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science/rdkit: update 2024_09_4 → 2025_03_1
This commit is contained in:
Yuri Victorovich
parent
ebdedab7bb
commit
d8e71b1111
5 changed files with 74 additions and 21 deletions
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@ -1,7 +1,6 @@
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PORTNAME= rdkit
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DISTVERSIONPREFIX= Release_
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DISTVERSION= 2024_09_4
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PORTREVISION= 1
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DISTVERSION= 2025_03_1
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CATEGORIES= science
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MASTER_SITES= LOCAL/yuri/:font # unstable, changing font file: https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font
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DISTFILES= ComicNeue-Regular.ttf:font
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@ -28,12 +27,16 @@ LIB_DEPENDS= libboost_system.so:devel/boost-libs \
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libfreetype.so:print/freetype2 \
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libmaeparser.so:science/maeparser
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USES= bison:build cmake:testing compiler:c++11-lang eigen:3 python
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USE_GITHUB= yes
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GH_TUPLE= rareylab:RingDecomposerLib:v1.1.3_rdkit:RingDecomposerLib/External/RingFamilies/RingDecomposerLib
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GH_TUPLE+= ncbi:pubchem-align3d:daefab3:align3d/External/pubchem_shape/pubchem-align3d
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USES= bison:build cmake:testing compiler:c++11-lang eigen:3 gnome python
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USE_GNOME= cairo
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USE_LDCONFIG= yes
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USE_GITHUB= yes
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GH_TUPLE= rareylab:RingDecomposerLib:v1.1.3_rdkit:RingDecomposerLib/External/RingFamilies/RingDecomposerLib
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GH_TUPLE+= ncbi:pubchem-align3d:daefab3:align3d/External/pubchem_shape/pubchem-align3d \
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aantron:better-enums:520d8ee:better_enums/better_enums
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CMAKE_ON= RDK_BUILD_CAIRO_SUPPORT
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CMAKE_OFF= RDK_INSTALL_INTREE RDK_USE_FLEXBISON \
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RDK_INSTALL_STATIC_LIBS RDK_SWIG_STATIC RDK_PGSQL_STATIC \
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RDK_OPTIMIZE_NATIVE \
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@ -42,6 +45,7 @@ CMAKE_ARGS= -DCATCH_DIR=${LOCALBASE}/include/catch2
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CFLAGS+= -D_GNU_SOURCE
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CXXFLAGS+= -D_GNU_SOURCE
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#-I${WRKSRC}/better_enums
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DATADIR= ${PREFIX}/share/RDKit
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DOCSDIR= ${PREFIX}/share/doc/RDKit
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@ -87,6 +91,7 @@ post-extract:
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@${MKDIR} ${WRKSRC}/External/rapidjson-1.1.0
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@cd ${WRKSRC}/External/rapidjson-1.1.0 && ${LN} -s ${LOCALBASE}/include/rapidjson include
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@cd ${WRKSRC}/Data/Fonts && ${CP} ${DISTDIR}/${DIST_SUBDIR}/ComicNeue-Regular.ttf .
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@${CP} ${WRKSRC}/better_enums/enum.h ${WRKSRC}/Code/RDGeneral
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post-install-PGSQL-on:
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@${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/postgresql/rdkit.so
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@ -1,9 +1,11 @@
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TIMESTAMP = 1734855089
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SHA256 (rdkit-2024.09.4/ComicNeue-Regular.ttf) = 4f0f67d826565ed55f91ca6512e5562d0f2a39030fc7208519354438bc783ff6
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SIZE (rdkit-2024.09.4/ComicNeue-Regular.ttf) = 21915
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SHA256 (rdkit-2024.09.4/rdkit-rdkit-Release_2024_09_4_GH0.tar.gz) = a5e8da75aae7e88f3a50d8577f9027c971187492a93a15085f797fe6fef74ad2
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SIZE (rdkit-2024.09.4/rdkit-rdkit-Release_2024_09_4_GH0.tar.gz) = 82055856
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SHA256 (rdkit-2024.09.4/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715
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SIZE (rdkit-2024.09.4/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931
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SHA256 (rdkit-2024.09.4/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = d7814a00a39f6a798bc1611d0f7bbd1abc91d754309527a9038a0dad42d848c0
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SIZE (rdkit-2024.09.4/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = 112376
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TIMESTAMP = 1744735395
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SHA256 (rdkit-2025.03.1/ComicNeue-Regular.ttf) = 4f0f67d826565ed55f91ca6512e5562d0f2a39030fc7208519354438bc783ff6
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SIZE (rdkit-2025.03.1/ComicNeue-Regular.ttf) = 21915
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SHA256 (rdkit-2025.03.1/rdkit-rdkit-Release_2025_03_1_GH0.tar.gz) = 947e5aa004047fbec4bf4ba93b84a50ca7f68e248a0654080d8ca0cdb06e3534
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SIZE (rdkit-2025.03.1/rdkit-rdkit-Release_2025_03_1_GH0.tar.gz) = 82192067
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SHA256 (rdkit-2025.03.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715
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SIZE (rdkit-2025.03.1/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931
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SHA256 (rdkit-2025.03.1/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = d7814a00a39f6a798bc1611d0f7bbd1abc91d754309527a9038a0dad42d848c0
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SIZE (rdkit-2025.03.1/ncbi-pubchem-align3d-daefab3_GH0.tar.gz) = 112376
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SHA256 (rdkit-2025.03.1/aantron-better-enums-520d8ee_GH0.tar.gz) = 29ef26e79eb489b3ef71f85f904f3f1173ffefc6c853219bee7520188805eca5
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SIZE (rdkit-2025.03.1/aantron-better-enums-520d8ee_GH0.tar.gz) = 136592
