science/rdkit: Update 2018_03_4 -> 2018_09_1

Approved by:	portscout

5 files changed, 90 insertions, 16 deletions

diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile
index 937ad122fc1a..c903ca89b0b2 100644
--- a/science/rdkit/Makefile
+++ b/science/rdkit/Makefile
@@ -2,7 +2,7 @@
 
 PORTNAME=	rdkit
 DISTVERSIONPREFIX=	Release_
-DISTVERSION=	2018_03_4
+DISTVERSION=	2018_09_1
 CATEGORIES=	science
 
 MAINTAINER=	yuri@FreeBSD.org
@@ -11,7 +11,8 @@ COMMENT=	Collection of cheminformatics and machine-learning software
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/license.txt
 
-BUILD_DEPENDS=	flex:textproc/flex \
+BUILD_DEPENDS=	catch>0:devel/catch \
+		flex:textproc/flex \
 		rapidjson>=0:devel/rapidjson
 LIB_DEPENDS=	libboost_system.so:devel/boost-libs
 
@@ -23,7 +24,7 @@ USE_LDCONFIG=	yes
 
 CMAKE_OFF=	RDK_INSTALL_INTREE RDK_USE_FLEXBISON \
 		RDK_INSTALL_STATIC_LIBS RDK_SWIG_STATIC RDK_PGSQL_STATIC
-CMAKE_ARGS=	-DFREEBSD_DOCSDIR:PATH=${DOCSDIR}
+CMAKE_ARGS=	-DFREEBSD_DOCSDIR:PATH=${DOCSDIR} -DCATCH_DIR=${LOCALBASE}
 
 DATADIR=	${PREFIX}/share/RDKit
 DOCSDIR=	${PREFIX}/share/doc/RDKit
@@ -48,4 +49,8 @@ post-extract:
 	@${MKDIR} ${WRKSRC}/External/rapidjson-1.1.0
 	@cd ${WRKSRC}/External/rapidjson-1.1.0 && ${LN} -s ${LOCALBASE}/include/rapidjson include
 
