Date: Thu, 22 Mar 2018 08:23:57 +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: r465265 - in head/science: . rdkit rdkit/files Message-ID: <201803220823.w2M8Nvt7031175@repo.freebsd.org>
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Author: yuri Date: Thu Mar 22 08:23:57 2018 New Revision: 465265 URL: https://svnweb.freebsd.org/changeset/ports/465265 Log: New port: science/rdkit: Collection of cheminformatics and machine-learning software Added: head/science/rdkit/ head/science/rdkit/Makefile (contents, props changed) head/science/rdkit/distinfo (contents, props changed) head/science/rdkit/files/ head/science/rdkit/files/patch-CMakeLists.txt (contents, props changed) head/science/rdkit/pkg-descr (contents, props changed) head/science/rdkit/pkg-plist (contents, props changed) Modified: head/science/Makefile Modified: head/science/Makefile ============================================================================== --- head/science/Makefile Thu Mar 22 08:15:51 2018 (r465264) +++ head/science/Makefile Thu Mar 22 08:23:57 2018 (r465265) @@ -189,6 +189,7 @@ SUBDIR += pynn SUBDIR += qcl SUBDIR += qtresistors + SUBDIR += rdkit SUBDIR += rubygem-ai4r SUBDIR += rubygem-cdo SUBDIR += rubygem-ruby-dcl Added: head/science/rdkit/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/rdkit/Makefile Thu Mar 22 08:23:57 2018 (r465265) @@ -0,0 +1,35 @@ +# $FreeBSD$ + +PORTNAME= rdkit +DISTVERSIONPREFIX= Release_ +DISTVERSION= 2017_09_3 +CATEGORIES= science +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Collection of cheminformatics and machine-learning software + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/license.txt + +BUILD_DEPENDS= flex:textproc/flex +LIB_DEPENDS= libboost_system.so:devel/boost-libs + +USES= bison:build cmake:outsource eigen:3 +USE_GITHUB= yes +USE_LDCONFIG= yes + +CMAKE_OFF= RDK_BUILD_PYTHON_WRAPPERS RDK_INSTALL_INTREE RDK_USE_FLEXBISON \ + RDK_INSTALL_STATIC_LIBS RDK_SWIG_STATIC RDK_PGSQL_STATIC +CMAKE_ARGS= -DFREEBSD_DOCSDIR:PATH=${DOCSDIR} + +DATADIR= ${PREFIX}/share/RDKit +DOCSDIR= ${PREFIX}/share/doc/RDKit + +OPTIONS_DEFINE= DOCS + +PORTDOCS= * + +PLIST_SUB= SHLIB_VER=${PORTVERSION} + +.include <bsd.port.mk> Added: head/science/rdkit/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/rdkit/distinfo Thu Mar 22 08:23:57 2018 (r465265) @@ -0,0 +1,3 @@ +TIMESTAMP = 1521697971 +SHA256 (rdkit-rdkit-Release_2017_09_3_GH0.tar.gz) = 6a4d9e9eb0ca06cbcdc20505f0c6ea0b1167b4dcdf7d1185871ba16ce701a5f4 +SIZE (rdkit-rdkit-Release_2017_09_3_GH0.tar.gz) = 29567648 Added: head/science/rdkit/files/patch-CMakeLists.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/rdkit/files/patch-CMakeLists.txt Thu Mar 22 08:23:57 2018 (r465265) @@ -0,0 +1,11 @@ +--- CMakeLists.txt.orig 2018-03-22 06:56:06 UTC ++++ CMakeLists.txt +@@ -338,7 +338,7 @@ if(NOT RDK_INSTALL_INTREE) + PATTERN ".svn" EXCLUDE + ) + install(DIRECTORY Docs DESTINATION +- ${RDKit_ShareDir} ++ ${FREEBSD_DOCSDIR} + COMPONENT docs + PATTERN ".svn" EXCLUDE + PATTERN "_build" EXCLUDE Added: head/science/rdkit/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/rdkit/pkg-descr Thu Mar 22 08:23:57 2018 (r465265) @@ -0,0 +1,21 @@ +Open source toolkit for cheminformatics. + +Features: +* Input/Output: SMILES/SMARTS, SDF, TDT, SLN 1, Corina mol2 1, PDB, + sequence notation, FASTA (peptides only), HELM (peptides only) +* Substructure searching +* Canonical SMILES +* Chirality support (i.e. R/S or E/Z labeling) +* Chemical transformations (e.g. remove matching