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https://github.com/rdkit/rdkit.git
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update to coordgen 2.0.0 (#3974)
change option name for setTreatAllBondsToMetalAsZOBs update expected minimizeOnly output (note: these new results don't look great)
This commit is contained in:
Greg Landrum
GitHub
13
External/CoordGen/CMakeLists.txt
vendored
13
External/CoordGen/CMakeLists.txt
vendored
@@ -82,8 +82,8 @@ if(RDK_BUILD_COORDGEN_SUPPORT)
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endif()
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if(NOT EXISTS "${COORDGEN_DIR}/sketcherMinimizer.h")
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set(RELEASE_NO "1.4.2")
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set(MD5 "47aa5fe6d8186b6c8d3b871d4400218a")
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set(RELEASE_NO "2.0.0")
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set(MD5 "d819cacd84b4938f49c0d5b486fcb653")
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downloadAndCheckMD5("https://github.com/schrodinger/coordgenlibs/archive/v${RELEASE_NO}.tar.gz"
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"${CMAKE_CURRENT_SOURCE_DIR}/coordgenlibs-${RELEASE_NO}.tar.gz" ${MD5})
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execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
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@@ -91,15 +91,6 @@ if(RDK_BUILD_COORDGEN_SUPPORT)
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WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
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file(RENAME "coordgenlibs-${RELEASE_NO}" "${COORDGEN_DIR}")
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# # FIX: this is a workaround until https://github.com/schrodinger/coordgenlibs/pull/76
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# # is merged and a new coordgen release is done
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# set(fileToPatch "${COORDGEN_DIR}/CoordgenFragmenter.h")
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# configure_file("${fileToPatch}" "${fileToPatch}.orig" COPYONLY)
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# file(READ "${fileToPatch}" buffer)
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# string(REPLACE "class CoordgenFragmenter"
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# "#include \"CoordgenConfig.hpp\"\nclass EXPORT_COORDGEN CoordgenFragmenter"
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# buffer "${buffer}")
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# file(WRITE "${fileToPatch}" "${buffer}")
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else()
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message("-- Found coordgenlibs source in ${COORDGEN_DIR}")
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endif()
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7
External/CoordGen/CoordGen.h
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7
External/CoordGen/CoordGen.h
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@@ -38,8 +38,8 @@ struct CoordGenParams {
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bool dbg_useConstrained = true; // debugging
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bool dbg_useFixed = false; // debugging
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bool minimizeOnly = false; // don't actually generate full coords
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bool treatBondsToMetalAsZeroOrder =
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false; // set all bonds to metal atoms to be zero-order bonds
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bool treatNonterminalBondsToMetalAsZeroOrder =
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false; // set non-terminal bonds to metal atoms to be zero-order bonds
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};
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static CoordGenParams defaultParams;
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@@ -77,7 +77,8 @@ unsigned int addCoords(T& mol, const CoordGenParams* params = nullptr) {
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sketcherMinimizer minimizer(params->minimizerPrecision);
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auto min_mol = new sketcherMinimizerMolecule();
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minimizer.setTreatAllBondsToMetalAsZOBs(params->treatBondsToMetalAsZeroOrder);
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minimizer.setTreatNonterminalBondsToMetalAsZOBs(
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params->treatNonterminalBondsToMetalAsZeroOrder);
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// FIX: only do this check once.
