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ESMTPS id 4YGG493hS1z13Df; Sun, 22 Dec 2024 09:26:17 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 4BM9QHd9010087; Sun, 22 Dec 2024 09:26:17 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 4BM9QHlN010082; Sun, 22 Dec 2024 09:26:17 GMT (envelope-from git) Date: Sun, 22 Dec 2024 09:26:17 GMT Message-Id: <202412220926.4BM9QHlN010082@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: b208f114255c - main - science/rdkit: update 2024_03_6 =?utf-8?Q?=E2=86=92?= 2024_09_4 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-all@freebsd.org Sender: owner-dev-commits-ports-all@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: b208f114255c6376eb0d8bf46c4d20f39bee9f6c Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=b208f114255c6376eb0d8bf46c4d20f39bee9f6c commit b208f114255c6376eb0d8bf46c4d20f39bee9f6c Author: Yuri Victorovich AuthorDate: 2024-12-22 09:09:28 +0000 Commit: Yuri Victorovich CommitDate: 2024-12-22 09:26:05 +0000 science/rdkit: update 2024_03_6 → 2024_09_4 --- science/rdkit/Makefile | 7 ++++--- science/rdkit/distinfo | 16 +++++++++------- science/rdkit/pkg-plist | 45 ++++++++++++++++++++++++++++++++++++--------- 3 files changed, 49 insertions(+), 19 deletions(-) diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile index c44922819a01..ea8192ecc72a 100644 --- a/science/rdkit/Makefile +++ b/science/rdkit/Makefile @@ -1,7 +1,6 @@ PORTNAME= rdkit DISTVERSIONPREFIX= Release_ -DISTVERSION= 2024_03_6 -PORTREVISION= 3 +DISTVERSION= 2024_09_4 CATEGORIES= science MASTER_SITES= LOCAL/yuri/:font # unstable, changing font file: https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font DISTFILES= ComicNeue-Regular.ttf:font @@ -10,7 +9,8 @@ EXTRACT_ONLY= ${DISTFILES:C/:.*//:N*.ttf} MAINTAINER= yuri@FreeBSD.org COMMENT= Collection of cheminformatics and machine-learning software -WWW= https://www.rdkit.org/ +WWW= https://www.rdkit.org/ \ + https://github.com/rdkit/rdkit LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt @@ -29,6 +29,7 @@ LIB_DEPENDS= libboost_system.so:devel/boost-libs \ USES= bison:build cmake:testing compiler:c++11-lang eigen:3 python USE_GITHUB= yes GH_TUPLE= rareylab:RingDecomposerLib:v1.1.3_rdkit:RingDecomposerLib/External/RingFamilies/RingDecomposerLib +GH_TUPLE+= ncbi:pubchem-align3d:daefab3:align3d/External/pubchem_shape/pubchem-align3d USE_LDCONFIG= yes CMAKE_OFF= RDK_INSTALL_INTREE RDK_USE_FLEXBISON \ diff --git a/science/rdkit/distinfo b/science/rdkit/distinfo index 1545d82058c4..bf713ecd6c60 100644 --- a/science/rdkit/distinfo +++ b/science/rdkit/distinfo @@ -1,7 +1,9 @@ -TIMESTAMP = 1725689837 -SHA256 (rdkit-2024.03.6/ComicNeue-Regular.ttf) = 4f0f67d826565ed55f91ca6512e5562d0f2a39030fc7208519354438bc783ff6 -SIZE (rdkit-2024.03.6/ComicNeue-Regular.ttf) = 21915 -SHA256 (rdkit-2024.03.6/rdkit-rdkit-Release_2024_03_6_GH0.tar.gz) = 5002ff97e59d9c08f4faa1c6a2e276a695f6874dfc93e28cbbd62dab4f0b40d7 -SIZE (rdkit-2024.03.6/rdkit-rdkit-Release_2024_03_6_GH0.tar.gz) = 80462644 -SHA256 (rdkit-2024.03.6/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715 -SIZE (rdkit-2024.03.6/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931 +TIMESTAMP = 1734855089 +SHA256 (rdkit-2024.09.4/ComicNeue-Regular.ttf) = 4f0f67d826565ed55f91ca6512e5562d0f2a39030fc7208519354438bc783ff6 +SIZE (rdkit-2024.09.4/ComicNeue-Regular.ttf) = 21915 +SHA256 (rdkit-2024.09.4/rdkit-rdkit-Release_2024_09_4_GH0.tar.gz) = a5e8da75aae7e88f3a50d8577f9027c971187492a93a15085f797fe6fef74ad2 +SIZE (rdkit-2024.09.4/rdkit-rdkit-Release_2024_09_4_GH0.tar.gz) = 82055856 +SHA256 (rdkit-2024.09.4/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715 +SIZE (rdkit-2024.09.4/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931 +SHA256 (rdkit-2024.09.4/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = d7814a00a39f6a798bc1611d0f7bbd1abc91d754309527a9038a0dad42d848c0 +SIZE (rdkit-2024.09.4/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = 112376 diff --git a/science/rdkit/pkg-plist b/science/rdkit/pkg-plist index 4fb73662f59c..02d0d907d04d 100644 --- a/science/rdkit/pkg-plist +++ b/science/rdkit/pkg-plist @@ -16,6 +16,7 @@ include/rdkit/DataStructs/DiscreteValueVect.h include/rdkit/DataStructs/ExplicitBitVect.h include/rdkit/DataStructs/FPBReader.h include/rdkit/DataStructs/MultiFPBReader.h +include/rdkit/DataStructs/RealValueVect.h include/rdkit/DataStructs/SparseBitVect.h include/rdkit/DataStructs/SparseIntVect.h include/rdkit/DataStructs/base64.h @@ -69,6 +70,7 @@ include/rdkit/Geometry/Transform.h include/rdkit/Geometry/Transform2D.h include/rdkit/Geometry/Transform3D.h include/rdkit/Geometry/UniformGrid3D.h +include/rdkit/Geometry/UniformRealValueGrid3D.h include/rdkit/Geometry/Utils.h include/rdkit/Geometry/point.h include/rdkit/GraphMol/Abbreviations/Abbreviations.h @@ -206,10 +208,12 @@ include/rdkit/GraphMol/MolEnumerator/LinkNode.h include/rdkit/GraphMol/MolEnumerator/MolEnumerator.h include/rdkit/GraphMol/MolHash/MolHash.h include/rdkit/GraphMol/MolHash/nmmolhash.h +include/rdkit/GraphMol/MolInteractionFields/MIFDescriptors.h include/rdkit/GraphMol/MolInterchange/MolInterchange.h include/rdkit/GraphMol/MolInterchange/details.h include/rdkit/GraphMol/MolOps.h include/rdkit/GraphMol/MolPickler.h +include/rdkit/GraphMol/MolProcessing/MolProcessing.h include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h @@ -221,6 +225,7 @@ include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h include/rdkit/GraphMol/MolStandardize/Metal.h include/rdkit/GraphMol/MolStandardize/MolStandardize.h include/rdkit/GraphMol/MolStandardize/Normalize.h +include/rdkit/GraphMol/MolStandardize/Pipeline.h include/rdkit/GraphMol/MolStandardize/Tautomer.h include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h @@ -234,6 +239,7 @@ include/rdkit/GraphMol/MonomerInfo.h include/rdkit/GraphMol/PartialCharges/GasteigerCharges.h include/rdkit/GraphMol/PartialCharges/GasteigerParams.h include/rdkit/GraphMol/PeriodicTable.h +include/rdkit/GraphMol/PubChemShape.hpp include/rdkit/GraphMol/QueryAtom.h include/rdkit/GraphMol/QueryBond.h include/rdkit/GraphMol/QueryOps.h @@ -258,11 +264,11 @@ include/rdkit/GraphMol/SanitException.h include/rdkit/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h include/rdkit/GraphMol/ShapeHelpers/ShapeEncoder.h include/rdkit/GraphMol/ShapeHelpers/ShapeUtils.h +include/rdkit/GraphMol/SmilesParse/CanonicalizeStereoGroups.h include/rdkit/GraphMol/SmilesParse/SmartsWrite.h include/rdkit/GraphMol/SmilesParse/SmilesParse.h include/rdkit/GraphMol/SmilesParse/SmilesParseOps.h include/rdkit/GraphMol/SmilesParse/SmilesWrite.h -include/rdkit/GraphMol/SmilesParse/primes.h include/rdkit/GraphMol/StereoGroup.h include/rdkit/GraphMol/Subgraphs/SubgraphUtils.h include/rdkit/GraphMol/Subgraphs/Subgraphs.h @@ -272,6 +278,13 @@ include/rdkit/GraphMol/Substruct/SubstructUtils.h include/rdkit/GraphMol/SubstructLibrary/PatternFactory.h include/rdkit/GraphMol/SubstructLibrary/SubstructLibrary.h include/rdkit/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h +include/rdkit/GraphMol/SynthonSpaceSearch/SearchResults.h +include/rdkit/GraphMol/SynthonSpaceSearch/Synthon.h +include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSet.h +include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpace.h +include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.h +include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.h +include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.h include/rdkit/GraphMol/TautomerQuery/TautomerQuery.h include/rdkit/GraphMol/Trajectory/Snapshot.h include/rdkit/GraphMol/Trajectory/Trajectory.h @@ -446,9 +459,15 @@ lib/libRDKitMolEnumerator.so.1.%%SHLIB_VER%% lib/libRDKitMolHash.so lib/libRDKitMolHash.so.1 lib/libRDKitMolHash.so.1.%%SHLIB_VER%% +lib/libRDKitMolInteractionFields.so +lib/libRDKitMolInteractionFields.so.1 +lib/libRDKitMolInteractionFields.so.1.%%SHLIB_VER%% lib/libRDKitMolInterchange.so lib/libRDKitMolInterchange.so.1 lib/libRDKitMolInterchange.so.1.%%SHLIB_VER%% +lib/libRDKitMolProcessing.so +lib/libRDKitMolProcessing.so.1 +lib/libRDKitMolProcessing.so.1.%%SHLIB_VER%% lib/libRDKitMolStandardize.so lib/libRDKitMolStandardize.so.1 lib/libRDKitMolStandardize.so.1.%%SHLIB_VER%% @@ -464,6 +483,9 @@ lib/libRDKitOptimizer.so.1.%%SHLIB_VER%% lib/libRDKitPartialCharges.so lib/libRDKitPartialCharges.so.1 lib/libRDKitPartialCharges.so.1.%%SHLIB_VER%% +lib/libRDKitPubChemShape.so +lib/libRDKitPubChemShape.so.1 +lib/libRDKitPubChemShape.so.1.%%SHLIB_VER%% %%PYTHON%%lib/libRDKitRDBoost.so %%PYTHON%%lib/libRDKitRDBoost.so.1 %%PYTHON%%lib/libRDKitRDBoost.so.1.%%SHLIB_VER%% @@ -512,6 +534,9 @@ lib/libRDKitSubstructLibrary.so.1.%%SHLIB_VER%% lib/libRDKitSubstructMatch.so lib/libRDKitSubstructMatch.so.1 lib/libRDKitSubstructMatch.so.1.%%SHLIB_VER%% +lib/libRDKitSynthonSpaceSearch.so +lib/libRDKitSynthonSpaceSearch.so.1 +lib/libRDKitSynthonSpaceSearch.so.1.%%SHLIB_VER%% lib/libRDKitTautomerQuery.so lib/libRDKitTautomerQuery.so.1 lib/libRDKitTautomerQuery.so.1.