science/rdkit: Update 2020.09.5 -> 2021.03.3

Reported by:	portscout

4 files changed, 72 insertions, 20 deletions

diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile
index a98f8046a3d1..98db77376579 100644
--- a/science/rdkit/Makefile
+++ b/science/rdkit/Makefile
@@ -1,8 +1,10 @@
 PORTNAME=	rdkit
 DISTVERSIONPREFIX=	Release_
-DISTVERSION=	2020_09_5
-PORTREVISION=	1
+DISTVERSION=	2021_03_3
 CATEGORIES=	science
+MASTER_SITES=	https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font
+DISTFILES=	Comic_Neue.zip:font
+DIST_SUBDIR=	${PORTNAME}-${PORTVERSION}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Collection of cheminformatics and machine-learning software
@@ -66,6 +68,7 @@ PLIST_SUB+=	LITTLE_ENDIAN="@comment "
 post-extract:
 	@${MKDIR} ${WRKSRC}/External/rapidjson-1.1.0
 	@cd ${WRKSRC}/External/rapidjson-1.1.0 && ${LN} -s ${LOCALBASE}/include/rapidjson include
+	@cd ${WRKSRC}/Data/Fonts && unzip ${DISTDIR}/${DIST_SUBDIR}/Comic_Neue.zip
 
