git: b208f114255c - main - science/rdkit: update 2024_03_6 → 2024_09_4
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Date: Sun, 22 Dec 2024 09:26:17 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=b208f114255c6376eb0d8bf46c4d20f39bee9f6c
commit b208f114255c6376eb0d8bf46c4d20f39bee9f6c
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2024-12-22 09:09:28 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
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