// // Copyright (C) 2020-2025 Greg Landrum and other RDKit contributors // @@ All Rights Reserved @@ // This file is part of the RDKit. // The contents are covered by the terms of the BSD license // which is included in the file license.txt, found at the root // of the RDKit source tree. // #include #include #include #include #include #include "RDGeneral/test.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include using namespace RDKit; TEST_CASE("Basic SVG Parsing", "[SVG][reader]") { SECTION("basics") { std::string svg = R"SVG( NH Cl O OH m1 )SVG"; std::unique_ptr mol(RDKitSVGToMol(svg)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 7); CHECK(mol->getNumConformers() == 1); CHECK_FALSE(mol->getConformer().is3D()); auto smiles = MolToSmiles(*mol); CHECK(smiles == "CN[C@H](Cl)C(=O)O"); } } TEST_CASE( "Github #2040: Failure to parse V3K mol file with bonds to multi-center " "linkage points", "[bug][reader]") { std::string rdbase = getenv("RDBASE"); SECTION("basics") { std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/github2040_1.mol"; std::unique_ptr mol( MolFileToMol(fName, false)); // don't sanitize yet REQUIRE(mol); CHECK(mol->getBondWithIdx(0)->getBondType() == Bond::SINGLE); CHECK( mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondEndPts)); CHECK(mol->getBondWithIdx(0)->getProp( common_properties::_MolFileBondEndPts) == "(3 5 4 3)"); CHECK( mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondAttach)); CHECK(mol->getBondWithIdx(0)->getProp( common_properties::_MolFileBondAttach) == "ANY"); CHECK(mol->getBondWithIdx(1)->getBondType() == Bond::AROMATIC); } } TEST_CASE("Github #2225: failure round-tripping mol block with Q atoms", "[bug][writer]") { std::string rdbase = getenv("RDBASE"); SECTION("basics") { std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/github2225_1.mol"; std::unique_ptr mol(MolFileToMol(fName)); REQUIRE(mol); REQUIRE(mol->getNumAtoms() == 7); REQUIRE(!mol->getAtomWithIdx(0)->hasQuery()); REQUIRE(mol->getAtomWithIdx(6)->hasQuery()); auto outBlock = MolToMolBlock(*mol); REQUIRE(outBlock.find(" Q ") != std::string::npos); REQUIRE(outBlock.find(" ALS ") == std::string::npos); std::unique_ptr mol2(MolBlockToMol(outBlock)); REQUIRE(mol2); REQUIRE(mol2->getNumAtoms() == 7); REQUIRE(!mol2->getAtomWithIdx(0)->hasQuery()); REQUIRE(mol2->getAtomWithIdx(6)->hasQuery()); auto outBlock2 = MolToMolBlock(*mol2); REQUIRE(outBlock2.find(" Q ") != std::string::npos); REQUIRE(outBlock2.find(" ALS ") == std::string::npos); } SECTION("check that SMARTS still works") { std::unique_ptr mol(SmartsToMol("C[#8,#7]")); REQUIRE(mol); REQUIRE(mol->getNumAtoms() == 2); auto outBlock = MolToMolBlock(*mol); REQUIRE(outBlock.find(" Q ") == std::string::npos); REQUIRE(outBlock.find(" ALS ") != std::string::npos); std::unique_ptr mol2(MolBlockToMol(outBlock)); REQUIRE(mol2); auto smarts = MolToSmarts(*mol2); REQUIRE(smarts == "[#6][#8,#7]"); } SECTION("basics with v3K") { std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/github2225_2.mol"; std::unique_ptr mol(MolFileToMol(fName)); REQUIRE(mol); REQUIRE(mol->getNumAtoms() == 7); REQUIRE(!mol->getAtomWithIdx(0)->hasQuery()); REQUIRE(mol->getAtomWithIdx(6)->hasQuery()); bool includeStereo = true; int confId = -1; bool kekulize = true; bool forceV3000 = true; auto outBlock = MolToMolBlock(*mol, includeStereo, confId, kekulize, forceV3000); REQUIRE(outBlock.find(" Q ") != std::string::npos); REQUIRE(outBlock.find(" ALS ") == std::string::npos); std::unique_ptr mol2(MolBlockToMol(outBlock)); REQUIRE(mol2); REQUIRE(mol2->getNumAtoms() == 7); REQUIRE(!mol2->getAtomWithIdx(0)->hasQuery()); REQUIRE(mol2->getAtomWithIdx(6)->hasQuery()); auto outBlock2 = MolToMolBlock(*mol2, includeStereo, confId, kekulize, forceV3000); REQUIRE(outBlock2.find(" Q ") != std::string::npos); REQUIRE(outBlock2.find(" ALS ") == std::string::npos); } SECTION("check that SMARTS still works with v3K output") { std::unique_ptr mol(SmartsToMol("C[#8,#7]")); REQUIRE(mol); REQUIRE(mol->getNumAtoms() == 2); bool includeStereo = true; int confId = -1; bool kekulize = true; bool forceV3000 = true; auto outBlock = MolToMolBlock(*mol, includeStereo, confId, kekulize, forceV3000); REQUIRE(outBlock.find(" Q ") == std::string::npos); REQUIRE(outBlock.find(" [O,N] ") != std::string::npos); std::unique_ptr mol2(MolBlockToMol(outBlock)); REQUIRE(mol2); auto smarts = MolToSmarts(*mol2); REQUIRE(smarts == "[#6][#8,#7]"); } } TEST_CASE( "Github #2229: problem round-tripping mol files with bond topology info", "[bug][writer]") { std::string rdbase = getenv("RDBASE"); std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/github2229_1.mol"; std::unique_ptr mol(MolFileToMol(fName)); REQUIRE(mol); REQUIRE(mol->getNumBonds() == 9); REQUIRE(!mol->getBondWithIdx(0)->hasQuery()); REQUIRE(mol->getBondWithIdx(7)->hasQuery()); SECTION("basics") { auto outBlock = MolToMolBlock(*mol); REQUIRE(outBlock.find(" 7 8 1 0 0 2") != std::string::npos); std::unique_ptr mol2(MolBlockToMol(outBlock)); REQUIRE(mol2); REQUIRE(mol2->getNumBonds() == 9); REQUIRE(!mol2->getBondWithIdx(0)->hasQuery()); REQUIRE(mol2->getBondWithIdx(7)->hasQuery()); } SECTION("basics with v3k") { bool includeStereo = true; int confId = -1; bool kekulize = true; bool forceV3000 = true; auto outBlock = MolToMolBlock(*mol, includeStereo, confId, kekulize, forceV3000); REQUIRE(outBlock.find("1 7 8 TOPO=2") != std::string::npos); std::unique_ptr mol2(MolBlockToMol(outBlock)); REQUIRE(mol2); REQUIRE(mol2->getNumBonds() == 9); REQUIRE(!mol2->getBondWithIdx(0)->hasQuery()); REQUIRE(mol2->getBondWithIdx(7)->hasQuery()); } } TEST_CASE("preserve mol file properties on bonds", "[reader][ctab]") { SECTION("basics") { std::string molblock = R"CTAB( Mrv1810 02111915042D 4 3 0 0 0 0 999 V2000 -1.5625 1.6071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8480 2.0196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2770 2.0196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5625 0.7821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 0 0 0 1 2 6 0 0 0 0 1 4 1 1 0 0 0 M END )CTAB"; std::unique_ptr mol(MolBlockToMol(molblock)); REQUIRE(mol); CHECK(mol->getBondWithIdx(1)->getProp( common_properties::_MolFileBondType) == 6); CHECK(mol->getBondWithIdx(2)->getProp( common_properties::_MolFileBondType) == 1); CHECK(mol->getBondWithIdx(2)->getProp( common_properties::_MolFileBondStereo) == 1); } SECTION("basics-v3k") { std::string molblock = R"CTAB( Mrv1810 02111915102D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 4 3 0 0 0 M V30 BEGIN ATOM M V30 1 C -2.9167 3 0 0 M V30 2 C -1.583 3.77 0 0 M V30 3 C -4.2503 3.77 0 0 M V30 4 C -2.9167 1.46 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 3 M V30 2 6 1 2 M V30 3 1 1 4 CFG=1 M V30 END BOND M V30 END CTAB M END )CTAB"; std::unique_ptr mol(MolBlockToMol(molblock)); REQUIRE(mol); CHECK(mol->getBondWithIdx(1)->getProp( common_properties::_MolFileBondType) == 6); CHECK(mol->getBondWithIdx(2)->getProp( common_properties::_MolFileBondType) == 1); CHECK(mol->getBondWithIdx(2)->getProp( common_properties::_MolFileBondCfg) == 1); } } TEST_CASE("github #2277 : Failure when parsing mol block with M PXA", "[reader][ctab]") { std::string molblock = R"CTAB( Mrv1810 02151911552D 13 12 0 0 1 0 999 V2000 -3.6588 -26.0592 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9453 -27.2971 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9453 -26.4713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6588 -25.2360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9467 -24.8200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9467 -23.9968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2304 -25.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5102 -26.4716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7989 -25.2306 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7989 -26.0582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3730 -26.4732 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.2277 -26.0635 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.0839 -26.4708 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 0 0 0 3 2 2 0 0 0 0 1 4 1 1 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 8 10 1 0 0 0 0 10 9 2 0 0 0 0 3 12 1 0 0 0 0 12 8 1 0 0 0 0 11 1 1 0 0 0 0 10 13 1 0 0 0 0 M PXA 11 -5.0817 -26.0408 0.0000 H M END )CTAB"; std::unique_ptr mol(MolBlockToMol(molblock)); SECTION("basics, make sure we can parse the original data") { REQUIRE(mol); CHECK(mol->getAtomWithIdx(10)->hasProp("_MolFile_PXA")); CHECK(!mol->getAtomWithIdx(11)->hasProp("_MolFile_PXA")); } SECTION("basics, can we write it?") { REQUIRE(mol); std::string outmb = MolToMolBlock(*mol); CHECK(outmb.find("M PXA 11") != std::string::npos); } } TEST_CASE( "github #2266: missing stereo in adamantyl-like cages with " "exocyclic bonds", "[bug]") { SECTION("basics") { std::string molblock = R"CTAB( SciTegic12231509382D 14 16 0 0 0 0 999 V2000 1.5584 -5.7422 0.0000 C 0 0 2.2043 -5.0535 0.0000 C 0 0 2 0 0 0 2.3688 -5.5155 0.0000 C 0 0 1 0 0 0 2.9210 -5.3181 0.0000 C 0 0 3.1270 -5.8206 0.0000 C 0 0 3.6744 -5.1312 0.0000 C 0 0 2 0 0 0 2.3619 -4.6609 0.0000 C 0 0 2.9268 -3.9939 0.0000 C 0 0 2 0 0 0 2.1999 -4.2522 0.0000 C 0 0 3.6803 -4.3062 0.0000 C 0 0 2.9436 -3.1692 0.0000 N 0 0 4.4569 -5.4095 0.0000 H 0 0 2.3246 -6.3425 0.0000 H 0 0 1.4365 -4.7500 0.0000 H 0 0 1 2 1 0 1 3 1 0 2 4 1 0 3 5 1 0 4 6 1 0 5 6 1 0 7 8 1 0 3 7 1 0 2 9 1 0 6 10 1 0 10 8 1 0 8 9 1 0 8 11 1 1 6 12 1 6 3 13 1 1 2 14 1 6 M END)CTAB"; { std::unique_ptr mol(MolBlockToMol(molblock)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 11); CHECK(mol->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED); CHECK(mol->getAtomWithIdx(2)->getChiralTag() != Atom::CHI_UNSPECIFIED); CHECK(mol->getAtomWithIdx(5)->getChiralTag() != Atom::CHI_UNSPECIFIED); } { bool sanitize = true; bool removeHs = false; std::unique_ptr mol(MolBlockToMol(molblock, sanitize, removeHs)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 14); CHECK(mol->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED); CHECK(mol->getAtomWithIdx(2)->getChiralTag() != Atom::CHI_UNSPECIFIED); CHECK(mol->getAtomWithIdx(5)->getChiralTag() != Atom::CHI_UNSPECIFIED); } } SECTION("with F") { std::string molblock = R"CTAB( SciTegic12231509382D 14 16 0 0 0 0 999 V2000 1.5584 -5.7422 0.0000 C 0 0 2.2043 -5.0535 0.0000 C 0 0 2 0 0 0 2.3688 -5.5155 0.0000 C 0 0 1 0 0 0 2.9210 -5.3181 0.0000 C 0 0 3.1270 -5.8206 0.0000 C 0 0 3.6744 -5.1312 0.0000 C 0 0 2 0 0 0 2.3619 -4.6609 0.0000 C 0 0 2.9268 -3.9939 0.0000 C 0 0 2 0 0 0 2.1999 -4.2522 0.0000 C 0 0 3.6803 -4.3062 0.0000 C 0 0 2.9436 -3.1692 0.0000 N 0 0 4.4569 -5.4095 0.0000 F 0 0 2.3246 -6.3425 0.0000 F 0 0 1.4365 -4.7500 0.0000 F 0 0 1 2 1 0 1 3 1 0 2 4 1 0 3 5 1 0 4 6 1 0 5 6 1 0 7 8 1 0 3 7 1 0 2 9 1 0 6 10 1 0 10 8 1 0 8 9 1 0 8 11 1 1 6 12 1 6 3 13 1 1 2 14 1 6 M END)CTAB"; { std::unique_ptr mol(MolBlockToMol(molblock)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 14); CHECK(mol->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED); CHECK(mol->getAtomWithIdx(2)->getChiralTag() != Atom::CHI_UNSPECIFIED); CHECK(mol->getAtomWithIdx(5)->getChiralTag() != Atom::CHI_UNSPECIFIED); } } } TEST_CASE("workaround for broken MJ2009-MJ2011 molblocks", "[feature][sgroups]") { SECTION("molblock1 strictParsing true/false") { std::string molblock1 = R"CTAB( MJ201100 10 10 0 0 0 0 0 0 0 0999 V2000 -1.2946 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2946 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 1.2493 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.1342 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 -0.1796 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -0.6907 0.5348 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 1 1 0 0 0 0 6 8 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 M STY 1 1 SUP M SAL 1 4 7 8 9 10 M SMT 1 CF3 M SBL 1 1 7 M SAP 1 1 8 M END )CTAB"; std::string expectedMolblock1 = R"CTAB( RDKit 2D 10 10 0 1 0 0 0 0 0 0999 V2000 -1.2946 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2946 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 1.2493 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.1342 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 -0.1796 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -0.6907 0.5348 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 2 0 5 6 1 0 6 1 2 0 6 8 1 0 7 8 1 0 8 9 1 0 8 10 1 0 M STY 1 1 SUP M SAL 1 4 7 8 9 10 M SBL 1 1 7 M SMT 1 CF3 M SAP 1 1 8 6 M END )CTAB"; std::unique_ptr mol; REQUIRE_THROWS_AS(mol.reset(MolBlockToMol(molblock1)), FileParseException); REQUIRE_NOTHROW(mol.reset(MolBlockToMol(molblock1, true, true, false))); REQUIRE(mol); CHECK(MolToMolBlock(*mol) == expectedMolblock1); } SECTION("molblock1 strictParsing true/false no/bad SBL group") { std::string molblock1NoSBL = R"CTAB( MJ201100 10 10 0 0 0 0 0 0 0 0999 V2000 -1.2946 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2946 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 1.2493 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.1342 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 -0.1796 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -0.6907 0.5348 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 1 1 0 0 0 0 6 8 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 M STY 1 1 SUP M SAL 1 4 7 8 9 10 M SMT 1 CF3 M SAP 1 1 8 M END )CTAB"; std::string molblock1BadSBL = R"CTAB( MJ201100 10 10 0 0 0 0 0 0 0 0999 V2000 -1.2946 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2946 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 1.2493 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.1342 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 -0.1796 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -0.6907 0.5348 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 1 1 0 0 0 0 6 8 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 M STY 1 1 SUP M SAL 1 4 7 8 9 10 M SMT 1 CF3 M SAP 1 1 8 M SBL 1 2 7 8 M END )CTAB"; std::string expectedMolblock1NoSGroups = R"CTAB( RDKit 2D 10 10 0 0 0 0 0 0 0 0999 V2000 -1.2946 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2946 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 1.2493 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.1342 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 -0.1796 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -0.6907 0.5348 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 2 0 5 6 1 0 6 1 2 0 6 8 1 0 7 8 1 0 8 9 1 0 8 10 1 0 M END )CTAB"; std::unique_ptr mol; REQUIRE_THROWS_AS(mol.reset(MolBlockToMol(molblock1NoSBL)), FileParseException); REQUIRE_NOTHROW( mol.reset(MolBlockToMol(molblock1NoSBL, true, true, false))); REQUIRE(mol); CHECK(MolToMolBlock(*mol) == expectedMolblock1NoSGroups); REQUIRE_THROWS_AS(mol.reset(MolBlockToMol(molblock1BadSBL)), FileParseException); REQUIRE_NOTHROW( mol.reset(MolBlockToMol(molblock1BadSBL, true, true, false))); REQUIRE(mol); CHECK(MolToMolBlock(*mol) == expectedMolblock1NoSGroups); } SECTION("molblock2 strictParsing true/false") { std::string molblock2 = R"CTAB( MJ201100 13 13 0 0 0 0 0 0 0 0999 V2000 -1.2946 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2946 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 1.2493 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.1342 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 -0.1796 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -0.6907 0.5348 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -3.4380 -0.7027 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7235 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0091 -0.7027 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 1 1 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 6 8 1 0 0 0 0 3 12 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 M STY 2 1 SUP 2 SUP M SAL 1 4 7 8 9 10 M SMT 1 CF3 M SBL 1 1 7 M SAP 1 1 8 M SAL 2 3 11 12 13 M SMT 2 COOH M SBL 2 1 8 M SAP 2 1 12 M END )CTAB"; std::string expectedMolblock2 = R"CTAB( RDKit 2D 13 13 0 2 0 0 0 0 0 0999 V2000 -1.2946 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2946 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 1.2493 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.1342 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 -0.1796 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -0.6907 0.5348 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -3.4380 -0.7027 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7235 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0091 -0.7027 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 4 5 1 0 5 6 2 0 6 1 1 0 2 3 1 0 3 4 2 0 6 8 1 0 3 12 1 0 7 8 1 0 8 9 1 0 8 10 1 0 11 12 1 0 12 13 2 0 M STY 2 1 SUP 2 SUP M SAL 1 4 7 8 9 10 M SBL 1 1 7 M SMT 1 CF3 M SAP 1 1 8 6 M SAL 2 3 11 12 13 M SBL 2 1 8 M SMT 2 COOH M SAP 2 1 12 3 M END )CTAB"; std::unique_ptr mol; REQUIRE_THROWS_AS(mol.reset(MolBlockToMol(molblock2)), FileParseException); REQUIRE_NOTHROW(mol.reset(MolBlockToMol(molblock2, true, true, false))); REQUIRE(mol); CHECK(MolToMolBlock(*mol) == expectedMolblock2); } SECTION("molblock2 strictParsing true/false no/bad SBL group1") { std::string molblock2NoSBL = R"CTAB( MJ201100 13 13 0 0 0 0 0 0 0 0999 V2000 -1.2946 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2946 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 1.2493 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.1342 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 -0.1796 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -0.6907 0.5348 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -3.4380 -0.7027 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7235 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0091 -0.7027 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 1 1 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 6 8 1 0 0 0 0 3 12 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 M STY 2 1 SUP 2 SUP M SAL 1 4 7 8 9 10 M SMT 1 CF3 M SAP 1 1 8 M SAL 2 3 11 12 13 M SMT 2 COOH M SBL 2 1 8 M SAP 2 1 12 M END )CTAB"; std::string molblock2BadSBL = R"CTAB( MJ201100 13 13 0 0 0 0 0 0 0 0999 V2000 -1.2946 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2946 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 1.2493 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.1342 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 -0.1796 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -0.6907 0.5348 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -3.4380 -0.7027 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7235 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0091 -0.7027 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 1 1 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 6 8 1 0 0 0 0 3 12 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 M STY 2 1 SUP 2 SUP M SAL 1 4 7 8 9 10 M SMT 1 CF3 M SAP 1 1 8 M SBL 1 2 7 8 M SAL 2 3 11 12 13 M SMT 2 COOH M SBL 2 1 8 M SAP 2 1 12 M END )CTAB"; std::string expectedMolblock2NoSGroup1 = R"CTAB( RDKit 2D 13 13 0 1 0 0 0 0 0 0999 V2000 -1.2946 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0090 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2946 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5801 0.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 1.2493 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.1342 0.5348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5467 -0.1796 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -0.6907 0.5348 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -3.4380 -0.7027 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7235 -1.1152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0091 -0.7027 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 4 5 1 0 5 6 2 0 6 1 1 0 2 3 1 0 3 4 2 0 6 8 1 0 3 12 1 0 7 8 1 0 8 9 1 0 8 10 1 0 11 12 1 0 12 13 2 0 M STY 1 1 SUP M SAL 1 3 11 12 13 M SBL 1 1 8 M SMT 1 COOH M SAP 1 1 12 3 M END )CTAB"; std::unique_ptr mol; REQUIRE_THROWS_AS(mol.reset(MolBlockToMol(molblock2NoSBL)), FileParseException); REQUIRE_NOTHROW( mol.reset(MolBlockToMol(molblock2NoSBL, true, true, false))); REQUIRE(mol); CHECK(MolToMolBlock(*mol) == expectedMolblock2NoSGroup1); REQUIRE_THROWS_AS(mol.reset(MolBlockToMol(molblock2BadSBL)), FileParseException); REQUIRE_NOTHROW( mol.reset(MolBlockToMol(molblock2BadSBL, true, true, false))); REQUIRE(mol); CHECK(MolToMolBlock(*mol) == expectedMolblock2NoSGroup1); } } TEST_CASE( "do not throw but remove malformed V2000 SGroups when strictParsing is " "false", "[feature][sgroups]") { std::string molblock = R"CTAB( ChemDraw01072117362D 16 16 0 0 0 0 0 0 0 0999 V2000 -1.7862 0.7219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7862 -0.1031 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0717 -0.5156 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3572 -0.1031 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3572 0.7219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0717 1.1344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3572 2.3719 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3572 -0.5156 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0717 -0.1031 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3572 -1.3406 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0717 -1.7531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0717 -2.5781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7862 -1.3406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4289 1.3406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7145 1.7531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7145 2.5781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11 12 1 0 11 13 1 0 10 11 1 0 8 9 2 0 8 10 1 0 4 8 1 0 15 16 1 0 14 15 1 0 6 14 1 0 7 16 1 0 1 2 2 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 1 1 0 M STY 1 1 SUP M SLB 1 1 1 M SAL 1 6 8 9 10 11 12 13 M SBL 1 1 6 M SMT 1 COOiPr M SBV 1 6 -0.7145 0.4125 M STY 1 2 SUP M SLB 1 2 2 M SAL 2 3 14 15 16 M SBL 2 2 9 10 M SMT 2 (CH2)3 M SBV 2 9 0.3572 -0.2062 M SBV 2 10 0.3572 -0.2062 M END )CTAB"; SECTION("molblock strictParsing true") { std::unique_ptr mol(MolBlockToMol(molblock)); REQUIRE(mol); CHECK(getSubstanceGroups(*mol).size() == 2); } SECTION("molblock bad sgroup idx") { std::string molblockBad = boost::replace_all_copy( molblock, "M SBL 1 1 6", "M SBL 3 1 6"); std::unique_ptr mol; REQUIRE_THROWS(mol.reset(MolBlockToMol(molblockBad))); REQUIRE_NOTHROW(mol.reset(MolBlockToMol(molblockBad, true, true, false))); CHECK(getSubstanceGroups(*mol).size() == 1); } SECTION("molblock sgroup line too short (1)") { std::string molblockBad = boost::replace_all_copy( molblock, "M SBV 1 6 -0.7145 0.4125", "M SBV 1 6"); std::unique_ptr mol; REQUIRE_THROWS(mol.reset(MolBlockToMol(molblockBad))); REQUIRE_NOTHROW(mol.reset(MolBlockToMol(molblockBad, true, true, false))); CHECK(getSubstanceGroups(*mol).size() == 1); } SECTION("molblock sgroup line too short (2)") { std::string molblockBad = boost::replace_all_copy( molblock, "M SBL 2 2 9 10", "M SBL 2 3 9 10"); std::unique_ptr mol; REQUIRE_THROWS(mol.reset(MolBlockToMol(molblockBad))); REQUIRE_NOTHROW(mol.reset(MolBlockToMol(molblockBad, true, true, false))); CHECK(getSubstanceGroups(*mol).size() == 1); } SECTION("molblock sgroup bad bond idx") { std::string molblockBad = boost::replace_all_copy( molblock, "M SBL 2 2 9 10", "M SBL 2 2 9 99"); std::unique_ptr mol; REQUIRE_THROWS(mol.reset(MolBlockToMol(molblockBad))); REQUIRE_NOTHROW(mol.reset(MolBlockToMol(molblockBad, true, true, false))); CHECK(getSubstanceGroups(*mol).size() == 1); } SECTION("molblock sgroup bad atom idx") { std::string molblockBad = boost::replace_all_copy( molblock, "M SAL 2 3 14 15 16", "M SAL 2 3 14 15 99"); std::unique_ptr mol; REQUIRE_THROWS(mol.reset(MolBlockToMol(molblockBad))); REQUIRE_NOTHROW(mol.reset(MolBlockToMol(molblockBad, true, true, false))); CHECK(getSubstanceGroups(*mol).size() == 1); } } TEST_CASE( "do not throw but remove malformed V3000 SGroups when strictParsing is " "false", "[feature][sgroups]") { std::string molblock = R"CTAB( RDKit 2D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 16 16 2 0 0 M V30 BEGIN ATOM M V30 1 C -1.786200 0.721900 0.000000 0 M V30 2 C -1.786200 -0.103100 0.000000 0 M V30 3 C -1.071700 -0.515600 0.000000 0 M V30 4 C -0.357200 -0.103100 0.000000 0 M V30 5 C -0.357200 0.721900 0.000000 0 M V30 6 C -1.071700 1.134400 0.000000 0 M V30 7 O -0.357200 2.371900 0.000000 0 M V30 8 C 0.357200 -0.515600 0.000000 0 M V30 9 O 1.071700 -0.103100 0.000000 0 M V30 10 O 0.357200 -1.340600 0.000000 0 M V30 11 C 1.071700 -1.753100 0.000000 0 M V30 12 C 1.071700 -2.578100 0.000000 0 M V30 13 C 1.786200 -1.340600 0.000000 0 M V30 14 C -1.428900 1.340600 0.000000 0 M V30 15 C -0.714500 1.753100 0.000000 0 M V30 16 C -0.714500 2.578100 0.000000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 11 12 M V30 2 1 11 13 M V30 3 1 10 11 M V30 4 2 8 9 M V30 5 1 8 10 M V30 6 1 4 8 M V30 7 1 15 16 M V30 8 1 14 15 M V30 9 1 6 14 M V30 10 1 7 16 M V30 11 2 1 2 M V30 12 1 2 3 M V30 13 2 3 4 M V30 14 1 4 5 M V30 15 2 5 6 M V30 16 1 6 1 M V30 END BOND M V30 BEGIN SGROUP M V30 1 SUP 1 ATOMS=(6 8 9 10 11 12 13) XBONDS=(1 6) LABEL=COOiPr CSTATE=(4 6 - M V30 -0.7145 0.4125 0) M V30 2 SUP 2 ATOMS=(3 14 15 16) XBONDS=(2 9 10) LABEL=(CH2)3 CSTATE=(4 9 0.35- M V30 72 -0.2062 0) CSTATE=(4 10 0.3572 -0.2062 0) M V30 END SGROUP M V30 END CTAB M END )CTAB"; SECTION("molblock strictParsing true") { std::unique_ptr mol(MolBlockToMol(molblock)); REQUIRE(mol); CHECK(getSubstanceGroups(*mol).size() == 2); } SECTION("molblock sgroup line too short (1)") { std::string molblockBad = boost::replace_all_copy(molblock, "XBONDS=(1 6)", "XBONDS=(2 6)"); std::unique_ptr mol; REQUIRE_THROWS(mol.reset(MolBlockToMol(molblockBad))); REQUIRE_NOTHROW(mol.reset(MolBlockToMol(molblockBad, true, true, false))); CHECK(getSubstanceGroups(*mol).size() == 1); } SECTION("molblock sgroup line too short (2)") { std::string molblockBad = boost::replace_all_copy( molblock, "ATOMS=(6 8 9 10 11 12 13)", "ATOMS=(7 8 9 10 11 12 13)"); std::unique_ptr mol; REQUIRE_THROWS(mol.reset(MolBlockToMol(molblockBad))); REQUIRE_NOTHROW(mol.reset(MolBlockToMol(molblockBad, true, true, false))); CHECK(getSubstanceGroups(*mol).size() == 1); } SECTION("molblock sgroup bad bond idx") { std::string molblockBad = boost::replace_all_copy(molblock, "XBONDS=(2 9 10)", "XBONDS=(2 9 99)"); std::unique_ptr mol; REQUIRE_THROWS(mol.reset(MolBlockToMol(molblockBad))); REQUIRE_NOTHROW(mol.reset(MolBlockToMol(molblockBad, true, true, false))); CHECK(getSubstanceGroups(*mol).size() == 1); } SECTION("molblock sgroup bad atom idx") { std::string molblockBad = boost::replace_all_copy( molblock, "ATOMS=(3 14 15 16)", "ATOMS=(3 14 15 99)"); std::unique_ptr mol; REQUIRE_THROWS(mol.reset(MolBlockToMol(molblockBad))); REQUIRE_NOTHROW(mol.reset(MolBlockToMol(molblockBad, true, true, false))); CHECK(getSubstanceGroups(*mol).size() == 1); } } TEST_CASE("parsing of SCN lines", "[bug][sgroups]") { SECTION("basics") { std::string molblock = R"CTAB( MJ171200 76 80 0 0 0 0 0 0 0 0999 V2000 -6.4802 2.6494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8927 3.3638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7177 3.3638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1302 2.6494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7177 1.9349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8927 1.9349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2426 1.9349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6552 2.6494 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -6.4802 1.2203 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.6552 1.2203 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0051 1.2203 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4176 1.9349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2426 0.5060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4176 0.5060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8927 0.5060 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4802 -0.2085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6552 -0.2085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1302 1.2203 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -6.8927 -0.9230 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4802 -1.6374 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6552 -1.6374 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0051 -1.6374 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2426 -2.3519 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.4176 -2.3519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0051 -3.0663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1801 -3.0663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7676 -3.7808 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4176 -3.7808 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0051 -4.4953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1801 -4.4953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3243 -3.7791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7368 -3.0648 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5619 -3.0648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9744 -3.7791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5619 -4.4936 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7368 -4.4936 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3243 -5.2082 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -7.9744 -5.2082 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5619 -5.9226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7368 -5.9226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9744 -2.3503 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7994 -2.3503 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.7994 -3.7791 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.9487 -5.1497 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3243 -6.6371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3705 -2.2987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9580 -1.5842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1329 -1.5842 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2796 -2.2987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1329 -3.0132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9580 -3.0132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1329 -0.1553 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2796 -0.8698 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3705 -3.7276 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.2796 -3.7276 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1329 -4.4420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9580 -4.4420 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3705 -5.1566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8575 -2.2792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4450 -1.5648 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6200 -1.5648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2073 -2.2792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6200 -2.9937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4450 -2.9937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3789 -3.8003 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3797 -5.2304 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8445 -5.2489 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3318 -2.2987 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2075 -3.7082 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8195 -3.7288 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3448 -2.2597 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1706 -0.8729 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3860 -0.6179 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 3.2997 -0.0580 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1046 -2.2987 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9675 -0.6233 0.0000 Na 0 3 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 1 6 1 0 0 0 0 9 10 1 0 0 0 0 7 10 1 0 0 0 0 8 1 1 0 0 0 0 6 9 1 0 0 0 0 11 12 1 0 0 0 0 13 14 1 0 0 0 0 11 14 2 0 0 0 0 10 13 2 0 0 0 0 12 7 2 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 13 17 1 0 0 0 0 5 18 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 16 19 1 0 0 0 0 23 24 1 0 0 0 0 22 24 2 0 0 0 0 21 23 1 0 0 0 0 25 26 1 0 0 0 0 25 24 1 1 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 27 30 1 0 0 0 0 25 28 1 0 0 0 0 27 26 1 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 33 34 1 0 0 0 0 34 35 1 0 0 0 0 35 36 1 0 0 0 0 31 36 1 0 0 0 0 39 40 2 0 0 0 0 37 40 1 0 0 0 0 35 38 1 1 0 0 0 36 37 1 6 0 0 0 41 42 1 0 0 0 0 34 43 1 6 0 0 0 33 41 1 1 0 0 0 44 38 1 1 0 0 0 40 45 1 0 0 0 0 46 47 1 0 0 0 0 47 48 1 0 0 0 0 48 49 1 0 0 0 0 49 50 1 0 0 0 0 50 51 1 0 0 0 0 46 51 1 0 0 0 0 52 53 1 0 0 0 0 48 53 1 1 0 0 0 56 57 2 0 0 0 0 54 57 1 0 0 0 0 51 54 1 6 0 0 0 50 55 1 1 0 0 0 57 58 1 0 0 0 0 59 60 1 0 0 0 0 60 61 1 0 0 0 0 61 62 1 0 0 0 0 62 63 1 0 0 0 0 63 64 1 0 0 0 0 59 64 1 0 0 0 0 28 65 1 6 0 0 0 31 65 1 1 0 0 0 29 66 1 1 0 0 0 30 67 1 6 0 0 0 27 55 1 1 0 0 0 46 68 1 1 0 0 0 62 68 1 6 0 0 0 63 69 1 1 0 0 0 64 70 1 6 0 0 0 59 71 1 1 0 0 0 61 72 1 1 0 0 0 72 73 1 0 0 0 0 72 74 2 0 0 0 0 49 75 1 6 0 0 0 M STY 3 1 SRU 2 SRU 3 SRU M SCN 3 1 HT 2 HT 3 HT M SAL 1 15 55 50 51 54 57 58 56 46 68 62 63 69 64 70 61 M SAL 1 11 72 74 73 60 47 48 53 52 49 75 59 M SMT 1 b M SBL 1 2 71 76 M SAL 2 15 27 26 25 28 65 31 36 37 40 45 39 35 34 43 33 M SAL 2 15 41 42 32 29 66 24 22 23 21 20 19 16 17 13 10 M SAL 2 15 7 12 11 9 6 1 8 2 3 4 5 18 14 15 30 M SAL 2 2 67 38 M SMT 2 a M SBL 2 2 71 46 M SAL 3 15 38 35 36 37 40 45 39 31 65 28 25 24 22 23 21 M SAL 3 15 20 19 16 17 13 10 7 12 11 9 6 1 8 2 3 M SAL 3 15 4 5 18 14 15 26 27 55 50 51 54 57 58 56 46 M SAL 3 15 68 62 63 69 64 70 61 72 74 73 60 47 48 53 52 M SAL 3 13 49 75 30 67 29 66 32 33 41 42 34 43 59 M SMT 3 n M SBL 3 2 46 76 M END )CTAB"; std::unique_ptr mol(MolBlockToMol(molblock)); REQUIRE(mol); } } TEST_CASE("A couple more S group problems", "[bug][sgroups]") { std::string molblock = R"CTAB(CHEMBL3666739 SciTegic05171617282D 35 40 0 0 0 0 999 V2000 -3.6559 5.8551 0.0000 O 0 0 -2.6152 5.2576 0.0000 C 0 0 -2.6120 3.7568 0.0000 N 0 0 -3.9097 3.0028 0.0000 C 0 0 -5.2093 3.7519 0.0000 C 0 0 -6.5078 3.0010 0.0000 C 0 0 -6.5067 1.5010 0.0000 C 0 0 -5.2071 0.7519 0.0000 C 0 0 -3.9086 1.5029 0.0000 C 0 0 -2.6111 0.7486 0.0000 C 0 0 -2.6111 -0.7486 0.0000 N 0 0 -1.2964 -1.4973 0.0000 C 0 0 -1.2907 -2.9981 0.0000 N 0 0 -2.5870 -3.7544 0.0000 C 0 0 -2.5748 -5.2506 0.0000 C 0 0 -3.8815 -6.0264 0.0000 C 0 0 -5.1819 -5.2707 0.0000 C 0 0 -6.6004 -5.7374 0.0000 N 0 0 -7.4849 -4.5227 0.0000 N 0 0 -6.6189 -3.3309 0.0000 C 0 0 -5.1934 -3.7757 0.0000 C 0 0 -3.9049 -3.0000 0.0000 C 0 0 0.0000 -0.7486 0.0000 C 0 0 1.2964 -1.4973 0.0000 C 0 0 2.5929 -0.7486 0.0000 C 0 0 2.5929 0.7486 0.0000 C 0 0 1.2964 1.4973 0.0000 C 0 0 0.0000 0.7486 0.0000 C 0 0 -1.2964 1.4973 0.0000 N 0 0 -1.3175 6.0116 0.0000 C 0 0 -1.3185 7.5117 0.0000 C 0 0 -0.0200 8.2626 0.0000 C 0 0 1.2795 7.5135 0.0000 N 0 0 1.2806 6.0135 0.0000 C 0 0 -0.0178 5.2626 0.0000 C 0 0 1 2 2 0 2 3 1 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 4 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 1 0 19 20 2 0 20 21 1 0 17 21 1 0 21 22 2 0 14 22 1 0 12 23 2 0 23 24 1 0 24 25 2 0 25 26 1 0 26 27 2 0 27 28 1 0 23 28 1 0 28 29 2 0 10 29 1 0 2 30 1 0 30 31 2 0 31 32 1 0 32 33 2 0 33 34 1 0 34 35 2 0 30 35 1 0 M STY 1 1 DAT M SLB 1 1 1 M SAL 1 1 33 M SDT 1 FAKE_MRV_IMPLICIT_H M SDD 1 0.5304 -0.4125 DR ALL 0 0 M SED 1 IMPL_H1 M END )CTAB"; SECTION("spaces in count lines") { std::unique_ptr mol(MolBlockToMol(molblock)); REQUIRE(mol); } SECTION("short SDT lines") { std::unique_ptr mol(MolBlockToMol(molblock)); REQUIRE(mol); const auto &sgroups = getSubstanceGroups(*mol); CHECK(sgroups.size() == 1); CHECK(sgroups[0].hasProp("TYPE")); CHECK(sgroups[0].getProp("TYPE") == "DAT"); CHECK(sgroups[0].hasProp("FIELDNAME")); CHECK(sgroups[0].getProp("FIELDNAME") == "FAKE_MRV_IMPLICIT_H"); } } TEST_CASE("Github #2527: handling of \"R\" in CTABs", "[rgroups]") { std::string molblock = R"CTAB(example Mrv1902 07031913362D 2 1 0 0 0 0 999 V2000 -1.1418 0.0687 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0 -1.9668 0.0687 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 M END )CTAB"; SECTION("basics") { bool sanitize = false; std::unique_ptr mol(MolBlockToMol(molblock, sanitize)); REQUIRE(mol); auto *at = static_cast(mol->getAtomWithIdx(1)); REQUIRE(at->hasQuery()); CHECK(at->getQuery()->getDescription() == "AtomNull"); } } TEST_CASE("CML writer", "[CML][writer]") { SECTION("basics") { std::unique_ptr mol{new RWMol{}}; mol->setProp(common_properties::_Name, "S-lactic acid"); for (auto z : {6u, 1u, 1u, 1u, 6u, 1u, 8u, 1u, 6u, 8u, 8u}) { auto *a = new Atom{z}; mol->addAtom(a, false, true); } mol->getAtomWithIdx(7u)->setIsotope(2u); mol->getAtomWithIdx(10u)->setFormalCharge(-1); mol->addBond(0u, 1u, Bond::SINGLE); mol->addBond(0u, 2u, Bond::SINGLE); mol->addBond(0u, 3u, Bond::SINGLE); mol->addBond(0u, 4u, Bond::SINGLE); mol->addBond(4u, 5u, Bond::SINGLE); mol->addBond(4u, 6u, Bond::SINGLE); mol->addBond(4u, 8u, Bond::SINGLE); mol->addBond(6u, 7u, Bond::SINGLE); mol->addBond(8u, 9u, Bond::DOUBLE); mol->addBond(8u, 10u, Bond::SINGLE); auto *conf = new Conformer{11u}; conf->setId(0u); conf->setAtomPos(0u, RDGeom::Point3D{-0.95330, 0.60416, 1.01609}); conf->setAtomPos(1u, RDGeom::Point3D{-1.00832, 1.68746, 0.83520}); conf->setAtomPos(2u, RDGeom::Point3D{-1.96274, 0.16103, 0.94471}); conf->setAtomPos(3u, RDGeom::Point3D{-0.57701, 0.44737, 2.04167}); conf->setAtomPos(4u, RDGeom::Point3D{0.00000, 0.00000, 0.00000}); conf->setAtomPos(5u, RDGeom::Point3D{-0.43038, 0.18596, -1.01377}); conf->setAtomPos(6u, RDGeom::Point3D{0.22538, -1.36531, 0.19373}); conf->setAtomPos(7u, RDGeom::Point3D{1.21993, -1.33937, 0.14580}); conf->setAtomPos(8u, RDGeom::Point3D{1.38490, 0.73003, 0.00000}); conf->setAtomPos(9u, RDGeom::Point3D{1.38490, 1.96795, 0.00000}); conf->setAtomPos(10u, RDGeom::Point3D{2.35253, -0.07700, 0.00000}); mol->addConformer(conf); mol->updatePropertyCache(); MolOps::assignStereochemistryFrom3D(*mol); const std::string cmlblock = MolToCMLBlock(*mol); const std::string cmlblock_expected = R"CML( S-lactic acid 1 )CML"; CHECK(cmlblock == cmlblock_expected); } SECTION("chirality1") { auto mol = R"CTAB( Mrv1921 04232106262D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 4 0 0 1 M V30 BEGIN ATOM M V30 1 I 0.8918 -1.0472 0 0 M V30 2 C 0.8918 0.4928 0 0 M V30 3 Br 0.8918 2.0328 0 0 M V30 4 F 2.4318 0.4928 0 0 M V30 5 Cl -0.6482 0.4928 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 2 1 M V30 2 1 2 3 CFG=3 M V30 3 1 2 4 CFG=1 M V30 4 1 2 5 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); const std::string cmlblock = MolToCMLBlock(*mol); const std::string cmlblock_expected = R"CML( 1 )CML"; CHECK(cmlblock == cmlblock_expected); } SECTION("chirality2") { auto mol = R"CTAB( Mrv1921 04232106262D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 4 0 0 1 M V30 BEGIN ATOM M V30 1 I 0.8918 -1.0472 0 0 M V30 2 C 0.8918 0.4928 0 0 M V30 3 Br 0.8918 2.0328 0 0 M V30 4 F 2.4318 0.4928 0 0 M V30 5 Cl -0.6482 0.4928 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 2 1 M V30 2 1 2 3 CFG=1 M V30 3 1 2 4 CFG=3 M V30 4 1 2 5 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); const std::string cmlblock = MolToCMLBlock(*mol); const std::string cmlblock_expected = R"CML( -1 )CML"; CHECK(cmlblock == cmlblock_expected); } SECTION("no conformer") { auto mol = "C[C@](O)(F)Cl"_smiles; REQUIRE(mol); const std::string cmlblock = MolToCMLBlock(*mol); const std::string cmlblock_expected = R"CML( 1 )CML"; CHECK(cmlblock == cmlblock_expected); } } TEST_CASE("XYZ", "[XYZ][writer]") { SECTION("basics") { std::unique_ptr mol{new RWMol{}}; mol->setProp(common_properties::_Name, "methane\nthis part should not be output"); for (unsigned z : {6, 1, 1, 1, 1}) { auto *a = new Atom{z}; mol->addAtom(a, false, true); } auto *conf = new Conformer{5}; conf->setId(0); conf->setAtomPos(0, RDGeom::Point3D{0.000, 0.000, 0.000}); conf->setAtomPos(1, RDGeom::Point3D{-0.635, -0.635, 0.635}); conf->setAtomPos(2, RDGeom::Point3D{-0.635, 0.635, -0.635}); conf->setAtomPos(3, RDGeom::Point3D{0.635, -0.635, -0.635}); conf->setAtomPos(4, RDGeom::Point3D{0.635, 0.635, 0.635}); mol->addConformer(conf); const std::string xyzblock = MolToXYZBlock(*mol); std::string xyzblock_expected = R"XYZ(5 methane C 0.000000 0.000000 0.000000 H -0.635000 -0.635000 0.635000 H -0.635000 0.635000 -0.635000 H 0.635000 -0.635000 -0.635000 H 0.635000 0.635000 0.635000 )XYZ"; CHECK(xyzblock == xyzblock_expected); } SECTION("precistion") { std::unique_ptr mol{new RWMol{}}; mol->setProp(common_properties::_Name, "CHEMBL506259"); for (unsigned z : {8, 6, 8, 6, 9, 9, 9}) { auto *a = new Atom{z}; mol->addAtom(a, false, true); } auto *conf = new Conformer{7}; conf->setId(0); conf->setAtomPos(0, RDGeom::Point3D{0.402012650000000, -0.132994360000000, 1.000000170000000}); conf->setAtomPos(1, RDGeom::Point3D{0.876222600000000, 0.997390900000000, 1.000000030000000}); conf->setAtomPos(2, RDGeom::Point3D{0.366137990000000, 2.110718500000000, 0.999999820000000}); conf->setAtomPos(3, RDGeom::Point3D{2.486961570000000, 1.004799350000000, 0.999999990000000}); conf->setAtomPos(4, RDGeom::Point3D{3.033118410000000, 2.237399550000000, 1.000000100000000}); conf->setAtomPos(5, RDGeom::Point3D{3.007723370000000, 0.373992940000000, 2.077133250000000}); conf->setAtomPos(6, RDGeom::Point3D{3.007723400000000, 0.373993120000000, -0.077133360000000}); mol->addConformer(conf); const std::string xyzblock = MolToXYZBlock(*mol, 0, 15); std::string xyzblock_expected = R"XYZ(7 CHEMBL506259 O 0.402012650000000 -0.132994360000000 1.000000170000000 C 0.876222600000000 0.997390900000000 1.000000030000000 O 0.366137990000000 2.110718500000000 0.999999820000000 C 2.486961570000000 1.004799350000000 0.999999990000000 F 3.033118410000000 2.237399550000000 1.000000100000000 F 3.007723370000000 0.373992940000000 2.077133250000000 F 3.007723400000000 0.373993120000000 -0.077133360000000 )XYZ"; CHECK(xyzblock == xyzblock_expected); } } TEST_CASE("valence writing 1", "[bug][writer]") { SECTION("carbon") { std::string molblock = R"CTAB(carbon atom 1 0 0 0 0 0 999 V2000 -0.3958 -0.0542 0.0000 C 0 0 0 0 0 15 M END)CTAB"; bool sanitize = false; bool removeHs = false; std::unique_ptr mol(MolBlockToMol(molblock, sanitize, removeHs)); REQUIRE(mol); mol->updatePropertyCache(); CHECK(mol->getAtomWithIdx(0)->getNoImplicit()); CHECK(mol->getAtomWithIdx(0)->getValence(Atom::ValenceType::EXPLICIT) == 0); CHECK(mol->getAtomWithIdx(0)->getTotalValence() == 0); auto outBlock = MolToMolBlock(*mol); REQUIRE(outBlock.find("0 0 15") != std::string::npos); } SECTION("P valences") { std::string molblock = R"CTAB(H2PO2 3 2 0 0 0 0 999 V2000 0.2667 -0.4167 0.0000 P 0 0 0 0 0 5 0.2667 1.1083 0.0000 O 0 0 -1.0958 -1.0042 0.0000 O 0 0 2 1 2 0 3 1 1 0 M END)CTAB"; bool sanitize = false; bool removeHs = false; std::unique_ptr mol(MolBlockToMol(molblock, sanitize, removeHs)); REQUIRE(mol); mol->updatePropertyCache(); CHECK(mol->getAtomWithIdx(0)->getNoImplicit()); CHECK(mol->getAtomWithIdx(0)->getValence(Atom::ValenceType::EXPLICIT) == 5); CHECK(mol->getAtomWithIdx(0)->getTotalValence() == 5); auto outBlock = MolToMolBlock(*mol); REQUIRE(outBlock.find("0 0 5") != std::string::npos); } } TEST_CASE("Github #2695: Error when a squiggle bond is in an aromatic ring", "[bug][reader]") { SECTION("reported") { auto ctab = R"CTAB( -ISIS- -- StrEd -- 19 22 0 0 0 0 0 0 0 0999 V2000 -3.1355 -0.9331 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.6355 -1.7990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6356 -1.7990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1356 -0.9331 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6356 -0.0671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6355 -0.0671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1355 0.7991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6355 1.6651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6356 1.6651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1356 0.7991 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.1354 0.7991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4523 1.6080 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.4034 1.2991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2693 1.7990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1355 1.2991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1355 0.2991 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.2693 -0.2011 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4034 0.2991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4523 -0.0099 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 1 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 10 9 1 4 0 0 0 5 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 13 18 1 0 0 0 0 18 19 2 0 0 0 0 11 19 1 0 0 0 0 M END)CTAB"; std::unique_ptr mol(MolBlockToMol(ctab)); REQUIRE(mol); } } TEST_CASE("Github #2917: _ctab _mol2 and _pdb support", "[feature][reader]") { SECTION("_ctab") { auto mol = R"CTAB( Mrv1810 01292008292D 4 3 0 0 0 0 999 V2000 -3.7669 1.1053 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0524 1.5178 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3380 1.1053 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4814 1.5178 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 2 3 1 0 0 0 0 1 4 1 0 0 0 0 1 2 2 0 0 0 0 M END )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getNumAtoms() == 4); } SECTION("_ctab failure") { auto mol = R"CTAB( Mrv1810 01292008292D 4 3 0 0 0 0 999 V2000 -3.7669 1.1053 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0524 1.5178 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3380 1.1053 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4814 1.5178 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 3 1 1 0 0 0 0 M END )CTAB"_ctab; REQUIRE(!mol); } SECTION("_pdb") { auto mol = R"DATA(HEADER 2VNF_PROTEIN COMPND 2VNF_PROTEIN REMARK GENERATED BY X-TOOL on Wed Nov 21 18:02:19 2012 ATOM 1 N ALA A 225 10.250 -13.177 9.152 1.00 19.76 N ATOM 2 H ALA A 225 10.605 -14.082 8.782 1.00 0.00 H ATOM 3 CA ALA A 225 11.136 -12.000 9.236 1.00 21.97 C ATOM 4 HA ALA A 225 11.079 -11.589 10.244 1.00 0.00 H ATOM 5 C ALA A 225 10.683 -10.934 8.231 1.00 21.61 C ATOM 6 O ALA A 225 10.811 -9.723 8.485 1.00 20.83 O ATOM 7 CB ALA A 225 12.572 -12.399 8.956 1.00 22.98 C ATOM 8 HB1 ALA A 225 12.892 -13.138 9.690 1.00 0.00 H ATOM 9 HB2 ALA A 225 12.641 -12.825 7.955 1.00 0.00 H ATOM 10 HB3 ALA A 225 13.212 -11.519 9.022 1.00 0.00 H TER 11 ALA A 225 HETATM 12 O HOH 43 12.371 -9.746 8.354 0.50 30.13 O END )DATA"_pdb; REQUIRE(mol); CHECK(mol->getNumAtoms() == 6); } SECTION("_pdb failure") { auto mol_ok = R"DATA(HEADER TEST COMPND ACY REMARK invented HETATM 2779 C ACY A 404 15.911 -4.912 26.073 1.00 30.04 C HETATM 2780 O ACY A 404 15.855 -4.063 25.124 1.00 24.12 O HETATM 2781 OXT ACY A 404 16.514 -4.578 27.173 1.00 34.44 O HETATM 2782 CH3 ACY A 404 15.319 -6.258 25.820 1.00 30.60 C CONECT 2780 2781 END )DATA"_pdb; REQUIRE(mol_ok); CHECK(mol_ok->getNumAtoms() == 4); CHECK(mol_ok->getBondBetweenAtoms(1, 2)); auto mol_fail = R"DATA(HEADER TEST COMPND ACY REMARK invented HETATM 2779 C ACY A 404 15.911 -4.912 26.073 1.00 30.04 C HETATM 2780 O ACY A 404 15.855 -4.063 25.124 1.00 24.12 O HETATM 2781 OXT ACY A 404 16.514 -4.578 27.173 1.00 34.44 O HETATM 2782 CH3 ACY A 404 15.319 -6.258 25.820 1.00 30.60 C CONECT 2780 2781 CONECT 2780 2779 CONECT 2780 2782 END )DATA"_pdb; REQUIRE(!mol_fail); } SECTION("_mol2") { auto mol = R"DATA(@MOLECULE UNK 6 4 0 0 0 SMALL GASTEIGER @ATOM 1 Na 0.0000 0.0000 0.0000 Na 1 UNL 1.0000 2 C 0.0000 0.0000 0.0000 C.3 1 UNL -0.0305 3 H 0.0000 0.0000 0.0000 H 1 UNL 0.0265 4 H 0.0000 0.0000 0.0000 H 1 UNL 0.0265 5 H 0.0000 0.0000 0.0000 H 1 UNL 0.0265 6 H 0.0000 0.0000 0.0000 H 1 UNL 0.0265 @BOND 1 2 3 1 2 2 4 1 3 2 5 1 4 2 6 1 )DATA"_mol2; REQUIRE(mol); CHECK(mol->getNumAtoms() == 2); } SECTION("_mol2 failure") { // this one checks that the C-Na bond is not automatically converted // to dative when parsing Mol2 files auto mol = R"DATA(@MOLECULE UNK 6 5 0 0 0 SMALL GASTEIGER @ATOM 1 Na 0.0000 0.0000 0.0000 Na 1 UNL 1.0000 2 C 0.0000 0.0000 0.0000 C.3 1 UNL -0.0305 3 H 0.0000 0.0000 0.0000 H 1 UNL 0.0265 4 H 0.0000 0.0000 0.0000 H 1 UNL 0.0265 5 H 0.0000 0.0000 0.0000 H 1 UNL 0.0265 6 H 0.0000 0.0000 0.0000 H 1 UNL 0.0265 @BOND 1 2 3 1 2 2 4 1 3 2 5 1 4 2 6 1 5 2 1 1 )DATA"_mol2; REQUIRE(!mol); } } TEST_CASE("handling STBOX properties from v3k ctabs", "[feature][v3k]") { SECTION("atoms and bonds") { auto mol = R"CTAB(basic test Mrv1810 01292006422D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 4 3 0 0 0 M V30 BEGIN ATOM M V30 1 C -7.0316 2.0632 0 0 STBOX=1 M V30 2 C -5.6979 2.8332 0 0 STBOX=1 M V30 3 O -4.3642 2.0632 0 0 M V30 4 F -8.3653 2.8332 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 2 3 M V30 2 1 1 4 M V30 3 2 1 2 STBOX=1 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getNumAtoms() == 4); int val = 0; CHECK(mol->getAtomWithIdx(0)->getPropIfPresent( common_properties::molStereoCare, val)); CHECK(val == 1); CHECK(mol->getAtomWithIdx(1)->getPropIfPresent( common_properties::molStereoCare, val)); CHECK(val == 1); CHECK(!mol->getAtomWithIdx(2)->hasProp(common_properties::molStereoCare)); REQUIRE(mol->getBondBetweenAtoms(0, 1)); CHECK(mol->getBondBetweenAtoms(0, 1)->getPropIfPresent( common_properties::molStereoCare, val)); CHECK(val == 1); } SECTION("bonds set if the atoms are also set 1") { auto mol = R"CTAB(basic test Mrv1810 01292006422D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 4 3 0 0 0 M V30 BEGIN ATOM M V30 1 C -7.0316 2.0632 0 0 STBOX=1 M V30 2 C -5.6979 2.8332 0 0 STBOX=1 M V30 3 O -4.3642 2.0632 0 0 M V30 4 F -8.3653 2.8332 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 2 3 M V30 2 1 1 4 M V30 3 2 1 2 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getNumAtoms() == 4); REQUIRE(mol->getBondBetweenAtoms(0, 1)); int val = 0; CHECK(mol->getBondBetweenAtoms(0, 1)->getPropIfPresent( common_properties::molStereoCare, val)); CHECK(val == 1); } SECTION("bonds set if the atoms are also set 2") { auto mol = R"CTAB(basic test Mrv1810 01292006422D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 4 3 0 0 0 M V30 BEGIN ATOM M V30 1 C -7.0316 2.0632 0 0 STBOX=0 M V30 2 C -5.6979 2.8332 0 0 STBOX=0 M V30 3 O -4.3642 2.0632 0 0 M V30 4 F -8.3653 2.8332 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 2 3 M V30 2 1 1 4 M V30 3 2 1 2 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getNumAtoms() == 4); REQUIRE(mol->getBondBetweenAtoms(0, 1)); CHECK(!mol->getBondBetweenAtoms(0, 1)->hasProp( common_properties::molStereoCare)); } SECTION("bonds set if the atoms are also set 2") { auto mol = R"CTAB(basic test Mrv1810 01292006422D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 4 3 0 0 0 M V30 BEGIN ATOM M V30 1 C -7.0316 2.0632 0 0 STBOX=1 M V30 2 C -5.6979 2.8332 0 0 STBOX=0 M V30 3 O -4.3642 2.0632 0 0 M V30 4 F -8.3653 2.8332 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 2 3 M V30 2 1 1 4 M V30 3 2 1 2 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getNumAtoms() == 4); REQUIRE(mol->getBondBetweenAtoms(0, 1)); CHECK(!mol->getBondBetweenAtoms(0, 1)->hasProp( common_properties::molStereoCare)); } SECTION("bonds set if the atoms are also set v2k") { auto mol = R"CTAB(basic test Mrv1810 01292015042D 4 3 0 0 0 0 999 V2000 -3.7669 1.1053 0.0000 C 0 0 0 0 1 0 0 0 0 0 0 0 -3.0524 1.5178 0.0000 C 0 0 0 0 1 0 0 0 0 0 0 0 -2.3380 1.1053 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4814 1.5178 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 2 3 1 0 0 0 0 1 4 1 0 0 0 0 1 2 2 0 0 0 0 M END )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getNumAtoms() == 4); REQUIRE(mol->getBondBetweenAtoms(0, 1)); int val = 0; CHECK(mol->getBondBetweenAtoms(0, 1)->getPropIfPresent( common_properties::molStereoCare, val)); CHECK(val == 1); } } TEST_CASE("github #2829: support MRV_IMPLICIT_H", "[feature][sgroups]") { SECTION("basics v2k") { auto mol = R"CTAB( Mrv1810 01302015262D 5 5 0 0 0 0 999 V2000 1.1387 -1.3654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6538 -0.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1387 -0.0305 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.9233 -0.2854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9233 -1.1104 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 4 0 0 0 0 2 3 4 0 0 0 0 3 4 4 0 0 0 0 1 5 4 0 0 0 0 4 5 4 0 0 0 0 M STY 1 1 DAT M SAL 1 1 3 M SDT 1 MRV_IMPLICIT_H M SDD 1 0.0000 0.0000 DR ALL 0 0 M SED 1 IMPL_H1 M END )CTAB"_ctab; REQUIRE(mol); CHECK(MolToSmiles(*mol) == "c1cc[nH]c1"); } SECTION("basics v3k") { auto mol = R"CTAB( Mrv1810 01302015452D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 5 1 0 0 M V30 BEGIN ATOM M V30 1 C 2.1256 -2.5487 0 0 M V30 2 C 1.2204 -1.3027 0 0 M V30 3 N 2.1256 -0.0569 0 0 M V30 4 C 3.5902 -0.5327 0 0 M V30 5 C 3.5902 -2.0727 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 4 1 2 M V30 2 4 2 3 M V30 3 4 3 4 M V30 4 4 1 5 M V30 5 4 4 5 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 3) FIELDNAME=MRV_IMPLICIT_H - M V30 FIELDDISP=" 0.0000 0.0000 DR ALL 0 0" - M V30 FIELDDATA=IMPL_H1 M V30 END SGROUP M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); CHECK(MolToSmiles(*mol) == "c1cc[nH]c1"); // we removed all the S groups: CHECK(getSubstanceGroups(*mol).empty()); } SECTION("v3k two groups") { auto mol = R"CTAB( Mrv1810 01302016392D 12 14 0 0 0 0 999 V2000 1.1387 -1.3654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6538 -0.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1387 -0.0305 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.9233 -0.2854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9233 -1.1104 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6378 0.1271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6378 -1.5229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3522 -1.1104 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3522 -0.2854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1369 -1.3653 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.1369 -0.0305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6218 -0.6979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 4 0 0 0 0 2 3 4 0 0 0 0 3 4 4 0 0 0 0 1 5 4 0 0 0 0 4 5 4 0 0 0 0 7 8 1 0 0 0 0 6 9 1 0 0 0 0 5 7 1 0 0 0 0 6 4 1 0 0 0 0 11 12 4 0 0 0 0 10 12 4 0 0 0 0 9 11 4 0 0 0 0 10 8 4 0 0 0 0 8 9 4 0 0 0 0 M STY 2 1 DAT 2 DAT M SAL 1 1 3 M SDT 1 MRV_IMPLICIT_H M SDD 1 0.0000 0.0000 DR ALL 0 0 M SED 1 IMPL_H1 M SAL 2 1 10 M SDT 2 MRV_IMPLICIT_H M SDD 2 0.0000 0.0000 DR ALL 0 0 M SED 2 IMPL_H1 M END )CTAB"_ctab; REQUIRE(mol); CHECK(MolToSmiles(*mol) == "c1cc2c([nH]1)Cc1cc[nH]c1C2"); // we removed all the S groups: CHECK(getSubstanceGroups(*mol).empty()); } SECTION("removal leaves other s groups intact") { auto mol = R"CTAB( Mrv1810 02022006062D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 6 6 2 0 0 M V30 BEGIN ATOM M V30 1 C 2.1256 -2.5487 0 0 M V30 2 C 1.2204 -1.3027 0 0 M V30 3 N 2.1256 -0.0569 0 0 M V30 4 C 3.5902 -0.5327 0 0 M V30 5 C 3.5902 -2.0727 0 0 M V30 6 C 4.8361 -2.9778 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 4 1 2 M V30 2 4 2 3 M V30 3 4 3 4 M V30 4 4 1 5 M V30 5 4 4 5 M V30 6 1 5 6 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 6) FIELDNAME=some_data - M V30 FIELDDISP=" 4.8361 -2.9778 DAU ALL 0 0" - M V30 MRV_FIELDDISP=0 FIELDDATA=foo M V30 2 DAT 0 ATOMS=(1 3) FIELDNAME=MRV_IMPLICIT_H - M V30 FIELDDISP=" 0.0000 0.0000 DR ALL 0 0" - M V30 FIELDDATA=IMPL_H1 M V30 END SGROUP M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); CHECK(MolToSmiles(*mol) == "Cc1cc[nH]c1"); CHECK(getSubstanceGroups(*mol).size() == 1); } } TEST_CASE("extra v3k mol file properties", "[ctab][v3k]") { SECTION("ATTCHPT") { auto mol = R"CTAB( Mrv2007 03132014352D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 3 2 0 0 0 M V30 BEGIN ATOM M V30 1 C -16.625 7.1667 0 0 ATTCHPT=2 M V30 2 C -15.2913 7.9367 0 0 ATTCHPT=1 M V30 3 N -13.9576 7.1667 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getAtomWithIdx(0)->getProp( common_properties::molAttachPoint) == 2); CHECK(mol->getAtomWithIdx(1)->getProp( common_properties::molAttachPoint) == 1); auto molb = MolToV3KMolBlock(*mol); CHECK(molb.find("ATTCHPT=1") != std::string::npos); CHECK(molb.find("ATTCHPT=2") != std::string::npos); } SECTION("others") { // this is not reasonable; just there to ensure that the reading/writing is // working auto mol = R"CTAB(really fake Mrv2007 03132015062D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 4 0 0 0 M V30 BEGIN ATOM M V30 1 C -22.5833 11.0833 0 0 EXACHG=1 M V30 2 C -21.2497 11.8533 0 0 INVRET=2 M V30 3 C -23.917 11.8533 0 0 ATTCHORD=3 M V30 4 C -25.2507 11.0833 0 0 CLASS=foo M V30 5 C -26.5844 11.8533 0 0 SEQID=4 SEQNAME=foo1 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 1 3 M V30 3 1 3 4 M V30 4 1 4 5 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getAtomWithIdx(0)->getProp( common_properties::molRxnExactChange) == 1); CHECK(mol->getAtomWithIdx(1)->getProp( common_properties::molInversionFlag) == 2); CHECK(mol->getAtomWithIdx(2)->getProp( common_properties::molAttachOrder) == 3); CHECK(mol->getAtomWithIdx(3)->getProp( common_properties::molAtomClass) == "foo"); CHECK(mol->getAtomWithIdx(4)->getProp( common_properties::molAtomSeqId) == 4); CHECK(mol->getAtomWithIdx(4)->getProp( common_properties::molAtomSeqName) == "foo1"); auto molb = MolToV3KMolBlock(*mol); CHECK(molb.find("EXACHG=1") != std::string::npos); CHECK(molb.find("INVRET=2") != std::string::npos); CHECK(molb.find("ATTCHORD=3") != std::string::npos); CHECK(molb.find("CLASS=foo") != std::string::npos); CHECK(molb.find("SEQID=4") != std::string::npos); CHECK(molb.find("SEQNAME=foo1") != std::string::npos); } SECTION("SUBST") { auto mol = R"CTAB(test Mrv2007 03132018122D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 4 3 0 0 0 M V30 BEGIN ATOM M V30 1 C -16.6248 7.1666 0 0 SUBST=3 M V30 2 C -15.2911 7.9366 0 0 SUBST=-2 M V30 3 N -13.9574 7.1666 0 0 SUBST=-1 M V30 4 C -17.9585 7.9366 0 0 SUBST=6 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 1 4 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); auto smarts = MolToSmarts(*mol); CHECK(smarts == "[#6&D3](-[#6&D2]-[#7&D0])-[#6&D{6-}]"); auto molb = MolToV3KMolBlock(*mol); CHECK(molb.find("SUBST=3") != std::string::npos); CHECK(molb.find("SUBST=-2") != std::string::npos); CHECK(molb.find("SUBST=-1") != std::string::npos); } SECTION("RBCNT") { auto mol = R"CTAB(test Mrv2007 03132018122D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 4 3 0 0 0 M V30 BEGIN ATOM M V30 1 C -16.6248 7.1666 0 0 RBCNT=3 M V30 2 C -15.2911 7.9366 0 0 RBCNT=-2 M V30 3 N -13.9574 7.1666 0 0 RBCNT=-1 M V30 4 C -17.9585 7.9366 0 0 RBCNT=4 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 1 4 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); auto smarts = MolToSmarts(*mol); CHECK(smarts == "[#6&x3](-[#6&x0]-[#7&x0])-[#6&x4]"); auto molb = MolToV3KMolBlock(*mol); CHECK(molb.find("RBCNT=3") != std::string::npos); CHECK(molb.find("RBCNT=-2") != std::string::npos); CHECK(molb.find("RBCNT=-1") != std::string::npos); } SECTION("bond props") { auto mol = R"CTAB(bogus example Mrv2007 03132017102D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 8 7 0 0 0 M V30 BEGIN ATOM M V30 1 C -28.125 8.2067 0 0 M V30 2 C -26.7913 7.4367 0 0 M V30 3 C -26.7913 5.8967 0 0 M V30 4 C -28.125 5.1267 0 0 M V30 5 N -29.4587 5.8967 0 0 M V30 6 C -29.4587 7.4367 0 0 M V30 7 * -27.2359 7.18 0 0 M V30 8 R# -25.2354 8.335 0 0 RGROUPS=(1 1) M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 2 2 3 M V30 3 1 3 4 M V30 4 2 4 5 M V30 5 1 5 6 M V30 6 2 1 6 RXCTR=1 M V30 7 1 7 8 ENDPTS=(3 1 2 3) ATTACH=ANY M V30 END BOND M V30 END CTAB M END)CTAB"_ctab; REQUIRE(mol); auto molb = MolToV3KMolBlock(*mol); CHECK(molb.find("ENDPTS=(3 1 2 3) ATTACH=ANY") != std::string::npos); CHECK(molb.find("RXCTR=1") != std::string::npos); } } TEST_CASE( "Problems parsing SGroup abbreviations with multiple attachment points", "[bug][reader]") { std::string rdbase = getenv("RDBASE"); SECTION("basics") { std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/sgroup_ap_bug.mol"; std::unique_ptr mol(MolFileToMol(fName)); REQUIRE(mol); const auto &sgroups = getSubstanceGroups(*mol); CHECK(sgroups.size() == 3); CHECK(sgroups[0].hasProp("TYPE")); CHECK(sgroups[0].getProp("TYPE") == "SUP"); CHECK(sgroups[0].getAttachPoints().size() == 1); CHECK(sgroups[1].hasProp("TYPE")); CHECK(sgroups[1].getProp("TYPE") == "SUP"); CHECK(sgroups[1].getAttachPoints().size() == 1); CHECK(sgroups[2].hasProp("TYPE")); CHECK(sgroups[2].getProp("TYPE") == "SUP"); CHECK(sgroups[2].getAttachPoints().size() == 2); } } TEST_CASE( "github #3207: Attachment point info not being read from V2000 mol blocks", "[ctab][bug]") { SECTION("ATTCHPT") { auto mol = R"CTAB( Mrv1824 06092009122D 3 2 0 0 0 0 999 V2000 -8.9061 3.8393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1917 4.2518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4772 3.8393 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 M APO 2 1 2 2 1 M END )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getAtomWithIdx(0)->getProp( common_properties::molAttachPoint) == 2); CHECK(mol->getAtomWithIdx(1)->getProp( common_properties::molAttachPoint) == 1); auto molb = MolToV3KMolBlock(*mol); CHECK(molb.find("ATTCHPT=1") != std::string::npos); CHECK(molb.find("ATTCHPT=2") != std::string::npos); } SECTION("Val=-1") { auto mol = R"CTAB( Mrv1824 06092009122D 3 2 0 0 0 0 999 V2000 -8.9061 