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@ -1,6 +1,6 @@
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--- CMakeLists.txt.orig 2024-12-20 08:56:08 UTC
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--- CMakeLists.txt.orig 2025-03-31 18:11:10 UTC
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+++ CMakeLists.txt
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@@ -76,12 +76,12 @@ if(NOT MSVC)
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@@ -78,12 +78,12 @@ if(NOT MSVC)
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if(NOT MSVC)
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if(RDK_OPTIMIZE_POPCNT)
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@ -17,7 +17,26 @@
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endif()
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endif()
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endif()
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@@ -516,12 +516,14 @@ if(NOT RDK_INSTALL_INTREE)
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@@ -166,18 +166,6 @@ endif()
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FetchContent_MakeAvailable(Catch2)
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endif()
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-#include better-enums
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-find_package(better_enums 0 QUIET)
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-if(NOT better_enums)
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- Include(FetchContent)
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-
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- FetchContent_Declare(
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- better_enums
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- GIT_REPOSITORY https://github.com/aantron/better-enums.git
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- GIT_TAG c35576bed0295689540b39873126129adfa0b4c8 # 0.11.3
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- )
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-endif()
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-
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if(RDK_INSTALL_INTREE)
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set(RDKit_BinDir "${CMAKE_SOURCE_DIR}/bin")
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set(RDKit_LibDir "${CMAKE_SOURCE_DIR}/lib")
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@@ -530,12 +518,14 @@ if(NOT RDK_INSTALL_INTREE)
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COMPONENT data
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PATTERN ".svn" EXCLUDE
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)
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14
science/rdkit/files/patch-Code_RDGeneral_CMakeLists.txt
Normal file
14
science/rdkit/files/patch-Code_RDGeneral_CMakeLists.txt
Normal file
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@ -0,0 +1,14 @@
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--- Code/RDGeneral/CMakeLists.txt.orig 2025-04-15 16:44:12 UTC
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+++ Code/RDGeneral/CMakeLists.txt
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@@ -5,11 +5,6 @@ CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/RDConfig.h.
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CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/RDConfig.h.cmake
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${CMAKE_CURRENT_SOURCE_DIR}/RDConfig.h)
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-FetchContent_MakeAvailable(better_enums)
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-if (NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/enum.h)
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- file(COPY ${better_enums_SOURCE_DIR}/enum.h DESTINATION ${CMAKE_CURRENT_SOURCE_DIR})
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-endif (NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/enum.h)
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-
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rdkit_library(RDGeneral
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Invariant.cpp types.cpp utils.cpp RDGeneralExceptions.cpp RDLog.cpp
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LocaleSwitcher.cpp versions.cpp SHARED)
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@ -22,12 +22,9 @@ include/rdkit/DataStructs/SparseIntVect.h
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include/rdkit/DataStructs/base64.h
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include/rdkit/DistGeom/BoundsMatrix.h
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include/rdkit/DistGeom/ChiralSet.h
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include/rdkit/DistGeom/ChiralViolationContrib.h
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include/rdkit/DistGeom/ChiralViolationContribs.h
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include/rdkit/DistGeom/DistGeomUtils.h
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include/rdkit/DistGeom/DistViolationContrib.h
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include/rdkit/DistGeom/DistViolationContribs.h
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include/rdkit/DistGeom/FourthDimContrib.h
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include/rdkit/DistGeom/FourthDimContribs.h
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include/rdkit/DistGeom/TriangleSmooth.h
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include/rdkit/Features/Feature.h
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@ -100,6 +97,7 @@ include/rdkit/GraphMol/ChemReactions/ReactionUtils.h
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include/rdkit/GraphMol/ChemReactions/SanitizeRxn.h
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include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h
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include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h
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include/rdkit/GraphMol/ChemTransforms/MolFragmenterJSONParser.h
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include/rdkit/GraphMol/Chirality.h
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include/rdkit/GraphMol/Conformer.h
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include/rdkit/GraphMol/CoordGen.h
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@ -199,6 +197,7 @@ include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeature.h
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include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h
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include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h
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include/rdkit/GraphMol/MolDraw2D/MolDraw2D.h
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include/rdkit/GraphMol/MolDraw2D/MolDraw2DCairo.h