substructures) +* Chemical reactions +* Molecular serialization (e.g. mol <-> text) +* 2D depiction, including constrained depiction +* Fingerprinting: Daylight-like, atom pairs, topological torsions, + Morgan algorithm, "MACCS keys", extended reduced graphs, etc. +* Similarity/diversity picking +* Gasteiger-Marsili charges +* Bemis and Murcko scaffold determination +* Salt stripping +* Functional-group filters + +WWW: http://www.rdkit.org/ Added: head/science/rdkit/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/rdkit/pkg-plist Thu Mar 22 08:23:57 2018 (r465265) @@ -0,0 +1,516 @@ +include/rdkit/Catalogs/Catalog.h +include/rdkit/Catalogs/CatalogEntry.h +include/rdkit/Catalogs/CatalogParams.h +include/rdkit/ChemicalFeatures/ChemicalFeature.h +include/rdkit/ChemicalFeatures/FreeChemicalFeature.h +include/rdkit/DataManip/MetricMatrixCalc/MetricFuncs.h +include/rdkit/DataManip/MetricMatrixCalc/MetricMatrixCalc.h +include/rdkit/DataStructs/BitOps.h +include/rdkit/DataStructs/BitVect.h +include/rdkit/DataStructs/BitVectUtils.h +include/rdkit/DataStructs/BitVects.h +include/rdkit/DataStructs/DatastructsException.h +include/rdkit/DataStructs/DiscreteDistMat.h +include/rdkit/DataStructs/DiscreteValueVect.h +include/rdkit/DataStructs/ExplicitBitVect.h +include/rdkit/DataStructs/FPBReader.h +include/rdkit/DataStructs/MultiFPBReader.h +include/rdkit/DataStructs/SparseBitVect.h +include/rdkit/DataStructs/SparseIntVect.h +include/rdkit/DataStructs/base64.h +include/rdkit/DistGeom/BoundsMatrix.h +include/rdkit/DistGeom/ChiralSet.h +include/rdkit/DistGeom/ChiralViolationContrib.h +include/rdkit/DistGeom/DistGeomUtils.h +include/rdkit/DistGeom/DistViolationContrib.h +include/rdkit/DistGeom/FourthDimContrib.h +include/rdkit/DistGeom/TriangleSmooth.h +include/rdkit/Features/Feature.h +include/rdkit/ForceField/Contrib.h +include/rdkit/ForceField/ForceField.h +include/rdkit/ForceField/MMFF/AngleBend.h +include/rdkit/ForceField/MMFF/AngleConstraint.h +include/rdkit/ForceField/MMFF/BondStretch.h +include/rdkit/ForceField/MMFF/Contribs.h +include/rdkit/ForceField/MMFF/DistanceConstraint.h +include/rdkit/ForceField/MMFF/Nonbonded.h +include/rdkit/ForceField/MMFF/OopBend.h +include/rdkit/ForceField/MMFF/Params.h +include/rdkit/ForceField/MMFF/PositionConstraint.h +include/rdkit/ForceField/MMFF/StretchBend.h +include/rdkit/ForceField/MMFF/TorsionAngle.h +include/rdkit/ForceField/MMFF/TorsionConstraint.h +include/rdkit/ForceField/UFF/AngleBend.h +include/rdkit/ForceField/UFF/AngleConstraint.h +include/rdkit/ForceField/UFF/BondStretch.h +include/rdkit/ForceField/UFF/Contribs.h +include/rdkit/ForceField/UFF/DistanceConstraint.h +include/rdkit/ForceField/UFF/Inversion.h +include/rdkit/ForceField/UFF/Nonbonded.h +include/rdkit/ForceField/UFF/Params.h +include/rdkit/ForceField/UFF/PositionConstraint.h +include/rdkit/ForceField/UFF/TorsionAngle.h +include/rdkit/ForceField/UFF/TorsionConstraint.h +include/rdkit/Geometry/Grid3D.h +include/rdkit/Geometry/GridUtils.h +include/rdkit/Geometry/Transform.h +include/rdkit/Geometry/Transform2D.h +include/rdkit/Geometry/Transform3D.h +include/rdkit/Geometry/UniformGrid3D.h +include/rdkit/Geometry/Utils.h +include/rdkit/Geometry/point.h +include/rdkit/GraphMol/Atom.h +include/rdkit/GraphMol/AtomIterators.h +include/rdkit/GraphMol/Bond.h +include/rdkit/GraphMol/BondIterators.h +include/rdkit/GraphMol/Canon.h +include/rdkit/GraphMol/ChemReactions/CartesianProduct.h +include/rdkit/GraphMol/ChemReactions/Enumerate.h +include/rdkit/GraphMol/ChemReactions/EnumerateBase.h +include/rdkit/GraphMol/ChemReactions/EnumerationPickler.h +include/rdkit/GraphMol/ChemReactions/EnumerationStrategyBase.h +include/rdkit/GraphMol/ChemReactions/PreprocessRxn.h +include/rdkit/GraphMol/ChemReactions/RandomSample.h +include/rdkit/GraphMol/ChemReactions/RandomSampleAllBBs.h +include/rdkit/GraphMol/ChemReactions/Reaction.h +include/rdkit/GraphMol/ChemReactions/ReactionFingerprints.h +include/rdkit/GraphMol/ChemReactions/ReactionParser.h +include/rdkit/GraphMol/ChemReactions/ReactionPickler.h +include/rdkit/GraphMol/ChemReactions/ReactionRunner.h +include/rdkit/GraphMol/ChemReactions/ReactionUtils.h +include/rdkit/GraphMol/ChemReactions/SanitizeRxn.h +include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h +include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h +include/rdkit/GraphMol/Chirality.h +include/rdkit/GraphMol/Conformer.h +include/rdkit/GraphMol/Depictor/DepictUtils.h +include/rdkit/GraphMol/Depictor/EmbeddedFrag.h +include/rdkit/GraphMol/Depictor/RDDepictor.h +include/rdkit/GraphMol/Descriptors/AUTOCORR2D.h +include/rdkit/GraphMol/Descriptors/AUTOCORR3D.h +include/rdkit/GraphMol/Descriptors/ConnectivityDescriptors.h +include/rdkit/GraphMol/Descriptors/Crippen.h +include/rdkit/GraphMol/Descriptors/Data3Ddescriptors.h +include/rdkit/GraphMol/Descriptors/GETAWAY.h +include/rdkit/GraphMol/Descriptors/Lipinski.h +include/rdkit/GraphMol/Descriptors/MORSE.h +include/rdkit/GraphMol/Descriptors/MQN.h +include/rdkit/GraphMol/Descriptors/MolData3Ddescriptors.h +include/rdkit/GraphMol/Descriptors/MolDescriptors.h +include/rdkit/GraphMol/Descriptors/MolDescriptors3D.h +include/rdkit/GraphMol/Descriptors/MolSurf.h +include/rdkit/GraphMol/Descriptors/PBF.h +include/rdkit/GraphMol/Descriptors/PMI.h +include/rdkit/GraphMol/Descriptors/Property.h +include/rdkit/GraphMol/Descriptors/RDF.h +include/rdkit/GraphMol/Descriptors/RegisterDescriptor.h +include/rdkit/GraphMol/Descriptors/USRDescriptor.h +include/rdkit/GraphMol/Descriptors/WHIM.h +include/rdkit/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h +include/rdkit/GraphMol/DistGeomHelpers/Embedder.h +include/rdkit/GraphMol/FMCS/FMCS.h +include/rdkit/GraphMol/FMCS/Graph.h +include/rdkit/GraphMol/FMCS/MatchTable.h +include/rdkit/GraphMol/FMCS/MaximumCommonSubgraph.h +include/rdkit/GraphMol/FMCS/RingMatchTableSet.h +include/rdkit/GraphMol/FMCS/Seed.h +include/rdkit/GraphMol/FMCS/SeedSet.h +include/rdkit/GraphMol/FMCS/SubstructMatchCustom.h +include/rdkit/GraphMol/FMCS/SubstructureCache.h +include/rdkit/GraphMol/FileParsers/FileParserUtils.h +include/rdkit/GraphMol/FileParsers/FileParsers.h +include/rdkit/GraphMol/FileParsers/MolFileStereochem.h +include/rdkit/GraphMol/FileParsers/MolSupplier.h +include/rdkit/GraphMol/FileParsers/MolWriters.h +include/rdkit/GraphMol/FileParsers/SequenceParsers.h +include/rdkit/GraphMol/FileParsers/SequenceWriters.h +include/rdkit/GraphMol/FilterCatalog/FilterCatalog.h +include/rdkit/GraphMol/FilterCatalog/FilterCatalogEntry.h +include/rdkit/GraphMol/FilterCatalog/FilterMatcherBase.h +include/rdkit/GraphMol/FilterCatalog/FilterMatchers.h +include/rdkit/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h +include/rdkit/GraphMol/Fingerprints/AtomPairs.h +include/rdkit/GraphMol/Fingerprints/Fingerprints.h +include/rdkit/GraphMol/Fingerprints/MACCS.h +include/rdkit/GraphMol/Fingerprints/MorganFingerprints.h +include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h 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