3.8393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1917 4.2518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4772 3.8393 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 M APO 2 1 3 2 1 M END )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getAtomWithIdx(0)->getProp( common_properties::molAttachPoint) == -1); CHECK(mol->getAtomWithIdx(1)->getProp( common_properties::molAttachPoint) == 1); auto molb = MolToV3KMolBlock(*mol); CHECK(molb.find("ATTCHPT=1") != std::string::npos); CHECK(molb.find("ATTCHPT=-1") != std::string::npos); } } TEST_CASE("XBHEAD and XBCORR causing parser failures", "[bug][reader]") { std::string rdbase = getenv("RDBASE"); SECTION("basics") { std::string fName = rdbase + "/Code/GraphMol/FileParsers/sgroup_test_data/repeat_groups_query1.mol"; std::unique_ptr mol(MolFileToMol(fName)); REQUIRE(mol); const auto &sgroups = getSubstanceGroups(*mol); CHECK(sgroups.size() == 1); CHECK(sgroups[0].hasProp("TYPE")); CHECK(sgroups[0].getProp("TYPE") == "SRU"); CHECK(sgroups[0].hasProp("XBHEAD")); auto v = sgroups[0].getProp>("XBHEAD"); CHECK(v.size() == 2); CHECK(v[0] == 5); CHECK(v[1] == 0); CHECK(sgroups[0].hasProp("XBCORR")); CHECK(sgroups[0].getProp>("XBCORR").size() == 4); auto mb = MolToV3KMolBlock(*mol); CHECK(mb.find("XBHEAD=(2 6 1)") != std::string::npos); CHECK(mb.find("XBCORR=(4 6 6 1 1)") != std::string::npos); } } TEST_CASE("LINKNODE information being ignored", "[ctab][bug]") { SECTION("v3000") { auto mol = R"CTAB( Mrv2007 06212005162D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 5 0 0 0 M V30 BEGIN ATOM M V30 1 C -3.25 12.2683 0 0 M V30 2 C -4.4959 11.3631 0 0 M V30 3 C -4.02 9.8986 0 0 M V30 4 C -2.48 9.8986 0 0 M V30 5 C -2.0041 11.3631 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 3 4 M V30 4 1 4 5 M V30 5 1 1 5 M V30 END BOND M V30 LINKNODE 1 3 2 1 2 1 5 M V30 LINKNODE 1 4 2 4 3 4 5 M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getProp(common_properties::molFileLinkNodes) == "1 3 2 1 2 1 5|1 4 2 4 3 4 5"); auto molb = MolToV3KMolBlock(*mol); CHECK(molb.find("LINKNODE 1 3 2 1 2 1 5") != std::string::npos); CHECK(molb.find("LINKNODE 1 4 2 4 3 4 5") != std::string::npos); } SECTION("v2000") { auto mol = R"CTAB( Mrv2007 06222015182D 5 5 0 0 0 0 999 V2000 -1.7411 6.5723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4085 6.0874 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1536 5.3028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3286 5.3028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0736 6.0874 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 1 5 1 0 0 0 0 M LIN 2 1 3 2 5 4 4 3 5 M END )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getProp(common_properties::molFileLinkNodes) == "1 3 2 1 2 1 5|1 4 2 4 3 4 5"); auto molb = MolToV3KMolBlock(*mol); CHECK(molb.find("LINKNODE 1 3 2 1 2 1 5") != std::string::npos); CHECK(molb.find("LINKNODE 1 4 2 4 3 4 5") != std::string::npos); } } TEST_CASE("more complex queries in CTAB parsers", "[ctab]") { SECTION("v3000") { auto mol = R"CTAB(*.*.*.*.*.*.*.* |$;Q_e;M_p;X_p;AH_p;QH_p;MH_p;XH_p$| manual 06272007272D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 8 0 0 0 0 M V30 BEGIN ATOM M V30 1 A -3.2083 5.25 0 0 M V30 2 Q -0.25 6 0 0 M V30 3 M 4.5417 6.0417 0 0 M V30 4 X 1.2917 4.2083 0 0 M V30 5 AH -4.2083 5.25 0 0 M V30 6 QH -1.25 6 0 0 M V30 7 MH 3.5417 6.0417 0 0 M V30 8 XH 0.2917 4.2083 0 0 M V30 END ATOM M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); for (const auto atom : mol->atoms()) { REQUIRE(atom->hasQuery()); CHECK(!atom->getQuery()->getTypeLabel().empty()); } std::string pkl; MolPickler::pickleMol(*mol, pkl); ROMol cp(pkl); for (const auto atom : cp.atoms()) { REQUIRE(atom->hasQuery()); CHECK(!atom->getQuery()->getTypeLabel().empty()); CHECK(atom->getQuery()->getTypeLabel() == mol->getAtomWithIdx(atom->getIdx())->getQuery()->getTypeLabel()); } auto molb = MolToV3KMolBlock(*mol); CHECK(molb.find(" A ") != std::string::npos); CHECK(molb.find(" AH ") != std::string::npos); CHECK(molb.find(" Q ") != std::string::npos); CHECK(molb.find(" QH ") != std::string::npos); CHECK(molb.find(" M ") != std::string::npos); CHECK(molb.find(" MH ") != std::string::npos); CHECK(molb.find(" X ") != std::string::npos); CHECK(molb.find(" XH ") != std::string::npos); } SECTION("v2000") { auto mol = R"CTAB(*.*.*.*.*.*.*.* |$;Q_e;M_p;X_p;AH_p;QH_p;MH_p;XH_p$| manual 06272007272D 8 0 0 0 0 0 999 V2000 -3.2083 5.2500 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0 -0.2500 6.0000 0.0000 Q 0 0 0 0 0 0 0 0 0 0 0 0 4.5417 6.0417 0.0000 M 0 0 0 0 0 0 0 0 0 0 0 0 1.2917 4.2083 0.0000 X 0 0 0 0 0 0 0 0 0 0 0 0 -4.2083 5.2500 0.0000 AH 0 0 0 0 0 0 0 0 0 0 0 0 -1.2500 6.0000 0.0000 QH 0 0 0 0 0 0 0 0 0 0 0 0 3.5417 6.0417 0.0000 MH 0 0 0 0 0 0 0 0 0 0 0 0 0.2917 4.2083 0.0000 XH 0 0 0 0 0 0 0 0 0 0 0 0 M END )CTAB"_ctab; REQUIRE(mol); for (const auto atom : mol->atoms()) { REQUIRE(atom->hasQuery()); CHECK(!atom->getQuery()->getTypeLabel().empty()); } std::string pkl; MolPickler::pickleMol(*mol, pkl); ROMol cp(pkl); for (const auto atom : cp.atoms()) { REQUIRE(atom->hasQuery()); CHECK(!atom->getQuery()->getTypeLabel().empty()); CHECK(atom->getQuery()->getTypeLabel() == mol->getAtomWithIdx(atom->getIdx())->getQuery()->getTypeLabel()); } auto molb = MolToMolBlock(*mol); CHECK(molb.find(" A ") != std::string::npos); CHECK(molb.find(" AH ") != std::string::npos); CHECK(molb.find(" Q ") != std::string::npos); CHECK(molb.find(" QH ") != std::string::npos); CHECK(molb.find(" M ") != std::string::npos); CHECK(molb.find(" MH ") != std::string::npos); CHECK(molb.find(" X ") != std::string::npos); CHECK(molb.find(" XH ") != std::string::npos); /// SMARTS-based queries are not written for these: CHECK(molb.find("V ") == std::string::npos); } } #ifdef RDK_USE_BOOST_IOSTREAMS TEST_CASE("read metadata from PNG", "[reader][PNG]") { std::string rdbase = getenv("RDBASE"); SECTION("basics") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.png"; auto metadata = PNGFileToMetadata(fname); auto iter = std::find_if(metadata.begin(), metadata.end(), [](const std::pair &val) { return boost::starts_with(val.first, PNGData::smilesTag); }); REQUIRE(iter != metadata.end()); CHECK( iter->second == "COc1cc2c(-c3ccc(OC)c(=O)cc3[C@@H](NC(C)=O)CC2)c(OC)c1OC " "|(6.46024,1.03002,;5.30621,1.98825,;3.89934,1.46795,;2.74531,2.42618,;" "1.33844,1.90588,;1.0856,0.427343,;-0.228013,-0.296833,;0.1857,-1." "73865,;-0.683614,-2.96106,;-2.18134,-3.04357,;-2.75685,-4.42878,;-4." "24422,-4.62298,;-3.17967,-1.92404,;-4.62149,-2.33775,;-2.92683,-0." "445502,;-1.61322,0.278673,;-2.02693,1.72049,;-3.50547,1.97333,;-4." "02577,3.3802,;-5.50431,3.63304,;-3.06754,4.53423,;-1.15762,2.9429,;0." "340111,3.02541,;2.23963,-0.530891,;1.98679,-2.00943,;3.14082,-2.96766," ";3.6465,-0.0105878,;4.80053,-0.968822,;4.54769,-2.44736,)|"); } SECTION("no metadata") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png"; auto metadata = PNGFileToMetadata(fname); REQUIRE(metadata.empty()); } SECTION("bad PNG") { std::string text = "NOT A PNG"; REQUIRE_THROWS_AS(PNGStringToMetadata(text), FileParseException); } SECTION("truncated PNG") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.png"; auto istr = std::ifstream(fname, std::ios_base::binary); istr.seekg(0, istr.end); auto sz = istr.tellg(); istr.seekg(0, istr.beg); char *buff = new char[sz]; istr.read(buff, sz); std::string data(buff, sz); delete[] buff; auto metadata = PNGStringToMetadata(data); REQUIRE(!metadata.empty()); REQUIRE_THROWS_AS(PNGStringToMetadata(data.substr(1000)), FileParseException); } SECTION("compressed metadata") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.mrv.png"; auto metadata = PNGFileToMetadata(fname); auto iter = std::find_if(metadata.begin(), metadata.end(), [](const std::pair &val) { return val.first == "molSource"; }); REQUIRE(iter != metadata.end()); CHECK(iter->second.find("") != std::string::npos); } } TEST_CASE("write metadata to PNG", "[writer][PNG]") { std::string rdbase = getenv("RDBASE"); SECTION("basics") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png"; std::vector> metadata; metadata.push_back(std::make_pair( PNGData::smilesTag, std::string( "COc1cc2c(-c3ccc(OC)c(=O)cc3[C@@H](NC(C)=O)CC2)c(OC)c1OC " "|(6.46024,1.03002,;5.30621,1.98825,;3.89934,1.46795,;2.74531,2." "42618,;1.33844,1.90588,;1.0856,0.427343,;-0.228013,-0.296833,;0." "1857,-1.73865,;-0.683614,-2.96106,;-2.18134,-3.04357,;-2.75685,-4." "42878,;-4.24422,-4.62298,;-3.17967,-1.92404,;-4.62149,-2.33775,;-" "2.92683,-0.445502,;-1.61322,0.278673,;-2.02693,1.72049,;-3.50547," "1.97333,;-4.02577,3.3802,;-5.50431,3.63304,;-3.06754,4.53423,;-1." "15762,2.9429,;0.340111,3.02541,;2.23963,-0.530891,;1.98679,-2." "00943,;3.14082,-2.96766,;3.6465,-0.0105878,;4.80053,-0.968822,;4." "54769,-2.44736,)|"))); auto pngData = addMetadataToPNGFile(fname, metadata); std::ofstream ofs("write_metadata.png"); ofs.write(pngData.c_str(), pngData.size()); ofs.flush(); auto ometadata = PNGStringToMetadata(pngData); REQUIRE(ometadata.size() == metadata.size()); for (unsigned int i = 0; i < ometadata.size(); ++i) { CHECK(ometadata[i].first == metadata[i].first); CHECK(ometadata[i].second == metadata[i].second); } } } TEST_CASE("read molecule from PNG", "[reader][PNG]") { std::string rdbase = getenv("RDBASE"); SECTION("smiles") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.png"; std::unique_ptr mol(PNGFileToMol(fname)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 29); CHECK(mol->getNumConformers() == 1); } SECTION("mol") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.mol.png"; std::unique_ptr mol(PNGFileToMol(fname)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 29); CHECK(mol->getNumConformers() == 1); } SECTION("no metadata") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png"; REQUIRE_THROWS_AS(PNGFileToMol(fname), FileParseException); } } #endif TEST_CASE("write molecule to PNG", "[writer][PNG]") { std::string rdbase = getenv("RDBASE"); SECTION("basics") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png"; std::ifstream strm(fname, std::ios::in | std::ios::binary); auto colchicine = "COc1cc2c(c(OC)c1OC)-c1ccc(OC)c(=O)cc1[C@@H](NC(C)=O)CC2"_smiles; REQUIRE(colchicine); auto pngString = addMolToPNGStream(*colchicine, strm); // read it back out std::unique_ptr mol(PNGStringToMol(pngString)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 29); CHECK(mol->getNumConformers() == 0); } SECTION("use SMILES") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png"; std::ifstream strm(fname, std::ios::in | std::ios::binary); auto colchicine = "COc1cc2c(c(OC)c1OC)-c1ccc(OC)c(=O)cc1[C@@H](NC(C)=O)CC2"_smiles; REQUIRE(colchicine); bool includePkl = false; auto pngString = addMolToPNGStream(*colchicine, strm, includePkl); // read it back out std::unique_ptr mol(PNGStringToMol(pngString)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 29); CHECK(mol->getNumConformers() == 0); } SECTION("use MOL") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png"; std::ifstream strm(fname, std::ios::in | std::ios::binary); auto colchicine = "COc1cc2c(c(OC)c1OC)-c1ccc(OC)c(=O)cc1[C@@H](NC(C)=O)CC2"_smiles; REQUIRE(colchicine); bool includePkl = false; bool includeSmiles = false; bool includeMol = true; auto pngString = addMolToPNGStream(*colchicine, strm, includePkl, includeSmiles, includeMol); // read it back out std::unique_ptr mol(PNGStringToMol(pngString)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 29); CHECK(mol->getNumConformers() == 1); } SECTION("use PKL") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png"; auto colchicine = "COc1cc2c(c(OC)c1OC)-c1ccc(OC)c(=O)cc1[C@@H](NC(C)=O)CC2"_smiles; REQUIRE(colchicine); RDDepict::compute2DCoords(*colchicine); CHECK(colchicine->getNumConformers() == 1); static const std::string propertyName("property"); static const std::string propertyValue("value"); colchicine->setProp(propertyName, propertyValue); PNGMetadataParams params; params.includePkl = true; params.includeSmiles = false; params.includeMol = false; { std::ifstream strm(fname, std::ios::in | std::ios::binary); params.propertyFlags = PicklerOps::PropertyPickleOptions::NoProps; auto pngString = addMolToPNGStream(*colchicine, strm, params); // read it back out std::unique_ptr mol(PNGStringToMol(pngString)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 29); CHECK(mol->getNumConformers() == 1); CHECK(!mol->hasProp(propertyName)); } { std::ifstream strm(fname, std::ios::in | std::ios::binary); params.propertyFlags = PicklerOps::PropertyPickleOptions::AllProps; auto pngString = addMolToPNGStream(*colchicine, strm, params); // read it back out std::unique_ptr mol(PNGStringToMol(pngString)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 29); CHECK(mol->getNumConformers() == 1); CHECK(mol->hasProp(propertyName)); CHECK(mol->getProp(propertyName) == propertyValue); } { std::ifstream strm(fname, std::ios::in | std::ios::binary); params.includePkl = false; params.includeSmiles = true; params.cxSmilesFlags = SmilesWrite::CXSmilesFields::CX_ALL_BUT_COORDS; auto pngString = addMolToPNGStream(*colchicine, strm, params); // read it back out std::unique_ptr mol(PNGStringToMol(pngString)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 29); CHECK(mol->getNumConformers() == 0); CHECK(!mol->hasProp(propertyName)); } } SECTION("use original wedging") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png"; auto colchicineUnusualWedging = R"CTAB( RDKit 2D 29 31 0 0 0 0 0 0 0 0999 V2000 6.4602 1.0300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3062 1.9883 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8993 1.4680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7453 2.4262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3384 1.9059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0856 0.4273 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2396 -0.5309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9868 -2.0094 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1408 -2.9677 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6465 -0.0106 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8005 -0.9688 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5477 -2.4474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2280 -0.2968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1857 -1.7387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6836 -2.9611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1813 -3.0436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7569 -4.4288 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2442 -4.6230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1797 -1.9240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6215 -2.3378 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9268 -0.4455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6132 0.2787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0269 1.7205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5055 1.9733 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.0258 3.3802 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5043 3.6330 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0675 4.5342 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1576 2.9429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3401 3.0254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 8 9 1 0 7 10 2 0 10 11 1 0 11 12 1 0 6 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 1 0 16 19 1 0 19 20 2 0 19 21 1 0 21 22 2 0 23 