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Date:      Sun, 8 Jul 2018 04:45:25 +0000 (UTC)
From:      Yuri Victorovich <yuri@FreeBSD.org>
To:        ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org
Subject:   svn commit: r474154 - in head/science: . coot coot/files
Message-ID:  <201807080445.w684jPdI002541@repo.freebsd.org>

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Author: yuri
Date: Sun Jul  8 04:45:25 2018
New Revision: 474154
URL: https://svnweb.freebsd.org/changeset/ports/474154

Log:
  New port: science/coot: Crystallographic Object-Oriented Toolkit

Added:
  head/science/coot/
  head/science/coot/Makefile   (contents, props changed)
  head/science/coot/distinfo   (contents, props changed)
  head/science/coot/files/
  head/science/coot/files/patch-src_cc-interface-image.hh   (contents, props changed)
  head/science/coot/files/patch-src_rama__plot.cc   (contents, props changed)
  head/science/coot/pkg-descr   (contents, props changed)
  head/science/coot/pkg-plist   (contents, props changed)
Modified:
  head/science/Makefile

Modified: head/science/Makefile
==============================================================================
--- head/science/Makefile	Sun Jul  8 01:51:36 2018	(r474153)
+++ head/science/Makefile	Sun Jul  8 04:45:25 2018	(r474154)
@@ -46,6 +46,7 @@
     SUBDIR += clhep
     SUBDIR += clipper
     SUBDIR += colt
+    SUBDIR += coot
     SUBDIR += crf++
     SUBDIR += dcl
     SUBDIR += devisor

Added: head/science/coot/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/coot/Makefile	Sun Jul  8 04:45:25 2018	(r474154)
@@ -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>

Added: head/science/coot/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/coot/distinfo	Sun Jul  8 04:45:25 2018	(r474154)
@@ -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

Added: head/science/coot/files/patch-src_cc-interface-image.hh
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/coot/files/patch-src_cc-interface-image.hh	Sun Jul  8 04:45:25 2018	(r474154)
@@ -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

Added: head/science/coot/files/patch-src_rama__plot.cc
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/coot/files/patch-src_rama__plot.cc	Sun Jul  8 04:45:25 2018	(r474154)
@@ -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

Added: head/science/coot/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/coot/pkg-descr	Sun Jul  8 04:45:25 2018	(r474154)
@@ -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/

Added: head/science/coot/pkg-plist
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/coot/pkg-plist	Sun Jul  8 04:45:25 2018	(r474154)
@@ -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
+%%PYTHON_SITELIBDIR%%/coot/clear_backup.pyc
+%%PYTHON_SITELIBDIR%%/coot/clear_backup.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/coot/cns2coot.py
+%%PYTHON_SITELIBDIR%%/coot/cns2coot.pyc
+%%PYTHON_SITELIBDIR%%/coot/cns2coot.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/coot/contact_score_isolated_ligand.py
+%%PYTHON_SITELIBDIR%%/coot/contact_score_isolated_ligand.pyc
+%%PYTHON_SITELIBDIR%%/coot/contact_score_isolated_ligand.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/coot/coot_gui.py
+%%PYTHON_SITELIBDIR%%/coot/coot_gui.pyc
+%%PYTHON_SITELIBDIR%%/coot/coot_gui.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/coot/coot_load_modules.py
+%%PYTHON_SITELIBDIR%%/coot/coot_load_modules.pyc
+%%PYTHON_SITELIBDIR%%/coot/coot_load_modules.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/coot/coot_lsq.py
+%%PYTHON_SITELIBDIR%%/coot/coot_lsq.pyc
+%%PYTHON_SITELIBDIR%%/coot/coot_lsq.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/coot/coot_toolbuttons.py
+%%PYTHON_SITELIBDIR%%/coot/coot_toolbuttons.pyc
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