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// std::cerr << " TEMPLATES: " << templateFileDir << std::endl;
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5
External/CoordGen/Wrap/rdCoordGen.cpp
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5
External/CoordGen/Wrap/rdCoordGen.cpp
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@@ -91,8 +91,9 @@ struct coordgen_wrapper {
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.def_readwrite("minimizerPrecision",
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&CoordGen::CoordGenParams::minimizerPrecision,
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"controls sketcher precision")
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.def_readwrite("treatBondsToMetalAsZOBs",
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&CoordGen::CoordGenParams::treatBondsToMetalAsZeroOrder);
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.def_readwrite(
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"treatNonterminalBondsToMetalAsZOBs",
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&CoordGen::CoordGenParams::treatNonterminalBondsToMetalAsZeroOrder);
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python::def("SetDefaultTemplateFileDir", SetDefaultTemplateFileDir);
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docString =
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"Add 2D coordinates.\n"
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100
External/CoordGen/Wrap/testCoordGen.py
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100
External/CoordGen/Wrap/testCoordGen.py
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@@ -79,65 +79,58 @@ class TestCase(unittest.TestCase) :
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def testMinimizeOnly(self):
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m = Chem.MolFromMolBlock('''
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Mrv2014 08052005392D
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Mrv2014 03252113022D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 14 15 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -1.4287 -1.4523 0 0
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M V30 2 C -2.9638 -1.5752 0 0
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M V30 3 C -3.8377 -0.3072 0 0
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M V30 4 C -3.1766 1.0837 0 0
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M V30 5 C -1.6416 1.2066 0 0
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M V30 6 C -0.7675 -0.0614 0 0
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M V30 7 C 0.7675 0.0614 0 0
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M V30 8 C 1.6416 -1.2066 0 0
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M V30 9 C 0.9804 -2.5975 0 0
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M V30 10 N 3.1766 -1.0837 0 0
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M V30 11 C 3.8377 0.3072 0 0
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M V30 12 C 2.9638 1.5752 0 0
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M V30 13 C 1.4287 1.4523 0 0
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M V30 14 F -0.5548 -2.7203 0 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 2 1 2
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M V30 2 1 2 3
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M V30 3 2 3 4
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M V30 4 1 4 5
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M V30 5 2 5 6
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M V30 6 1 6 7
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M V30 7 2 7 8
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M V30 8 1 8 9
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M V30 9 1 8 10
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M V30 10 2 10 11
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M V30 11 1 11 12
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M V30 12 2 12 13
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M V30 13 1 6 1
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M V30 14 1 13 7
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M V30 15 1 1 14
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M V30 END BOND
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M V30 END CTAB
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14 15 0 0 0 0 999 V2000
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-0.7654 -0.7780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.5877 -0.8439 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.0559 -0.1646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.7017 0.5805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.8794 0.6464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.4112 -0.0329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.4112 0.0329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.8794 -0.6464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.7771 -1.4237 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.7017 -0.5805 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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2.0559 0.1646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.5877 0.8439 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.7654 0.7780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.7654 -1.6519 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 2 0 0 0 0
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2 3 1 0 0 0 0
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3 4 2 0 0 0 0
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4 5 1 0 0 0 0
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5 6 2 0 0 0 0
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6 7 1 0 0 0 0
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7 8 2 0 0 0 0
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8 9 1 0 0 0 0
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8 10 1 0 0 0 0
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10 11 2 0 0 0 0
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11 12 1 0 0 0 0
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12 13 2 0 0 0 0
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6 1 1 0 0 0 0
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13 7 1 0 0 0 0
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1 14 1 0 0 0 0
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M END
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''')
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ref = Chem.MolFromMolBlock('''
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RDKit 2D
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14 15 0 0 0 0 0 0 0 0999 V2000
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-1.5379 -1.4859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-3.1218 -1.5958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-3.9595 -0.2554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-3.2641 1.1663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.6778 1.2217 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.7941 -0.0886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.7983 0.0383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.7524 -1.2209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.1246 -2.6443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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3.3306 -1.0787 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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3.9439 0.3747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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3.0337 1.6656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.4617 1.4692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.6924 -2.7917 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
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-0.5957 -0.8221 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.4185 -0.8441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.8520 -0.1434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.4595 0.5814 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.6368 0.6072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.2063 -0.0955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.2087 -0.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.7102 -0.7158 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.4040 -1.4774 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.5259 -0.6099 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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1.8401 0.1516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.3405 0.8062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.5252 0.6981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.1735 -1.5240 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 2 0
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2 3 1 0
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3 4 2 0
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@@ -153,7 +146,8 @@ M END
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6 1 1 0
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13 7 1 0
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1 14 1 0
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M END''')
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M END
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''')
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ps = rdCoordGen.CoordGenParams()
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ps.minimizeOnly = True
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m2 = Chem.Mol(m)
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2
External/CoordGen/test.cpp
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2
External/CoordGen/test.cpp
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@@ -607,7 +607,7 @@ M END
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}
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CoordGen::CoordGenParams ps;
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ps.treatBondsToMetalAsZeroOrder = true;
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ps.treatNonterminalBondsToMetalAsZeroOrder = true;
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CoordGen::addCoords(*m1, &ps);
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{
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// the ZOB behavior screws up the double bond stereo here... detect that
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