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include/rdkit/GraphMol/MolDraw2D/MolDraw2DHelpers.h
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include/rdkit/GraphMol/MolDraw2D/MolDraw2DJS.h
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include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h
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@ -246,6 +245,7 @@ include/rdkit/GraphMol/QueryOps.h
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include/rdkit/GraphMol/RDKitBase.h
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include/rdkit/GraphMol/RDKitQueries.h
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include/rdkit/GraphMol/RGroupDecomposition/RGroupDecomp.h
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include/rdkit/GraphMol/RGroupDecomposition/RGroupDecompJSONParsers.h
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include/rdkit/GraphMol/RGroupDecomposition/RGroupDecompParams.h
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include/rdkit/GraphMol/ROMol.h
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include/rdkit/GraphMol/RWMol.h
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@ -266,6 +266,7 @@ include/rdkit/GraphMol/ShapeHelpers/ShapeEncoder.h
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include/rdkit/GraphMol/ShapeHelpers/ShapeUtils.h
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include/rdkit/GraphMol/SmilesParse/CanonicalizeStereoGroups.h
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include/rdkit/GraphMol/SmilesParse/SmartsWrite.h
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include/rdkit/GraphMol/SmilesParse/SmilesJSONParsers.h
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include/rdkit/GraphMol/SmilesParse/SmilesParse.h
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include/rdkit/GraphMol/SmilesParse/SmilesParseOps.h
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include/rdkit/GraphMol/SmilesParse/SmilesWrite.h
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@ -283,6 +284,7 @@ include/rdkit/GraphMol/SynthonSpaceSearch/Synthon.h
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include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSet.h
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include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpace.h
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include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.h
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include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceRascalSearcher.h
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include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.h
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include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.h
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include/rdkit/GraphMol/TautomerQuery/TautomerQuery.h
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@ -320,9 +322,11 @@ include/rdkit/Query/XOrQuery.h
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%%PYTHON%%include/rdkit/RDBoost/python.h
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%%PYTHON%%include/rdkit/RDBoost/python_streambuf.h
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include/rdkit/RDGeneral/BadFileException.h
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include/rdkit/RDGeneral/BetterEnums.h
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include/rdkit/RDGeneral/BoostEndInclude.h
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include/rdkit/RDGeneral/BoostStartInclude.h
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include/rdkit/RDGeneral/ConcurrentQueue.h
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include/rdkit/RDGeneral/ControlCHandler.h
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include/rdkit/RDGeneral/Dict.h
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include/rdkit/RDGeneral/Exceptions.h
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include/rdkit/RDGeneral/FileParseException.h
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@ -339,6 +343,7 @@ include/rdkit/RDGeneral/RDValue-taggedunion.h
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include/rdkit/RDGeneral/RDValue.h
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include/rdkit/RDGeneral/Ranking.h
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include/rdkit/RDGeneral/StreamOps.h
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include/rdkit/RDGeneral/enum.h
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include/rdkit/RDGeneral/export.h
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include/rdkit/RDGeneral/hanoiSort.h
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include/rdkit/RDGeneral/hash/detail/float_functions.hpp
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@ -360,6 +365,10 @@ lib/cmake/rdkit/rdkit-config-version.cmake
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lib/cmake/rdkit/rdkit-config.cmake
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lib/cmake/rdkit/rdkit-targets-%%CMAKE_BUILD_TYPE%%.cmake
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lib/cmake/rdkit/rdkit-targets.cmake
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lib/cmake/rdkitpython/rdkitpython-config-version.cmake
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lib/cmake/rdkitpython/rdkitpython-config.cmake
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lib/cmake/rdkitpython/rdkitpython-targets-%%CMAKE_BUILD_TYPE%%.cmake
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lib/cmake/rdkitpython/rdkitpython-targets.cmake
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lib/libRDKitAbbreviations.so
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lib/libRDKitAbbreviations.so.1
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lib/libRDKitAbbreviations.so.1.%%SHLIB_VER%%
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@ -1064,6 +1073,10 @@ lib/libRDKitga.so.1.%%SHLIB_VER%%
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%%DATADIR%%/Contrib/SA_Score/data/zim.100.txt
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%%DATADIR%%/Contrib/SA_Score/fpscores.pkl.gz
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%%DATADIR%%/Contrib/SA_Score/sascorer.py
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%%DATADIR%%/Contrib/efgs/README.md
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%%DATADIR%%/Contrib/efgs/ch33query.sql
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%%DATADIR%%/Contrib/efgs/efgs.py
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%%DATADIR%%/Contrib/efgs/try_efgs.py
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%%DATADIR%%/Contrib/fraggle/atomcontrib.py
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%%DATADIR%%/Contrib/fraggle/cxn_tversky.py
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%%DATADIR%%/Contrib/fraggle/data/ChEMBL_11265_actives.smi
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