+post-stage: # https://github.com/rdkit/rdkit/issues/2094
+	#@${MKDIR} ${STAGEDIR}${PREFIX}/lib/cmake
+	#@${MV} ${STAGEDIR}${PREFIX}/lib/*.cmake ${STAGEDIR}${PREFIX}/lib/cmake
+
 .include <bsd.port.mk>
diff --git a/science/rdkit/distinfo b/science/rdkit/distinfo
index a9945215c64b..4cf1a71cbf08 100644
--- a/science/rdkit/distinfo
+++ b/science/rdkit/distinfo
@@ -1,6 +1,6 @@
-TIMESTAMP = 1534554734
-SHA256 (rdkit-rdkit-Release_2018_03_4_GH0.tar.gz) = 9e1a63f3b8c64b9754416073a20292ea79d33ac8aa1485259df1b8db2bfa0113
-SIZE (rdkit-rdkit-Release_2018_03_4_GH0.tar.gz) = 30304198
+TIMESTAMP = 1540446187
+SHA256 (rdkit-rdkit-Release_2018_09_1_GH0.tar.gz) = 61c14652a05a6f6b216ff099381c4dd32048861ba9d96f75a017084e81848baa
+SIZE (rdkit-rdkit-Release_2018_09_1_GH0.tar.gz) = 54640418
 SHA256 (schrodinger-maeparser-1.0.0_GH0.tar.gz) = f21e49d25fda5fb2ba4d698f104aa3fbfdd131d92f0807f3e617c15ebfc314aa
 SIZE (schrodinger-maeparser-1.0.0_GH0.tar.gz) = 26292
 SHA256 (schrodinger-coordgenlibs-ede3191_GH0.tar.gz) = 85b1ab66647a523a87bee584533fa81315ea82fde42542aa59e1e08bdf734471
diff --git a/science/rdkit/files/patch-CMakeLists.txt b/science/rdkit/files/patch-CMakeLists.txt
index f8281f7a554f..8a8804edd64f 100644
--- a/science/rdkit/files/patch-CMakeLists.txt
+++ b/science/rdkit/files/patch-CMakeLists.txt
@@ -1,6 +1,6 @@
---- CMakeLists.txt.orig	2018-03-22 06:56:06 UTC
+--- CMakeLists.txt.orig	2018-10-22 02:29:34 UTC
 +++ CMakeLists.txt
-@@ -338,7 +338,7 @@ if(NOT RDK_INSTALL_INTREE)
+@@ -410,7 +410,7 @@ if(NOT RDK_INSTALL_INTREE)
        PATTERN ".svn" EXCLUDE
        )
    install(DIRECTORY Docs DESTINATION
diff --git a/science/rdkit/files/patch-External_catch_CMakeLists.txt b/science/rdkit/files/patch-External_catch_CMakeLists.txt
new file mode 100644
index 000000000000..a3040cbed672
--- /dev/null
+++ b/science/rdkit/files/patch-External_catch_CMakeLists.txt
@@ -0,0 +1,17 @@
+--- External/catch/CMakeLists.txt.orig	2018-10-22 02:29:34 UTC
++++ External/catch/CMakeLists.txt
+@@ -3,7 +3,7 @@ add_custom_target(catch ALL)
+ if(NOT DEFINED CATCH_DIR)
+   set(CATCH_DIR "${CMAKE_CURRENT_SOURCE_DIR}/catch")
+ endif()
+-if(NOT EXISTS "${CATCH_DIR}/single_include")
++if(NOT EXISTS "${CATCH_DIR}/include/catch2")
+     include(RDKitUtils)
+     set(RELEASE_NO "2.1.2")
+     downloadAndCheckMD5("https://github.com/catchorg/Catch2/archive/v${RELEASE_NO}.tar.gz"
+@@ -17,4 +17,4 @@ else()
+   message("-- Found Catch2 source in ${CATCH_DIR}")
+ endif()
+ 
+-set(CATCH_INCLUDE_DIR "${CATCH_DIR}/single_include" PARENT_SCOPE)
++set(CATCH_INCLUDE_DIR "${CATCH_DIR}/include/catch2" PARENT_SCOPE)
diff --git a/science/rdkit/pkg-plist b/science/rdkit/pkg-plist
index 73dbd246e98e..696ac2f6e051 100644
--- a/science/rdkit/pkg-plist
+++ b/science/rdkit/pkg-plist
@@ -92,6 +92,7 @@ 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/EEM.h
 include/rdkit/GraphMol/Descriptors/GETAWAY.h
 include/rdkit/GraphMol/Descriptors/Lipinski.h
 include/rdkit/GraphMol/Descriptors/MORSE.h
@@ -130,10 +131,16 @@ 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/AtomPairGenerator.h
 include/rdkit/GraphMol/Fingerprints/AtomPairs.h
+include/rdkit/GraphMol/Fingerprints/FingerprintGenerator.h
+include/rdkit/GraphMol/Fingerprints/FingerprintUtil.h
 include/rdkit/GraphMol/Fingerprints/Fingerprints.h
 include/rdkit/GraphMol/Fingerprints/MACCS.h
 include/rdkit/GraphMol/Fingerprints/MorganFingerprints.h
+include/rdkit/GraphMol/Fingerprints/MorganGenerator.h
+include/rdkit/GraphMol/Fingerprints/RDKitFPGenerator.h
+include/rdkit/GraphMol/Fingerprints/TopologicalTorsionGenerator.h
 include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h
 include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h
 include/rdkit/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h
@@ -164,14 +171,30 @@ include/rdkit/GraphMol/MolDraw2D/MolDraw2DDetails.h
 include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h