22 1 1 23 24 1 0 24 25 1 0 25 26 1 0 25 27 2 0 23 28 1 0 28 29 1 0 10 3 1 0 22 13 1 0 29 5 1 0 M END )CTAB"_ctab; REQUIRE(colchicineUnusualWedging); CHECK(colchicineUnusualWedging->getNumConformers() == 1); SmilesWriteParams ps; CHECK(MolToCXSmiles(*colchicineUnusualWedging).find("wU:22.24|") != std::string::npos); CHECK(MolToCXSmiles(*colchicineUnusualWedging, ps, SmilesWrite::CX_ALL, RestoreBondDirOptionTrue) .find("wU:22.23|") != std::string::npos); PNGMetadataParams params; params.includePkl = true; params.includeSmiles = true; params.includeMol = true; params.propertyFlags = PicklerOps::PropertyPickleOptions::AtomProps | PicklerOps::PropertyPickleOptions::BondProps; { std::ifstream strm(fname, std::ios::in | std::ios::binary); auto pngString = addMolToPNGStream(*colchicineUnusualWedging, strm, params); // read it back out std::unique_ptr mol(PNGStringToMol(pngString)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 29); CHECK(mol->getNumConformers() == 1); CHECK( MolToCXSmiles(*mol, ps, SmilesWrite::CX_ALL, RestoreBondDirOptionTrue) .find("wU:22.23|") != std::string::npos); auto metadata = PNGStringToMetadata(pngString); auto smilesFound = false; auto ctabFound = false; auto pklFound = false; for (const auto &[key, value] : metadata) { if (key.substr(0, 6) == "SMILES") { smilesFound = true; CHECK(value.find("wU:22.24|") != std::string::npos); } else if (key.substr(0, 3) == "MOL") { ctabFound = true; CHECK(value.find(" 23 24 1 1") != std::string::npos); } else if (key.substr(0, 8) == "rdkitPKL") { pklFound = true; RWMol molFromPkl(value); CHECK(MolToMolBlock(molFromPkl).find(" 23 24 1 1") != std::string::npos); Chirality::reapplyMolBlockWedging(molFromPkl); CHECK(MolToMolBlock(molFromPkl).find(" 23 22 1 1") != std::string::npos); } } CHECK((smilesFound && ctabFound && pklFound)); } { params.restoreBondDirs = RestoreBondDirOptionTrue; std::ifstream strm(fname, std::ios::in | std::ios::binary); auto pngString = addMolToPNGStream(*colchicineUnusualWedging, strm, params); // read it back out std::unique_ptr mol(PNGStringToMol(pngString)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 29); CHECK(mol->getNumConformers() == 1); CHECK( MolToCXSmiles(*mol, ps, SmilesWrite::CX_ALL, RestoreBondDirOptionTrue) .find("wU:22.23|") != std::string::npos); auto metadata = PNGStringToMetadata(pngString); auto smilesFound = false; auto ctabFound = false; auto pklFound = false; for (const auto &[key, value] : metadata) { if (key.substr(0, 6) == "SMILES") { smilesFound = true; CHECK(value.find("wU:22.23|") != std::string::npos); } else if (key.substr(0, 3) == "MOL") { ctabFound = true; CHECK(value.find(" 23 22 1 1") != std::string::npos); } else if (key.substr(0, 8) == "rdkitPKL") { pklFound = true; RWMol molFromPkl(value); CHECK(MolToMolBlock(molFromPkl).find(" 23 24 1 1") != std::string::npos); Chirality::reapplyMolBlockWedging(molFromPkl); CHECK(MolToMolBlock(molFromPkl).find(" 23 22 1 1") != std::string::npos); } } CHECK((smilesFound && ctabFound && pklFound)); } } } TEST_CASE("multiple molecules in the PNG", "[writer][PNG]") { std::string rdbase = getenv("RDBASE"); std::vector smiles = {"c1ccccc1", "CCCOC", "c1ncccc1"}; std::vector> mols; for (const auto &smi : smiles) { mols.emplace_back(SmilesToMol(smi)); } SECTION("pickles") { std::vector> metadata; for (const auto &mol : mols) { std::string pkl; MolPickler::pickleMol(*mol, pkl); metadata.push_back(std::make_pair(PNGData::pklTag, pkl)); } // for the purposes of this test we'll add the metadata to an unrelated // PNG std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png"; std::ifstream strm(fname, std::ios::in | std::ios::binary); auto png = addMetadataToPNGStream(strm, metadata); std::stringstream pngstrm(png); auto molsRead = PNGStreamToMols(pngstrm); REQUIRE(molsRead.size() == mols.size()); for (unsigned i = 0; i < molsRead.size(); ++i) { CHECK(MolToSmiles(*molsRead[i]) == MolToSmiles(*mols[i])); } } SECTION("SMILES") { std::vector> metadata; for (const auto &mol : mols) { std::string pkl = "BOGUS"; // add bogus pickle data so we know that's not being read metadata.push_back(std::make_pair(PNGData::pklTag, pkl)); metadata.push_back(std::make_pair(PNGData::smilesTag, MolToSmiles(*mol))); } // for the purposes of this test we'll add the metadata to an unrelated // PNG std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png"; std::ifstream strm(fname, std::ios::in | std::ios::binary); auto png = addMetadataToPNGStream(strm, metadata); std::stringstream pngstrm(png); auto molsRead = PNGStreamToMols(pngstrm, PNGData::smilesTag); REQUIRE(molsRead.size() == mols.size()); for (unsigned i = 0; i < molsRead.size(); ++i) { CHECK(MolToSmiles(*molsRead[i]) == MolToSmiles(*mols[i])); } } } TEST_CASE("multiple molecules in the PNG, second example", "[writer][PNG]") { std::string rdbase = getenv("RDBASE"); std::vector smiles = {"c1ccccc1", "CCO", "CC(=O)O", "c1ccccn1"}; std::vector> mols; for (const auto &smi : smiles) { mols.emplace_back(SmilesToMol(smi)); } #ifdef RDK_USE_BOOST_IOSTREAMS SECTION("pickles") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/multiple_mols.png"; std::ifstream strm(fname, std::ios::in | std::ios::binary); auto molsRead = PNGStreamToMols(strm); REQUIRE(molsRead.size() == mols.size()); for (unsigned i = 0; i < molsRead.size(); ++i) { CHECK(MolToSmiles(*molsRead[i]) == MolToSmiles(*mols[i])); } } #endif SECTION("SMILES") { std::vector> metadata; for (const auto &mol : mols) { std::string pkl = "BOGUS"; // add bogus pickle data so we know that's not being read metadata.push_back(std::make_pair(PNGData::pklTag, pkl)); metadata.push_back(std::make_pair(PNGData::smilesTag, MolToSmiles(*mol))); } // for the purposes of this test we'll add the metadata to an unrelated // PNG std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png"; std::ifstream strm(fname, std::ios::in | std::ios::binary); auto png = addMetadataToPNGStream(strm, metadata); std::stringstream pngstrm(png); auto molsRead = PNGStreamToMols(pngstrm, PNGData::smilesTag); REQUIRE(molsRead.size() == mols.size()); for (unsigned i = 0; i < molsRead.size(); ++i) { CHECK(MolToSmiles(*molsRead[i]) == MolToSmiles(*mols[i])); } } } TEST_CASE("github #3413: V3K mol blocks with no atoms fail to parse", "[bug]") { SECTION("basics") { auto m = R"CTAB(6065 RDKit 2D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 0 0 0 0 0 M V30 BEGIN ATOM M V30 END ATOM M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); CHECK(m->getNumAtoms() == 0); CHECK(m->getNumBonds() == 0); } } TEST_CASE("github #3415: problem parsing SGroup data containing \" ", "[bug]") { SECTION("basics") { auto m = R"CTAB( Mrv2014 09172018222D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 6 6 1 0 0 M V30 BEGIN ATOM M V30 1 C 1.3337 2.31 0 0 M V30 2 C 2.6674 1.54 0 0 M V30 3 C 2.6674 -0 0 0 M V30 4 C 1.3337 -0.77 0 0 M V30 5 C 0 0 0 0 M V30 6 C 0 1.54 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 2 1 2 M V30 2 1 2 3 M V30 3 2 3 4 M V30 4 1 4 5 M V30 5 2 5 6 M V30 6 1 1 6 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 1) FIELDNAME=Tempstruct FIELDINFO="""" - M V30 FIELDDISP=" 2.1037 1.5400 DA ALL 0 0" QUERYOP="""" - M V30 FIELDDATA=Foo1 M V30 END SGROUP M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); CHECK(m->getNumAtoms() == 6); CHECK(m->getNumBonds() == 6); auto sgs = getSubstanceGroups(*m); REQUIRE(sgs.size() == 1); CHECK(sgs[0].getProp("TYPE") == "DAT"); CHECK(sgs[0].getProp("FIELDINFO") == "\""); CHECK(sgs[0].getProp("QUERYOP") == "\""); } SECTION("empty string") { auto m = R"CTAB( Mrv2014 09172018222D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 6 6 1 0 0 M V30 BEGIN ATOM M V30 1 C 1.3337 2.31 0 0 M V30 2 C 2.6674 1.54 0 0 M V30 3 C 2.6674 -0 0 0 M V30 4 C 1.3337 -0.77 0 0 M V30 5 C 0 0 0 0 M V30 6 C 0 1.54 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 2 1 2 M V30 2 1 2 3 M V30 3 2 3 4 M V30 4 1 4 5 M V30 5 2 5 6 M V30 6 1 1 6 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 1) FIELDNAME=Tempstruct FIELDINFO="" - M V30 FIELDDISP=" 2.1037 1.5400 DA ALL 0 0" QUERYOP="""" - M V30 FIELDDATA=Foo1 M V30 END SGROUP M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); CHECK(m->getNumAtoms() == 6); CHECK(m->getNumBonds() == 6); auto sgs = getSubstanceGroups(*m); REQUIRE(sgs.size() == 1); CHECK(sgs[0].getProp("TYPE") == "DAT"); CHECK(sgs[0].getProp("FIELDINFO").empty()); CHECK(sgs[0].getProp("QUERYOP") == "\""); } } TEST_CASE("github #3597: Scientific notation in SDF V3000 files", "[bug]") { SECTION("basics") { auto m = R"CTAB( Mrv2020 11302014062D 2 1 0 0 0 0 999 V2000 -2.8125 1.9196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0980 2.3321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 M END )CTAB"_ctab; REQUIRE(m); m->getConformer().getAtomPos(0).z = 1e-6; m->getConformer().getAtomPos(1).z = 1e-4; auto mb = MolToV3KMolBlock(*m); CHECK(mb.find("1e-06") == std::string::npos); } SECTION("toosmall") { auto m = R"CTAB( Mrv2020 11302014062D 2 1 0 0 0 0 999 V2000 -2.8125 1.9196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0980 2.3321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 M END )CTAB"_ctab; REQUIRE(m); m->getConformer().getAtomPos(0).z = 1e-17; m->getConformer().getAtomPos(1).z = 1e-4; auto mb = MolToV3KMolBlock(*m); // std::cerr<getPropIfPresent(common_properties::_MolFileChiralFlag, chiralFlag)); CHECK(chiralFlag == 1); auto mb = MolToV3KMolBlock(*m); CHECK(mb.find("4 3 0 0 1") != std::string::npos); } } TEST_CASE("test bond flavors when writing PDBs", "[bug]") { SECTION("basics") { std::unique_ptr m{SequenceToMol("G")}; REQUIRE(m); int confId = -1; { int flavor = 0; auto pdb = MolToPDBBlock(*m, confId, flavor); CHECK(pdb.find("CONECT 1 2\n") != std::string::npos); CHECK(pdb.find("CONECT 3 4 4 5\n") != std::string::npos); } { int flavor = 2; auto pdb = MolToPDBBlock(*m, confId, flavor); CHECK(pdb.find("CONECT 1 2\n") == std::string::npos); CHECK(pdb.find("CONECT 3 4 4\n") != std::string::npos); } { int flavor = 8; auto pdb = MolToPDBBlock(*m, confId, flavor); CHECK(pdb.find("CONECT 1 2\n") != std::string::npos); CHECK(pdb.find("CONECT 3 4 5\n") != std::string::npos); } { int flavor = 2 | 8; auto pdb = MolToPDBBlock(*m, confId, flavor); CHECK(pdb.find("CONECT") == std::string::npos); } } } TEST_CASE("test output with incomplete monomer info", "[bug][writer]") { SECTION("basics") { { auto m = "Cl"_smiles; REQUIRE(m); std::string pdb = MolToPDBBlock(*m, -1); CHECK(pdb.find("HETATM 1 CL1 UNL 1") != std::string::npos); } { auto m = "Cl"_smiles; // will get deleted by ~Atom() AtomPDBResidueInfo *info = new AtomPDBResidueInfo(); info->setResidueName("HCL"); m->getAtomWithIdx(0)->setMonomerInfo(info); std::string pdb = MolToPDBBlock(*m, -1); CHECK(pdb.find("ATOM 1 CL1 HCL 0") != std::string::npos); } { auto m = "Cl"_smiles; // will get deleted by ~Atom() AtomPDBResidueInfo *info = new AtomPDBResidueInfo(); info->setResidueName("HCL"); info->setName("Cl1"); m->getAtomWithIdx(0)->setMonomerInfo(info); std::string pdb = MolToPDBBlock(*m, -1); CHECK(pdb.find("ATOM 1 Cl1 HCL 0") != std::string::npos); } { // 1. should add spaces for padding if the atom name is too short // 2. should add spaces for missing residue name. auto m = "Cl"_smiles; // will get deleted by ~Atom() AtomPDBResidueInfo *info = new AtomPDBResidueInfo(); info->setName("CL"); m->getAtomWithIdx(0)->setMonomerInfo(info); std::string pdb = MolToPDBBlock(*m, -1); CHECK(pdb.find("ATOM 1 CL 0") != std::string::npos); } { // 1. Test that atom names get truncated to 4 letters. // 2. Test that residue names get truncated to 3 letters. auto m = "Cl"_smiles; // will get deleted by ~Atom() AtomPDBResidueInfo *info = new AtomPDBResidueInfo(); info->setName("CHLORINE_ATOM1"); info->setResidueName("CHLORINE_MOLECULE1"); m->getAtomWithIdx(0)->setMonomerInfo(info); std::string pdb = MolToPDBBlock(*m, -1); std::cout << pdb << std::endl; CHECK(pdb.find("ATOM 1 CHLO CHL 0") != std::string::npos); } } } TEST_CASE( "github #3599: Add explicit support for remaining CTAB query bond types", "[feature]") { SECTION("basics V3K") { auto m = R"CTAB( Mrv2014 11302009242D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 6 6 0 0 0 M V30 BEGIN ATOM M V30 1 N 3.7917 -2.96 0 0 M V30 2 C 2.458 -3.73 0 0 M V30 3 O 2.458 -5.27 0 0 M V30 4 C 3.7917 -6.04 0 0 M V30 5 C 5.1253 -5.27 0 0 M V30 6 C 5.1253 -3.73 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 2 3 M V30 2 1 4 5 M V30 3 1 1 6 M V30 4 5 1 2 M V30 5 6 5 6 M V30 6 7 3 4 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); REQUIRE(m->getBondWithIdx(3)->hasQuery()); CHECK(m->getBondWithIdx(3)->getQuery()->getDescription() == "SingleOrDoubleBond"); REQUIRE(m->getBondWithIdx(4)->hasQuery()); CHECK(m->getBondWithIdx(4)->getQuery()->getDescription() == "SingleOrAromaticBond"); REQUIRE(m->getBondWithIdx(5)->hasQuery()); CHECK(m->getBondWithIdx(5)->getQuery()->getDescription() == "DoubleOrAromaticBond"); auto mb = MolToV3KMolBlock(*m); CHECK(mb.find("M V30 4 5 1 2") != std::string::npos); CHECK(mb.find("M V30 5 6 5 6") != std::string::npos); CHECK(mb.find("M V30 6 7 3 4") != std::string::npos); std::string pkl; MolPickler::pickleMol(*m, pkl); m.reset(new RWMol(pkl)); REQUIRE(m); REQUIRE(m->getBondWithIdx(3)->hasQuery()); CHECK(m->getBondWithIdx(3)->getQuery()->getDescription() == "SingleOrDoubleBond"); REQUIRE(m->getBondWithIdx(4)->hasQuery()); CHECK(m->getBondWithIdx(4)->getQuery()->getDescription() == "SingleOrAromaticBond"); REQUIRE(m->getBondWithIdx(5)->hasQuery()); CHECK(m->getBondWithIdx(5)->getQuery()->getDescription() == "DoubleOrAromaticBond"); auto smarts = MolToSmarts(*m); CHECK(smarts == "[#7]1-,=[#6]-[#8]=,:[#6]-[#6][#6]-1"); } SECTION("basics V2K") { auto m = R"CTAB( Mrv2014 11302009442D 6 6 0 0 0 0 999 V2000 2.0313 -1.5857 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.3168 -1.9982 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3168 -2.8232 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0313 -3.2357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7457 -2.8232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7457 -1.9982 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 3 1 0 0 0 0 4 5 1 0 0 0 0 1 6 1 0 0 0 0 1 2 5 0 0 0 0 5 6 6 0 0 0 0 3 4 7 0 0 0 0 M END )CTAB"_ctab; REQUIRE(m); REQUIRE(m->getBondWithIdx(3)->hasQuery()); CHECK(m->getBondWithIdx(3)->getQuery()->getDescription() == "SingleOrDoubleBond"); REQUIRE(m->getBondWithIdx(4)->hasQuery()); CHECK(m->getBondWithIdx(4)->getQuery()->getDescription() == "SingleOrAromaticBond"); REQUIRE(m->getBondWithIdx(5)->hasQuery()); CHECK(m->getBondWithIdx(5)->getQuery()->getDescription() == "DoubleOrAromaticBond"); auto mb = MolToMolBlock(*m); CHECK(mb.find(" 1 2 5") != std::string::npos); CHECK(mb.find(" 5 6 6") != std::string::npos); CHECK(mb.find(" 3 4 7") != std::string::npos); std::string pkl; MolPickler::pickleMol(*m, pkl); m.reset(new RWMol(pkl)); REQUIRE(m); REQUIRE(m->getBondWithIdx(3)->hasQuery()); CHECK(m->getBondWithIdx(3)->getQuery()->getDescription() == "SingleOrDoubleBond"); REQUIRE(m->getBondWithIdx(4)->hasQuery()); CHECK(m->getBondWithIdx(4)->getQuery()->getDescription() == "SingleOrAromaticBond"); REQUIRE(m->getBondWithIdx(5)->hasQuery()); CHECK(m->getBondWithIdx(5)->getQuery()->getDescription() == "DoubleOrAromaticBond"); } } TEST_CASE("supplier close methods") { std::string rdbase = getenv("RDBASE"); SECTION("SDF") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf"; { SDMolSupplier suppl(fname); std::unique_ptr