON_SITELIBDIR%%/coot/acedrg_link.pyc +%%PYTHON_SITELIBDIR%%/coot/acedrg_link.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/coot/americanisms.py +%%PYTHON_SITELIBDIR%%/coot/americanisms.pyc +%%PYTHON_SITELIBDIR%%/coot/americanisms.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/coot/background_demo.py +%%PYTHON_SITELIBDIR%%/coot/background_demo.pyc +%%PYTHON_SITELIBDIR%%/coot/background_demo.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/coot/bones_reader.py +%%PYTHON_SITELIBDIR%%/coot/bones_reader.pyc +%%PYTHON_SITELIBDIR%%/coot/bones_reader.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/coot/brute_lsqman.py +%%PYTHON_SITELIBDIR%%/coot/brute_lsqman.pyc +%%PYTHON_SITELIBDIR%%/coot/brute_lsqman.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/coot/check_for_updates.py +%%PYTHON_SITELIBDIR%%/coot/check_for_updates.pyc +%%PYTHON_SITELIBDIR%%/coot/check_for_updates.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/coot/chemical_feature_clusters.py +%%PYTHON_SITELIBDIR%%/coot/chemical_feature_clusters.pyc +%%PYTHON_SITELIBDIR%%/coot/chemical_feature_clusters.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/coot/cho_restraints_from_models.py +%%PYTHON_SITELIBDIR%%/coot/cho_restraints_from_models.pyc +%%PYTHON_SITELIBDIR%%/coot/cho_restraints_from_models.%%PYTHON_PYOEXTENSION%% +%%PYTHON_SITELIBDIR%%/coot/clear_backup.py 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