 include/rdkit/GraphMol/MolDraw2D/MolDraw2DUtils.h
 include/rdkit/GraphMol/MolDraw2D/MolDraw2Dwx.h
-include/rdkit/GraphMol/MolDrawing/DrawingToCairo.h
-include/rdkit/GraphMol/MolDrawing/DrawingToSVG.h
-include/rdkit/GraphMol/MolDrawing/MolDrawing.h
 include/rdkit/GraphMol/MolHash/MolHash.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/MolStandardize/AcidBaseCatalogEntry.h
+include/rdkit/GraphMol/MolStandardize/AcidBaseCatalogParams.h
+include/rdkit/GraphMol/MolStandardize/AcidBaseCatalogUtils.h
+include/rdkit/GraphMol/MolStandardize/Charge.h
+include/rdkit/GraphMol/MolStandardize/Fragment.h
+include/rdkit/GraphMol/MolStandardize/FragmentCatalogEntry.h
+include/rdkit/GraphMol/MolStandardize/FragmentCatalogParams.h
+include/rdkit/GraphMol/MolStandardize/FragmentCatalogUtils.h
+include/rdkit/GraphMol/MolStandardize/Metal.h
+include/rdkit/GraphMol/MolStandardize/MolStandardize.h
+include/rdkit/GraphMol/MolStandardize/Normalize.h
+include/rdkit/GraphMol/MolStandardize/Tautomer.h
+include/rdkit/GraphMol/MolStandardize/TautomerCatalogEntry.h
+include/rdkit/GraphMol/MolStandardize/TautomerCatalogParams.h
+include/rdkit/GraphMol/MolStandardize/TautomerCatalogUtils.h
+include/rdkit/GraphMol/MolStandardize/TransformCatalogEntry.h
+include/rdkit/GraphMol/MolStandardize/TransformCatalogParams.h
+include/rdkit/GraphMol/MolStandardize/TransformCatalogUtils.h
+include/rdkit/GraphMol/MolStandardize/Validate.h
 include/rdkit/GraphMol/MolTransforms/MolTransforms.h
 include/rdkit/GraphMol/MonomerInfo.h
 include/rdkit/GraphMol/PartialCharges/GasteigerCharges.h
@@ -200,6 +223,7 @@ 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/StructChecker/Pattern.h
 include/rdkit/GraphMol/StructChecker/ReCharge.h
 include/rdkit/GraphMol/StructChecker/Stereo.h
@@ -251,6 +275,7 @@ include/rdkit/RDGeneral/FileParseException.h
 include/rdkit/RDGeneral/Invariant.h
 include/rdkit/RDGeneral/LocaleSwitcher.h
 include/rdkit/RDGeneral/RDAny.h
+include/rdkit/RDGeneral/RDConfig.h
 include/rdkit/RDGeneral/RDLog.h
 include/rdkit/RDGeneral/RDProps.h
 include/rdkit/RDGeneral/RDThreads.h
@@ -259,18 +284,24 @@ include/rdkit/RDGeneral/RDValue-taggedunion.h
 include/rdkit/RDGeneral/RDValue.h
 include/rdkit/RDGeneral/Ranking.h
 include/rdkit/RDGeneral/StreamOps.h
+include/rdkit/RDGeneral/export.h
 include/rdkit/RDGeneral/hanoiSort.h
 include/rdkit/RDGeneral/hash/hash/detail/float_functions.hpp
 include/rdkit/RDGeneral/hash/hash/detail/hash_float.hpp
 include/rdkit/RDGeneral/hash/hash/extensions.hpp
 include/rdkit/RDGeneral/hash/hash/hash.hpp
 include/rdkit/RDGeneral/hash/hash/hash_fwd.hpp
+include/rdkit/RDGeneral/test.h
 include/rdkit/RDGeneral/types.h
 include/rdkit/RDGeneral/utils.h
 include/rdkit/RDGeneral/versions.h
 include/rdkit/SimDivPickers/DistPicker.h
 include/rdkit/SimDivPickers/HierarchicalClusterPicker.h
 include/rdkit/SimDivPickers/MaxMinPicker.h
+lib/cmake/rdkit/rdkit-config-version.cmake
+lib/cmake/rdkit/rdkit-config.cmake
+lib/cmake/rdkit/rdkit-targets-%%CMAKE_BUILD_TYPE%%.cmake
+lib/cmake/rdkit/rdkit-targets.cmake
 lib/libRDKitAlignment.so
 lib/libRDKitAlignment.so.1
 lib/libRDKitAlignment.so.1.%%SHLIB_VER%%
@@ -352,6 +383,9 @@ lib/libRDKitMolHash.so.1.%%SHLIB_VER%%
 lib/libRDKitMolInterchange.so
 lib/libRDKitMolInterchange.so.1
 lib/libRDKitMolInterchange.so.1.%%SHLIB_VER%%
+lib/libRDKitMolStandardize.so
+lib/libRDKitMolStandardize.so.1
+lib/libRDKitMolStandardize.so.1.%%SHLIB_VER%%
 lib/libRDKitMolTransforms.so
 lib/libRDKitMolTransforms.so.1
 lib/libRDKitMolTransforms.so.1.%%SHLIB_VER%%