%%SHLIB_VER%% @@ -525,6 +550,9 @@ lib/libRDKitga.so.1.%%SHLIB_VER%% %%LITTLE_ENDIAN%%lib/libRDKithc.so.1 %%LITTLE_ENDIAN%%lib/libRDKithc.so.1.%%SHLIB_VER%% %%PGSQL%%lib/postgresql/rdkit.so +%%PYTHON%%lib/libRDKitpubchem_align3d.so +%%PYTHON%%lib/libRDKitpubchem_align3d.so.1 +%%PYTHON%%lib/libRDKitpubchem_align3d.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Avalon/__init__.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/AllChem.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/AtomPairs/Pairs.py @@ -552,13 +580,7 @@ lib/libRDKitga.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Draw/MolDrawing.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Draw/SimilarityMaps.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Draw/__init__.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Draw/aggCanvas.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Draw/cairoCanvas.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Draw/canvasbase.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Draw/mplCanvas.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Draw/qtCanvas.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Draw/rdMolDraw2D.so -%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/Draw/spingCanvas.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/EState/AtomTypes.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/EState/EState.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/EState/EState_VSA.py @@ -652,7 +674,7 @@ lib/libRDKitga.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/fmcs/fmcs %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/fmcs/fmcs.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/inchi.py -%%PYTHON%%%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/nbtests/ChEMBL_quinolones.tsv +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/nbtests/ChEMBL_quinolones.tsv %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/nbtests/github4823.ipynb %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/nbtests/rdkit-structure-renderer.ipynb %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdAbbreviations.so @@ -668,6 +690,7 @@ lib/libRDKitga.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdForceFieldHelpers.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdGeneralizedSubstruct.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMHFPFingerprint.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMIF.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMMPA.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolAlign.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolCatalog.so @@ -676,14 +699,17 @@ lib/libRDKitga.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolEnumerator.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolHash.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolInterchange.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolProcessing.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolTransforms.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdPartialCharges.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdRGroupDecomposition.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdRascalMCES.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdReducedGraphs.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdSLNParse.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdShapeAlign.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdShapeHelpers.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdSubstructLibrary.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdSynthonSpaceSearch.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdTautomerQuery.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdchem.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdfiltercatalog.so @@ -1034,6 +1060,7 @@ lib/libRDKitga.so.1.%%SHLIB_VER%% %%DATADIR%%/Contrib/RxnRoleAssignment/utils.py %%DATADIR%%/Contrib/SA_Score/README %%DATADIR%%/Contrib/SA_Score/UnitTestSAScore.py +%%DATADIR%%/Contrib/SA_Score/build_sascore_db.py %%DATADIR%%/Contrib/SA_Score/data/zim.100.txt %%DATADIR%%/Contrib/SA_Score/fpscores.pkl.gz %%DATADIR%%/Contrib/SA_Score/sascorer.py @@ -1129,7 +1156,7 @@ lib/libRDKitga.so.1.%%SHLIB_VER%% %%PYTHON%%%%DATADIR%%/Projects/DbCLI/testData/bzr_q1.mol %%PYTHON%%%%DATADIR%%/Projects/DbCLI/testData/pubchem.200.sdf %%DATADIR%%/Projects/pytest.ini -%%DATADIR%%/README +%%DATADIR%%/README.md %%PYTHON%%%%DATADIR%%/Scripts/FeatFinderCLI.py %%PYTHON%%%%DATADIR%%/Scripts/PythonFormat.py %%PYTHON%%%%DATADIR%%/Scripts/README.md