 post-stage: # https://github.com/rdkit/rdkit/issues/2094
 	#@${MKDIR} ${STAGEDIR}${PREFIX}/lib/cmake
diff --git a/science/rdkit/distinfo b/science/rdkit/distinfo
index 6dbdf98eb071..9145c25037cf 100644
--- a/science/rdkit/distinfo
+++ b/science/rdkit/distinfo
@@ -1,5 +1,7 @@
-TIMESTAMP = 1614725230
-SHA256 (rdkit-rdkit-Release_2020_09_5_GH0.tar.gz) = 85cec9618e7ef6365b9b908ed674c073d898b6627521cc7fd8c2e05fea8a5def
-SIZE (rdkit-rdkit-Release_2020_09_5_GH0.tar.gz) = 58609591
-SHA256 (rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715
-SIZE (rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931
+TIMESTAMP = 1623403789
+SHA256 (rdkit-2021.03.3/Comic_Neue.zip) = 9f254e5cd219c1aa9b1f18e73c2588d8cd8587ac16997eeff9adb0d556fa6461
+SIZE (rdkit-2021.03.3/Comic_Neue.zip) = 179735
+SHA256 (rdkit-2021.03.3/rdkit-rdkit-Release_2021_03_3_GH0.tar.gz) = e95f07adaee9280df077cb147210ee75e16957d81687ab0836d62ebf1f6f715f
+SIZE (rdkit-2021.03.3/rdkit-rdkit-Release_2021_03_3_GH0.tar.gz) = 78186499
+SHA256 (rdkit-2021.03.3/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715
+SIZE (rdkit-2021.03.3/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931
diff --git a/science/rdkit/files/patch-CMakeLists.txt b/science/rdkit/files/patch-CMakeLists.txt
index 5b5bb0dde652..a4594f30ae57 100644
--- a/science/rdkit/files/patch-CMakeLists.txt
+++ b/science/rdkit/files/patch-CMakeLists.txt
@@ -1,17 +1,6 @@
---- CMakeLists.txt.orig	2021-03-01 16:43:06 UTC
+--- CMakeLists.txt.orig	2020-06-10 03:59:48 UTC
 +++ CMakeLists.txt
-@@ -68,8 +68,8 @@ if(NOT MSVC)
-   if(RDK_OPTIMIZE_POPCNT)
-     if(CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "aarch64")
-       message("RDK_OPTIMIZE_POPCNT is not available on aarch64")
--    elseif(CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "ppc64le")
--      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcntb")
-+    elseif(CMAKE_HOST_SYSTEM_PROCESSOR MATCHES "^(ppc64|powerpc64)")
-+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcntd")
-     else()
-       set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcnt")
-     endif()
-@@ -459,12 +459,14 @@ if(NOT RDK_INSTALL_INTREE)
+@@ -432,12 +432,14 @@ if(NOT RDK_INSTALL_INTREE)
        COMPONENT data
        PATTERN ".svn" EXCLUDE
        )
diff --git a/science/rdkit/pkg-plist b/science/rdkit/pkg-plist
index bfab6a8f37f5..a1d51f03145b 100644
--- a/science/rdkit/pkg-plist
+++ b/science/rdkit/pkg-plist
@@ -1,4 +1,5 @@
 include/rdkit/CIPLabeler/CIPLabeler.h
+include/rdkit/CIPLabeler/TooManyNodesException.h
 include/rdkit/Catalogs/Catalog.h
 include/rdkit/Catalogs/CatalogEntry.h
 include/rdkit/Catalogs/CatalogParams.h
@@ -185,6 +186,7 @@ include/rdkit/GraphMol/MolDraw2D/MolDraw2DJS.h
 include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h
 include/rdkit/GraphMol/MolDraw2D/MolDraw2DUtils.h
 include/rdkit/GraphMol/MolDraw2D/MolDraw2Dwx.h
+include/rdkit/GraphMol/MolEnumerator/LinkNode.h
 include/rdkit/GraphMol/MolEnumerator/MolEnumerator.h
 include/rdkit/GraphMol/MolHash/MolHash.h
 include/rdkit/GraphMol/MolHash/nmmolhash.h
@@ -293,6 +295,7 @@ include/rdkit/RDGeneral/Invariant.h
 include/rdkit/RDGeneral/LocaleSwitcher.h
 include/rdkit/RDGeneral/RDAny.h
 include/rdkit/RDGeneral/RDConfig.h
+include/rdkit/RDGeneral/RDExportMacros.h
 include/rdkit/RDGeneral/RDLog.h
 include/rdkit/RDGeneral/RDProps.h
 include/rdkit/RDGeneral/RDThreads.h
@@ -481,6 +484,9 @@ lib/libRDKitTautomerQuery.so.1.%%SHLIB_VER%%
 lib/libRDKitTrajectory.so
 lib/libRDKitTrajectory.so.1
 lib/libRDKitTrajectory.so.1.%%SHLIB_VER%%
+lib/libRDKitga.so
+lib/libRDKitga.so.1
+lib/libRDKitga.so.1.%%SHLIB_VER%%
 %%LITTLE_ENDIAN%%lib/libRDKithc.so
 %%LITTLE_ENDIAN%%lib/libRDKithc.so.1
 %%LITTLE_ENDIAN%%lib/libRDKithc.so.1.%%SHLIB_VER%%
@@ -940,6 +946,44 @@ lib/libRDKitTrajectory.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/utils/test3.gif
 %%DATADIR%%/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py
 %%DATADIR%%/Contrib/CMakeLists.txt
+%%DATADIR%%/Contrib/CalcLigRMSD/CalcLigRMSD.py
+%%DATADIR%%/Contrib/CalcLigRMSD/Examples_CalcLigRMSD.ipynb
+%%DATADIR%%/Contrib/CalcLigRMSD/README.md
+%%DATADIR%%/Contrib/CalcLigRMSD/data/1C9_renamed.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/3m11_AKI.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/3w2c_N15.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/4i23_1C9.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/4i24_1C9.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/4uzh_JVE.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/5dpv.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/5dt0.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/6c83.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_1.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/ACP_renamed.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/AKI_renamed.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/BEG_test.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/JVE_renamed.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/N15_renamed.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/SKE_crystal_aligned_1.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/SKE_renamed.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/crystal_aligned.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/data/lig_crystal_aligned.pdb
+%%DATADIR%%/Contrib/CalcLigRMSD/figures/1C9.png
+%%DATADIR%%/Contrib/CalcLigRMSD/figures/5dpv_complex.png
+%%DATADIR%%/Contrib/CalcLigRMSD/figures/6c83_complex.png
+%%DATADIR%%/Contrib/CalcLigRMSD/figures/AKI.png
+%%DATADIR%%/Contrib/CalcLigRMSD/figures/BEG.png
+%%DATADIR%%/Contrib/CalcLigRMSD/figures/JVE.png
+%%DATADIR%%/Contrib/CalcLigRMSD/figures/N15.png
 %%DATADIR%%/Contrib/ChiralPairs/ChiralDescriptors.py
 %%DATADIR%%/Contrib/ChiralPairs/README.txt
 %%DATADIR%%/Contrib/ConformerParser/CMakeLists.txt
@@ -975,6 +1019,13 @@ lib/libRDKitTrajectory.so.1.%%SHLIB_VER%%
 %%DATADIR%%/Contrib/M_Kossner/Frames.py
 %%DATADIR%%/Contrib/M_Kossner/README
 %%DATADIR%%/Contrib/MolVS/molvs_cli.py
+%%DATADIR%%/Contrib/NIBRSubstructureFilters/FilterSet_NIBR2019_wPubChemExamples.html
+%%DATADIR%%/Contrib/NIBRSubstructureFilters/README.md
+%%DATADIR%%/Contrib/NIBRSubstructureFilters/SubstructureFilter_HitTriaging_wPubChemExamples.csv
+%%DATADIR%%/Contrib/NIBRSubstructureFilters/assignSubstructureFilters.py
+%%DATADIR%%/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100.csv
+%%DATADIR%%/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100_out.csv
+%%DATADIR%%/Contrib/NIBRSubstructureFilters/filterExamples.png
 %%DATADIR%%/Contrib/NP_Score/README
 %%DATADIR%%/Contrib/NP_Score/npscorer.py
 %%DATADIR%%/Contrib/NP_Score/publicnp.model.gz
@@ -1047,6 +1098,13 @@ lib/libRDKitTrajectory.so.1.%%SHLIB_VER%%
 %%DATADIR%%/Data/DTDs/RD_Model.dtd
 %%DATADIR%%/Data/DTDs/validate.py
 %%DATADIR%%/Data/Fonts/Amadeus.ttf
+%%DATADIR%%/Data/Fonts/ComicNeue-Bold.ttf
+%%DATADIR%%/Data/Fonts/ComicNeue-BoldItalic.ttf
+%%DATADIR%%/Data/Fonts/ComicNeue-Italic.ttf
+%%DATADIR%%/Data/Fonts/ComicNeue-Light.ttf
+%%DATADIR%%/Data/Fonts/ComicNeue-LightItalic.ttf
+%%DATADIR%%/Data/Fonts/ComicNeue-Regular.ttf
+%%DATADIR%%/Data/Fonts/OFL.txt
 %%DATADIR%%/Data/Fonts/Telex-Regular.ttf
 %%DATADIR%%/Data/Fonts/amadeus_font_license.txt
 %%DATADIR%%/Data/Fonts/telex_font_license.txt