@@ -489,6 +523,19 @@ lib/libRDKitmaeparser.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolKey/InchiInfo.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolKey/MolKey.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolKey/__init__.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/__init__.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/charge.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/errors.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/fragment.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/metal.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/normalize.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/rdMolStandardize.so
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/resonance.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/standardize.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/tautomer.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/utils.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/validate.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/validations.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolSurf.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/PandasTools.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/PeriodicTable.py
@@ -538,6 +585,7 @@ lib/libRDKitmaeparser.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdDepictor.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdDistGeom.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdFMCS.so
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdFingerprintGenerator.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdForceFieldHelpers.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMMPA.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolAlign.so
@@ -696,7 +744,6 @@ lib/libRDKitmaeparser.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/VLib/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/__init__.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/_py2_pickle.py
-%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/epydoc.config
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/rdBase.so
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/six.py
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/sping/PDF/__init__.py
@@ -847,12 +894,10 @@ lib/libRDKitmaeparser.so.1.%%SHLIB_VER%%
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/utils/test1.gif
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/utils/test2.gif
 %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/utils/test3.gif
-lib/rdkit-config-version.cmake
-lib/rdkit-config.cmake
-lib/rdkit-targets-%%CMAKE_BUILD_TYPE%%.cmake
-lib/rdkit-targets.cmake
 %%DATADIR%%/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py
 %%DATADIR%%/Contrib/CMakeLists.txt
+%%DATADIR%%/Contrib/ChiralPairs/ChiralDescriptors.py
+%%DATADIR%%/Contrib/ChiralPairs/README.txt
 %%DATADIR%%/Contrib/ConformerParser/CMakeLists.txt
 %%DATADIR%%/Contrib/ConformerParser/ConformerParser.cpp
 %%DATADIR%%/Contrib/ConformerParser/ConformerParser.h
@@ -885,6 +930,7 @@ lib/rdkit-targets.cmake
 %%DATADIR%%/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef
 %%DATADIR%%/Contrib/M_Kossner/Frames.py
 %%DATADIR%%/Contrib/M_Kossner/README
+%%DATADIR%%/Contrib/MolVS/molvs_cli.py
 %%DATADIR%%/Contrib/NP_Score/README
 %%DATADIR%%/Contrib/NP_Score/npscorer.py
 %%DATADIR%%/Contrib/NP_Score/publicnp.model.gz
@@ -959,6 +1005,11 @@ lib/rdkit-targets.cmake
 %%DATADIR%%/Data/FragmentDescriptors.csv
 %%DATADIR%%/Data/FunctionalGroups.txt
 %%DATADIR%%/Data/Functional_Group_Hierarchy.txt
+%%DATADIR%%/Data/MolStandardize/acid_base_pairs.txt
+%%DATADIR%%/Data/MolStandardize/acid_base_pairs2.txt
+%%DATADIR%%/Data/MolStandardize/fragmentPatterns.txt
+%%DATADIR%%/Data/MolStandardize/normalizations.txt
+%%DATADIR%%/Data/MolStandardize/tautomerTransforms.in
 %%DATADIR%%/Data/NCI/first_200.props.sdf
 %%DATADIR%%/Data/NCI/first_200.tpsa.csv
 %%DATADIR%%/Data/NCI/first_5K.smi
@@ -995,4 +1046,5 @@ lib/rdkit-targets.cmake
 %%PYTHON%%%%DATADIR%%/Scripts/FeatFinderCLI.py
 %%PYTHON%%%%DATADIR%%/Scripts/PythonFormat.py
 %%PYTHON%%%%DATADIR%%/Scripts/README.md
+%%PYTHON%%%%DATADIR%%/Scripts/create_deb_packages.sh
 %%DATADIR%%/license.txt