mol{suppl.next()}; REQUIRE(mol); suppl.close(); #if INVARIANT_EXCEPTION_METHOD REQUIRE_THROWS_AS(suppl.next(), Invar::Invariant); #endif } { std::ifstream instr(fname); ForwardSDMolSupplier suppl(&instr, false); std::unique_ptr mol{suppl.next()}; REQUIRE(mol); suppl.close(); #if INVARIANT_EXCEPTION_METHOD REQUIRE_THROWS_AS(suppl.next(), Invar::Invariant); #endif } } SECTION("SMILES") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.2.csv"; { SmilesMolSupplier suppl(fname, ",", 1, 0, true); std::unique_ptr mol{suppl.next()}; REQUIRE(mol); suppl.close(); #if INVARIANT_EXCEPTION_METHOD REQUIRE_THROWS_AS(suppl.next(), Invar::Invariant); #endif } } SECTION("TDT") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/acd_few.tdt"; { TDTMolSupplier suppl(fname, "PN"); std::unique_ptr mol{suppl.next()}; REQUIRE(mol); suppl.close(); #if INVARIANT_EXCEPTION_METHOD REQUIRE_THROWS_AS(suppl.next(), Invar::Invariant); #endif } } #ifdef RDK_BUILD_MAEPARSER_SUPPORT SECTION("MAE") { std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.mae"; { MaeMolSupplier suppl(fname); std::unique_ptr mol{suppl.next()}; REQUIRE(mol); suppl.close(); #if INVARIANT_EXCEPTION_METHOD REQUIRE_THROWS_AS(suppl.next(), Invar::Invariant); #endif } } #endif } TEST_CASE( "github #3768: SubstanceGroup output doesn't properly quote double " "quotes") { SECTION("basics") { auto m = R"CTAB( Mrv2014 01292104542D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 1 0 0 M V30 BEGIN ATOM M V30 1 C -1.3343 -0.7691 0 0 M V30 2 C -1.333 0.7709 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 2 1 2 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 1) FIELDNAME=[DUP]Tempstruct FIELDINFO="""" - M V30 FIELDDISP=" -0.1770 -0.5034 DA ALL 0 0" - M V30 QUERYOP="""""" FIELDDATA=Foo1 M V30 END SGROUP M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); auto sgs = getSubstanceGroups(*m); REQUIRE(sgs.size() == 1); auto sg = sgs[0]; CHECK(sg.getProp("FIELDINFO") == "\""); CHECK(sg.getProp("QUERYOP") == "\"\""); auto mb = MolToV3KMolBlock(*m); CHECK(mb.find("FIELDINFO=\"\"\"\"") != std::string::npos); CHECK(mb.find("QUERYOP=\"\"\"\"\"") != std::string::npos); } SECTION("parens and quote not at beginning") { auto m = R"CTAB( Mrv2014 01292104542D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 1 0 0 M V30 BEGIN ATOM M V30 1 C -1.3343 -0.7691 0 0 M V30 2 C -1.333 0.7709 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 2 1 2 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 1) FIELDNAME=[DUP]Tempstruct FIELDINFO="foo""" - M V30 FIELDDISP=" -0.1770 -0.5034 DA ALL 0 0" - M V30 QUERYOP="(bar)" FIELDDATA=Foo1 M V30 END SGROUP M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); auto sgs = getSubstanceGroups(*m); REQUIRE(sgs.size() == 1); auto sg = sgs[0]; CHECK(sg.getProp("FIELDINFO") == "foo\""); CHECK(sg.getProp("QUERYOP") == "(bar)"); auto mb = MolToV3KMolBlock(*m); CHECK(mb.find("FIELDINFO=\"foo\"\"\"") != std::string::npos); CHECK(mb.find("QUERYOP=\"(bar)\"") != std::string::npos); } } TEST_CASE("github #3216: WedgeMolBonds() should prefer degree-1 atoms") { SECTION("basics") { auto m = R"CTAB( Mrv2007 06082008522D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 8 7 0 0 0 M V30 BEGIN ATOM M V30 1 C -17.7571 16.6703 0 0 M V30 2 C -16.4234 17.4403 0 0 M V30 3 C -15.0897 16.6703 0 0 CFG=1 M V30 4 C -13.7561 17.4403 0 0 CFG=2 M V30 5 Br -15.0897 15.1303 0 0 M V30 6 C -12.4225 16.6703 0 0 M V30 7 Cl -13.7561 18.9803 0 0 M V30 8 C -11.0888 17.4403 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 3 5 CFG=1 M V30 4 1 3 4 M V30 5 1 4 6 M V30 6 1 4 7 CFG=1 M V30 7 1 6 8 M V30 END BOND M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); Chirality::wedgeMolBonds(*m, &m->getConformer()); CHECK(m->getBondBetweenAtoms(2, 4)->getBondDir() != Bond::BondDir::NONE); CHECK(m->getBondBetweenAtoms(3, 6)->getBondDir() != Bond::BondDir::NONE); CHECK(m->getBondBetweenAtoms(2, 1)->getBondDir() == Bond::BondDir::NONE); CHECK(m->getBondBetweenAtoms(2, 3)->getBondDir() == Bond::BondDir::NONE); CHECK(m->getBondBetweenAtoms(3, 5)->getBondDir() == Bond::BondDir::NONE); } } TEST_CASE("Hydrogen bonds in CTABs") { SECTION("basics") { auto m = R"CTAB( Mrv2014 03022114422D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 8 8 0 0 0 M V30 BEGIN ATOM M V30 1 C -5.4583 -0.125 0 0 M V30 2 C -4.1247 0.645 0 0 M V30 3 C -2.791 -0.125 0 0 M V30 4 C -1.4573 0.645 0 0 M V30 5 O -2.791 -1.665 0 0 M V30 6 C -6.792 0.645 0 0 M V30 7 O -5.4583 -1.665 0 0 M V30 8 H -4.1247 -2.435 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 3 4 M V30 4 2 3 5 M V30 5 1 1 6 M V30 6 1 1 7 M V30 7 1 7 8 M V30 8 10 5 8 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); REQUIRE(m->getBondBetweenAtoms(4, 7)); CHECK(m->getBondBetweenAtoms(4, 7)->getBondType() == Bond::BondType::HYDROGEN); auto mb = MolToV3KMolBlock(*m); CHECK(mb.find("V30 8 10 5 8") != std::string::npos); CHECK(MolToSmiles(*m) == "CC1CC(C)O[H]~O=1"); // the SMILES writer still doesn't know what to // do with it } } TEST_CASE("Support empty FIELDNAMES in SDT lines") { SECTION("basics") { auto m = R"CTAB( Mrv2014 03112117322D 6 6 0 0 0 0 999 V2000 -1.8270 -1.5114 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2764 -0.8194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1002 -0.8626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4748 -1.5977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0255 -2.2896 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2016 -2.2465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 1 6 1 0 0 0 0 M STY 1 1 DAT M SAL 1 6 1 2 3 4 5 6 M SDT 1 M SDD 1 -2.4921 -3.0466 DA ALL 1 5 M SED 1 foo: 1234.6 M END )CTAB"_ctab; REQUIRE(m); auto sgs = getSubstanceGroups(*m); REQUIRE(sgs.size() == 1); { auto outctab = MolToMolBlock(*m); CHECK(outctab.find("1234.6") != std::string::npos); auto nm = MolBlockToMol(outctab); REQUIRE(nm); auto sgs = getSubstanceGroups(*nm); REQUIRE(sgs.size() == 1); delete nm; } { auto outctab = MolToV3KMolBlock(*m); CHECK(outctab.find("1234.6") != std::string::npos); auto nm = MolBlockToMol(outctab); REQUIRE(nm); auto sgs = getSubstanceGroups(*nm); REQUIRE(sgs.size() == 1); delete nm; } } } TEST_CASE("Support reading unambiguous short atom lines") { SECTION("basics") { std::string mb = R"CTAB( Mrv2014 03112117322D 2 1 0 0 0 0 999 V2000 -1.8270 -1.5114 0.0000 C -2.2764 -0.8194 0.0000 C 1 2 1 0 0 0 0 M END )CTAB"; // we fail when doing strict parsing REQUIRE_THROWS_AS(MolBlockToMol(mb), FileParseException); bool removeHs = true; bool sanitize = true; bool strictParsing = false; // but can read it with non-strict parsing std::unique_ptr m{ MolBlockToMol(mb, sanitize, removeHs, strictParsing)}; REQUIRE(m); CHECK(m->getNumAtoms() == 2); CHECK(m->getAtomWithIdx(0)->getAtomicNum() == 6); CHECK(m->getAtomWithIdx(1)->getAtomicNum() == 6); } SECTION("too short") { std::string mb = R"CTAB( Mrv2014 03112117322D 2 1 0 0 0 0 999 V2000 -1.8270 -1.5114 0.0000 -2.2764 -0.8194 0.0000 C 1 2 1 0 0 0 0 M END )CTAB"; // we fail when doing strict parsing REQUIRE_THROWS_AS(MolBlockToMol(mb), FileParseException); bool removeHs = true; bool sanitize = true; bool strictParsing = false; // fail even with non-strict parsing REQUIRE_THROWS_AS(MolBlockToMol(mb, sanitize, removeHs, strictParsing), FileParseException); } } TEST_CASE("Github #4099: HCount field in v2000 mol blocks ignored") { SECTION("basics") { auto mol = R"CTAB(Test 3 2 0 0 0 0 0 0 0 0999 V2000 2.7500 -7.9167 -0.0000 C 0 0 0 3 0 0 0 0 0 0 0 0 3.6160 -7.4167 -0.0000 N 0 0 0 1 0 0 0 0 0 0 0 0 4.4821 -7.9167 -0.0000 C 0 0 0 2 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 M END)CTAB"_ctab; REQUIRE(mol); CHECK(MolToSmarts(*mol) == "[#6&h{2-}]-[#7&h0]-[#6&h{1-}]"); } } TEST_CASE("Github #4131: HCOUNT from v3000 CTABS incorrectly interpreted") { SECTION("basics") { auto mol = R"CTAB( Mrv2108 05122108272D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 3 2 0 0 0 M V30 BEGIN ATOM M V30 1 C 5.458 -2.2567 0 0 HCOUNT=2 M V30 2 N 6.7916 -1.4867 0 0 HCOUNT=0 M V30 3 C 8.1254 -2.2567 0 0 HCOUNT=-1 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); CHECK(MolToSmarts(*mol) == "[#6&h{2-}]-[#7]-[#6&h0]"); } } TEST_CASE("sgroups and strict parsing") { SECTION("everything ok") { std::string ctab = R"CTAB( Mrv2108 06052107052D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 2 0 0 M V30 BEGIN ATOM M V30 1 C -6.875 1.0417 0 0 M V30 2 C -5.5413 1.8117 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 2) FIELDNAME=foo - M V30 FIELDDISP=" -5.5413 1.8117 DAU ALL 0 0" - M V30 MRV_FIELDDISP=0 FIELDDATA=bar M V30 2 DAT 0 ATOMS=(1 1) FIELDNAME=foo - M V30 FIELDDISP=" -6.8750 1.0417 DAU ALL 0 0" - M V30 MRV_FIELDDISP=0 FIELDDATA=baz M V30 END SGROUP M V30 END CTAB M END )CTAB"; std::unique_ptr m(MolBlockToMol(ctab)); CHECK(m); } SECTION("SGroups totally missing") { std::string ctab = R"CTAB( Mrv2108 06052107052D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 2 0 0 M V30 BEGIN ATOM M V30 1 C -6.875 1.0417 0 0 M V30 2 C -5.5413 1.8117 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 END BOND M V30 END CTAB M END )CTAB"; std::unique_ptr m; CHECK_THROWS_AS(m.reset(MolBlockToMol(ctab)), FileParseException); bool sanitize = true; bool removeHs = true; bool strictParsing = false; m.reset(MolBlockToMol(ctab, sanitize, removeHs, strictParsing)); CHECK(m); } SECTION("one SGroup missing") { std::string ctab = R"CTAB( Mrv2108 06052107052D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 2 0 0 M V30 BEGIN ATOM M V30 1 C -6.875 1.0417 0 0 M V30 2 C -5.5413 1.8117 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 END BOND M V30 BEGIN SGROUP M V30 2 DAT 0 ATOMS=(1 1) FIELDNAME=foo - M V30 FIELDDISP=" -6.8750 1.0417 DAU ALL 0 0" - M V30 MRV_FIELDDISP=0 FIELDDATA=baz M V30 END SGROUP M V30 END CTAB M END )CTAB"; std::unique_ptr m; // fails without an exception m.reset(MolBlockToMol(ctab)); CHECK(!m); bool sanitize = true; bool removeHs = true; bool strictParsing = false; m.reset(MolBlockToMol(ctab, sanitize, removeHs, strictParsing)); CHECK(m); } SECTION("END SGROUPS missing") { std::string ctab = R"CTAB( Mrv2108 06052107052D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 2 0 0 M V30 BEGIN ATOM M V30 1 C -6.875 1.0417 0 0 M V30 2 C -5.5413 1.8117 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 2) FIELDNAME=foo - M V30 FIELDDISP=" -5.5413 1.8117 DAU ALL 0 0" - M V30 MRV_FIELDDISP=0 FIELDDATA=bar M V30 2 DAT 0 ATOMS=(1 1) FIELDNAME=foo - M V30 FIELDDISP=" -6.8750 1.0417 DAU ALL 0 0" - M V30 MRV_FIELDDISP=0 FIELDDATA=baz M V30 END CTAB M END )CTAB"; std::unique_ptr m; CHECK_THROWS_AS(m.reset(MolBlockToMol(ctab)), FileParseException); bool sanitize = true; bool removeHs = true; bool strictParsing = false; m.reset(MolBlockToMol(ctab, sanitize, removeHs, strictParsing)); CHECK(m); } } TEST_CASE("double bond stereo should not be set when the coords are all zero") { auto m = R"CTAB( RDKit 2D 4 3 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 M END)CTAB"_ctab; REQUIRE(m); REQUIRE(m->getBondBetweenAtoms(1, 2)); CHECK(m->getBondBetweenAtoms(1, 2)->getStereo() == Bond::STEREOANY); } TEST_CASE("Handle MRV_COORDINATE_BOND_TYPE data Substance Groups") { SECTION( "Convert SDF V2000 MRV_COORDINATE_BOND_TYPE data Substance Groups " "into coordinate bonds") { auto m = R"CTAB( Mrv2111 06302118332D 9 9 0 0 0 0 999 V2000 -2.9465 0.7804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6609 0.3679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6609 -0.4572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9465 -0.8697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2320 -0.4572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2320 0.3679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5175 0.7804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9465 -1.6947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3754 0.7804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 1 1 0 0 0 0 6 7 8 0 0 0 0 4 8 8 0 0 0 0 2 9 8 0 0 0 0 M STY 3 1 DAT 2 DAT 3 DAT M SAL 1 2 6 7 M SDT 1 MRV_COORDINATE_BOND_TYPE M SDD 1 0.0000 0.0000 DR ALL 0 0 M SED 1 7 M SAL 2 2 4 8 M SDT 2 MRV_COORDINATE_BOND_TYPE M SDD 2 0.0000 0.0000 DR ALL 0 0 M SED 2 8 M SAL 3 2 2 9 M SDT 3 MRV_COORDINATE_BOND_TYPE M SDD 3 0.0000 0.0000 DR ALL 0 0 M SED 3 9 M END )CTAB"_ctab; REQUIRE(m); std::vector> coordinate_bonds{ {5, 6}, {3, 7}, {1, 8}}; for (const auto &bond_atoms : coordinate_bonds) { auto bnd = m->getBondBetweenAtoms(bond_atoms.first, bond_atoms.second); REQUIRE(bnd); CHECK(bnd->getBondType() == Bond::BondType::DATIVE); CHECK(typeid(*bnd) == typeid(Bond)); } CHECK(getSubstanceGroups(*m).empty()); } SECTION( "GitHub Issue #4473: MRV_COORDINATE_BOND_TYPE SGroup may reference bond " "index, instead of atom") { // Same input as previous test, just shuffled the bonds and changed // the indexes in the SGroups auto m1 = R"CTAB( Mrv2111 06302118332D 9 9 0 0 0 0 999 V2000 -2.9465 0.7804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6609 0.3679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6609 -0.4572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9465 -0.8697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2320 -0.4572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2320 0.3679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5175 0.7804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9465 -1.6947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3754 0.7804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 7 8 0 0 0 0 4 8 8 0 0 0 0 2 9 8 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 1 1 0 0 0 0 M STY 3 1 DAT 2 DAT 3 DAT M SAL 1 2 6 7 M SDT 1 MRV_COORDINATE_BOND_TYPE M SDD 1 0.0000 0.0000 DR ALL 0 0 M SED 1 1 M SAL 2 2 4 8 M SDT 2 MRV_COORDINATE_BOND_TYPE M SDD 2 0.0000 0.0000 DR ALL 0 0 M SED 2 2 M SAL 3 2 2 9 M SDT 3 MRV_COORDINATE_BOND_TYPE M SDD 3 0.0000 0.0000 DR ALL 0 0 M SED 3 3 M END )CTAB"_ctab; // Same input, but changing the type of 2 of the bonds, and giving // a random value to the other SGroup to check that we fail auto m2 = R"CTAB( Mrv2111 06302118332D 9 9 0 0 0 0 999 V2000 -2.9465 0.7804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6609 0.3679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6609 -0.4572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9465 -0.8697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2320 -0.4572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2320 0.3679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5175 0.7804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9465 -1.6947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3754 0.7804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 7 1 0 0 0 0 4 8 1 0 0 0 0 2 9 1 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 1 1 0 0 0 0 M STY 3 1 DAT 2 DAT 3 DAT M SAL 1 2 6 7 M SDT 1 MRV_COORDINATE_BOND_TYPE M SDD 1 0.0000 0.0000 DR ALL 0 0 M SED 1 1 M SAL 2 2 4 8 M SDT 2 MRV_COORDINATE_BOND_TYPE M SDD 2 0.0000 0.0000 DR ALL 0 0 M SED 2 2 M SAL 3 2 2 9 M SDT 3 MRV_COORDINATE_BOND_TYPE M SDD 3 0.0000 0.0000 DR ALL 0 0 M SED 3 100 M END )CTAB"_ctab; std::vector> coordinate_bonds{ {5, 6}, {3, 7}, {1, 8}}; for (const auto &bond_atoms : coordinate_bonds) { auto bnd = m1->getBondBetweenAtoms(bond_atoms.first, bond_atoms.second); REQUIRE(bnd); CHECK(bnd->getBondType() == Bond::BondType::DATIVE); CHECK(typeid(*bnd) == typeid(Bond)); } CHECK(getSubstanceGroups(*m1).empty()); REQUIRE(m2); for (const auto &bond_atoms : coordinate_bonds) { auto bnd = m2->getBondBetweenAtoms(bond_atoms.first, bond_atoms.second); REQUIRE(bnd); CHECK(bnd->getBondType() != Bond::BondType::DATIVE); } CHECK(getSubstanceGroups(*m2).empty()); } } TEST_CASE( "Github #4256: multiple ATTCHPT entries for one atom handled " "incorrectly") { SECTION("V3000") { std::string ctab = R"CTAB( Mrv2108 06172117542D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 0 0 0 M V30 BEGIN ATOM M V30 1 C -4.8333 3.5 0 0 M V30 2 C -3.4997 4.27 0 0 ATTCHPT=-1 ATTCHPT=3 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 END BOND M V30 END CTAB M END)CTAB"; { REQUIRE_THROWS_AS(MolBlockToMol(ctab), FileParseException); } { bool sanitize = true; bool removeHs = true; bool strictParsing = false; std::unique_ptr m{ MolBlockToMol(ctab, sanitize, removeHs, strictParsing)}; REQUIRE(m); auto atom = m->getAtomWithIdx(1); REQUIRE(atom->hasProp(common_properties::molAttachPoint)); REQUIRE(atom->getProp(common_properties::molAttachPoint) == -1); } } SECTION("V2000 1") { // Marvin doesn't actually do this, but might as well // test for it anyway std::string ctab = R"CTAB( Mrv2108 06212115462D 2 1 0 0 0 0 999 V2000 -2.5894 1.8751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8749 2.2876 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 M APO 2 2 3 2 2 M END )CTAB"; } SECTION("V2000 2") { // Marvin doesn't actually do this, but might as well // test for it anyway std::string ctab = R"CTAB( Mrv2108 06212115482D 2 1 0 0 0 0 999 V2000 -2.5894 1.8751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8749 2.2876 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 M APO 1 2 3 M APO 1 2 2 M END )CTAB"; } } TEST_CASE("Long lines in V3000 mol blocks") { SECTION("basics") { auto m = R"CTAB(query Mrv2108 07152116102D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 1 0 0 M V30 BEGIN ATOM M V30 1 C 3.5417 -5.875 0 0 M V30 2 C 4.8753 -5.105 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 2) - M V30 FIELDDISP=" 4.8753 -5.1050 DA ALL 0 0" - M V30 QUERYTYPE=SMARTSL QUERYOP== FIELDDATA=[#6;R] M V30 END SGROUP M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); CHECK(getSubstanceGroups(*m).size() == 1); auto mb = MolToV3KMolBlock(*m); std::unique_ptr m2(MolBlockToMol(mb)); REQUIRE(m2); CHECK(getSubstanceGroups(*m2).size() == 1); } SECTION("long data elements") { auto m = R"CTAB(query with bogus sgroups Mrv2108 07152116102D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 5 0 0 M V30 BEGIN ATOM M V30 1 C 3.5417 -5.875 0 0 M V30 2 C 4.8753 -5.105 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 2) - M V30 FIELDDISP=" 0.0000 0.0000 DR ALL 0 0" - M V30 QUERYTYPE=SMARTSR QUERYOP== - M V30 FIELDDATA="quite long piece of text that needs to be broken - M V30 across two lines" M V30 2 DAT 0 ATOMS=(1 1) - M V30 FIELDDISP=" 0.0000 0.0000 DR ALL 0 0" - M V30 QUERYTYPE=SMARTSR QUERYOP== - M V30 FIELDDATA="quite long piece of text that needs to be broken - M V30 across more than two lines because we really want to be sure - M V30 that we are doing this right" M V30 3 DAT 0 ATOMS=(1 1) - M V30 FIELDDISP=" 0.0000 0.0000 DR ALL 0 0" - M V30 QUERYTYPE=SMARTSR QUERYOP== - M V30 FIELDDATA="quite long piece of text that needs to be broken - M V30 across exactly two lines so that we can check the edge case - M V30 11111111111111111111" M V30 4 DAT 0 ATOMS=(1 1) - M V30 FIELDDISP=" 0.0000 0.0000 DR ALL 0 0" - M V30 QUERYTYPE=SMARTSR QUERYOP== - M V30 FIELDDATA="quite long piece of text that needs to be broken - M V30 across more than two lines because we really want to be sure - M V30 that we are doing this right" SEQID=1 M V30 5 DAT 0 ATOMS=(1 1) - M V30 FIELDDISP=" 0.0000 0.0000 DR ALL 0 0" - M V30 QUERYTYPE=SMARTSR QUERYOP== - M V30 FIELDDATA="quite long piece of text that needs to be broken - M V30 across exactly two lines so that we can check the edge case - M V30 11111111111111111111" SEQID=2 M V30 END SGROUP M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); CHECK(getSubstanceGroups(*m).size() == 5); auto mb = MolToV3KMolBlock(*m); std::unique_ptr m2(MolBlockToMol(mb)); REQUIRE(m2); CHECK(getSubstanceGroups(*m2).size() == 5); } SECTION( "GitHub Issue #4471: SDF SGroups may be missing the final space in the " "\"M V30 \" prefix") { auto m = R"CTAB(bogus mol with unspaced SGroup field Mrv2114 09022123382D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 1 0 0 M V30 BEGIN ATOM M V30 1 C -0.7917 0 0 0 M V30 END ATOM M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 1) FIELDNAME=Data - M V30 FIELDDISP=" 0.0000 0.0000 DRU ALL 0 0" - M V30 MRV_FIELDDISP=0 - M V30 FIELDDATA=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA- M V30 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA- M V30 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA- M V30 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA M V30 END SGROUP M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); CHECK(getSubstanceGroups(*m).size() == 1); auto mb = MolToV3KMolBlock(*m); std::unique_ptr m2(MolBlockToMol(mb)); REQUIRE(m2); CHECK(getSubstanceGroups(*m2).size() == 1); } SECTION( "GitHub Issue #4477: Same SDF SGroup lines may be written multiple " "times") { auto m = R"CTAB( Mrv2014 03112117322D 6 6 0 0 0 0 999 V2000 -1.8270 -1.5114 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2764 -0.8194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1002 -0.8626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4748 -1.5977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0255 -2.2896 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2016 -2.2465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 1 6 1 0 0 0 0 M STY 1 1 DAT M SAL 1 6 1 2 3 4 5 6 M SDT 1 M SDD 1 -2.4921 -3.0466 DA 123456789012345 ALL 1 5 M END)CTAB"_ctab; REQUIRE(m); CHECK(getSubstanceGroups(*m).size() == 1); auto mb = MolToV3KMolBlock(*m); auto pos = 0u; auto count = 0u; std::string target{"FIELDDISP"}; while (pos < mb.size()) { pos = mb.find(target, pos); if (pos < mb.size()) { pos += target.size(); ++count; } } CHECK(count == 1); } } TEST_CASE("github #4345: non-stereo bonds written with unspecified parity") { SECTION("basics") { auto m = "CC=C(F)F"_smiles; REQUIRE(m); auto mb = MolToV3KMolBlock(*m); CHECK(mb.find("CFG=2") == std::string::npos); mb = MolToMolBlock(*m); CHECK(mb.find(" 2 3 2 3") == std::string::npos); } SECTION("possible chirality") { auto m = "CC=C(O)F"_smiles; REQUIRE(m); auto mb = MolToV3KMolBlock(*m); CHECK(mb.find("CFG=2") != std::string::npos); mb = MolToMolBlock(*m); CHECK(mb.find(" 2 3 2 3") != std::string::npos); } SECTION("terminal") { auto m = "CC=C"_smiles; REQUIRE(m); auto mb = MolToV3KMolBlock(*m); CHECK(mb.find("CFG=2") == std::string::npos); mb = MolToMolBlock(*m); CHECK(mb.find(" 2 3 2 3") == std::string::npos); } SECTION("nitrogen") { auto m = "CC(C)=NF"_smiles; REQUIRE(m); auto mb = MolToV3KMolBlock(*m); CHECK(mb.find("CFG=2") == std::string::npos); mb = MolToMolBlock(*m); CHECK(mb.find(" 3 4 2 3") == std::string::npos); } SECTION("nitrogen with") { auto m = "CC=NF"_smiles; REQUIRE(m); auto mb = MolToV3KMolBlock(*m); CHECK(mb.find("CFG=2") != std::string::npos); mb = MolToMolBlock(*m); CHECK(mb.find(" 2 3 2 3") != std::string::npos); } SECTION("direction explicitly set should be ignored") { auto m = "CC=C(F)F"_smiles; REQUIRE(m); m->getBondWithIdx(0)->setBondDir(Bond::BondDir::ENDUPRIGHT); m->getBondWithIdx(2)->setBondDir(Bond::BondDir::ENDUPRIGHT); auto mb = MolToV3KMolBlock(*m); CHECK(mb.find("CFG=2") == std::string::npos); mb = MolToMolBlock(*m); CHECK(mb.find(" 2 3 2 3") == std::string::npos); } } TEST_CASE( "github #4476: Additional SDT properties not decoded if FIELDNAME is " "empty") { SECTION("basics") { auto m = R"CTAB(query Mrv2102 09032106302D 2 1 0 0 0 0 999 V2000 -0.4464 2.4334 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2680 2.8459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 M STY 1 1 DAT M SAL 1 1 2 M SDT 1 PQ= M SDD 1 0.0000 0.0000 DR ALL 0 0 M SED 1 [#6;R] M END )CTAB"_ctab; REQUIRE(m); REQUIRE(getSubstanceGroups(*m).size() == 1); const auto sg = getSubstanceGroups(*m)[0]; CHECK(sg.hasProp("QUERYTYPE")); CHECK(sg.getProp("QUERYTYPE") == "PQ"); CHECK(sg.hasProp("QUERYOP")); CHECK(sg.getProp("QUERYOP") == "="); } } TEST_CASE("github #4468: decode SMARTS in SGroups") { SECTION("parsing v3000") { auto m = R"CTAB(query Mrv2108 07152116012D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 1 0 0 M V30 BEGIN ATOM M V30 1 C -0.8333 4.5421 0 0 M V30 2 C 0.5003 5.3121 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 2) - M V30 FIELDDISP=" 0.0000 0.0000 DR ALL 0 0" - M V30 QUERYTYPE=SMARTSQ QUERYOP== FIELDDATA=[#6;R] M V30 END SGROUP M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); REQUIRE(m->getAtomWithIdx(1)->hasQuery()); CHECK(SmartsWrite::GetAtomSmarts( static_cast(m->getAtomWithIdx(1))) == "[#6&R]"); CHECK(getSubstanceGroups(*m).empty()); } SECTION("ensure bad SMARTS don't break things") { auto m = R"CTAB(query Mrv2108 07152116012D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 1 0 0 M V30 BEGIN ATOM M V30 1 C -0.8333 4.5421 0 0 M V30 2 C 0.5003 5.3121 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 2) - M V30 FIELDDISP=" 0.0000 0.0000 DR ALL 0 0" - M V30 QUERYTYPE=SMARTSQ QUERYOP== FIELDDATA=[#6;R M V30 END SGROUP M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); REQUIRE(!m->getAtomWithIdx(1)->hasQuery()); CHECK(getSubstanceGroups(*m).empty()); } SECTION("empty SMARTS") { auto m = R"CTAB(query Mrv2108 07152116012D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 1 0 0 M V30 BEGIN ATOM M V30 1 C -0.8333 4.5421 0 0 M V30 2 C 0.5003 5.3121 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 2) - M V30 FIELDDISP=" 0.0000 0.0000 DR ALL 0 0" - M V30 QUERYTYPE=SMARTSQ QUERYOP== FIELDDATA= M V30 END SGROUP M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); REQUIRE(!m->getAtomWithIdx(1)->hasQuery()); CHECK(getSubstanceGroups(*m).empty()); } SECTION("bad operator") { auto m = R"CTAB(query Mrv2108 07152116012D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 1 0 0 M V30 BEGIN ATOM M V30 1 C -0.8333 4.5421 0 0 M V30 2 C 0.5003 5.3121 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 2) - M V30 FIELDDISP=" 0.0000 0.0000 DR ALL 0 0" - M V30 QUERYTYPE=SMARTSQ QUERYOP=> FIELDDATA=[#6;R] M V30 END SGROUP M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); REQUIRE(!m->getAtomWithIdx(1)->hasQuery()); CHECK(getSubstanceGroups(*m).empty()); } SECTION("SMARTS with multiple atoms become recursive") { auto m = R"CTAB(query Mrv2108 07152116012D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 1 0 0 M V30 BEGIN ATOM M V30 1 C -0.8333 4.5421 0 0 M V30 2 C 0.5003 5.3121 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 2) - M V30 FIELDDISP=" 0.0000 0.0000 DR ALL 0 0" - M V30 QUERYTYPE=SMARTSQ QUERYOP== FIELDDATA=[#6;R]-[#8] M V30 END SGROUP M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); REQUIRE(m->getAtomWithIdx(1)->hasQuery()); CHECK(SmartsWrite::GetAtomSmarts(static_cast( m->getAtomWithIdx(1))) == "[$([#6&R]-[#8])]"); CHECK(getSubstanceGroups(*m).empty()); } SECTION("parsing v3000, v2000 compatibility version") { auto m = R"CTAB(query Mrv2108 07152116012D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 1 0 0 M V30 BEGIN ATOM M V30 1 C -0.8333 4.5421 0 0 M V30 2 C 0.5003 5.3121 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 2) - M V30 FIELDDISP=" 0.0000 0.0000 DR ALL 0 0" - M V30 QUERYTYPE=SQ QUERYOP== FIELDDATA=[#6;R] M V30 END SGROUP M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); REQUIRE(m->getAtomWithIdx(1)->hasQuery()); CHECK(SmartsWrite::GetAtomSmarts( static_cast(m->getAtomWithIdx(1))) == "[#6&R]"); CHECK(getSubstanceGroups(*m).empty()); } SECTION("parsing v2000") { auto m = R"CTAB(query Mrv2102 09032106302D 2 1 0 0 0 0 999 V2000 -0.4464 2.4334 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2680 2.8459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 M STY 1 1 DAT M SAL 1 1 2 M SDT 1 SQ= M SDD 1 0.0000 0.0000 DR ALL 0 0 M SED 1 [#6;R] M END )CTAB"_ctab; REQUIRE(m); REQUIRE(m->getAtomWithIdx(1)->hasQuery()); CHECK(SmartsWrite::GetAtomSmarts( static_cast(m->getAtomWithIdx(1))) == "[#6&R]"); CHECK(getSubstanceGroups(*m).empty()); } } TEST_CASE("Github #4561: failure to parse CTAB with LINKNODE and SGROUP") { SECTION("BASICS") { auto mol1 = R"CTAB( Mrv2108 09252106182D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 7 7 1 0 0 M V30 BEGIN ATOM M V30 1 C 12.719 -9.1518 0 0 M V30 2 O 14.0458 -9.9326 0 0 M V30 3 * 15.3857 -9.1735 0 0 M V30 4 * 11.379 -9.9108 0 0 M V30 5 C 12.7317 -7.6118 0 0 M V30 6 C 12.2558 -6.1472 0 0 M V30 7 C 13.7622 -6.4674 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 1 4 M V30 4 1 1 5 M V30 5 1 7 6 M V30 6 1 6 5 M V30 7 1 5 7 M V30 END BOND M V30 LINKNODE 1 2 2 7 5 7 6 M V30 BEGIN SGROUP M V30 1 SRU 0 ATOMS=(5 2 1 5 7 6) XBONDS=(2 2 3) BRKXYZ=(9 12.044 -10.2974 0 - M V30 12.044 -8.7593 0 0 0 0) BRKXYZ=(9 14.7161 -8.7854 0 14.7161 -10.3235 0 - M V30 0 0 0) CONNECT=HT LABEL=n M V30 END SGROUP M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol1); CHECK(getSubstanceGroups(*mol1).size() == 1); CHECK(mol1->hasProp(common_properties::molFileLinkNodes)); } } TEST_CASE( "Github #4785: MDL query with aromatic bond sets aromatic flag on atoms " "even though they are not in an aromatic ring") { SECTION("benzene") { auto mol = R"CTAB( Mrv2108 12102110572D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 6 6 0 0 0 M V30 BEGIN ATOM M V30 1 C 128.125 -103.585 0 0 M V30 2 C 126.7913 -104.355 0 0 M V30 3 C 126.7913 -105.895 0 0 M V30 4 C 128.125 -106.665 0 0 M V30 5 C 129.4587 -105.895 0 0 M V30 6 C 129.4587 -104.355 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 4 1 2 M V30 2 4 2 3 M V30 3 4 3 4 M V30 4 4 4 5 M V30 5 4 5 6 M V30 6 4 1 6 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getAtomWithIdx(0)->getIsAromatic()); CHECK(mol->getBondWithIdx(0)->getIsAromatic()); } SECTION("non-kekulizeable") { auto mol = R"CTAB( Mrv2108 12102110572D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 5 0 0 0 M V30 BEGIN ATOM M V30 1 C 128.125 -103.585 0 0 M V30 2 C 126.7913 -104.355 0 0 M V30 3 C 126.7913 -105.895 0 0 M V30 4 C 128.125 -106.665 0 0 M V30 5 C 129.4587 -105.895 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 4 1 2 M V30 2 4 2 3 M V30 3 4 3 4 M V30 4 4 4 5 M V30 5 4 5 1 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(!mol); } SECTION("as reported1") { auto mol = R"CTAB( MJ201100 2 1 0 0 0 0 0 0 0 0999 V2000 -0.3538 0.6163 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0668 0.2012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 4 0 0 1 0 M MRV SMA 1 [#6;a;a] M MRV SMA 2 [#6;a;a] M END)CTAB"_ctab; REQUIRE(mol); } SECTION("as reported2") { auto mol = R"CTAB( MJ201100 2 1 0 0 0 0 0 0 0 0999 V2000 -0.3538 0.6163 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0 -1.0668 0.2012 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0 1 2 4 0 0 1 0 M END)CTAB"_ctab; REQUIRE(mol); } SECTION("as reported3") { auto mol = R"CTAB( RDKit 2D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 0 0 0 M V30 BEGIN ATOM M V30 1 A -0.353800 0.616300 0.000000 0 M V30 2 A -1.066800 0.201200 0.000000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 4 1 2 TOPO=1 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); } } TEST_CASE("checking array bounds") { SECTION("XBONDS") { auto mb = R"CTAB( Mrv2108 01202214292D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 4 3 1 0 0 M V30 BEGIN ATOM M V30 1 * -6.6667 7.5833 0 0 M V30 2 C -5.333 8.3533 0 0 M V30 3 C -3.9993 7.5833 0 0 M V30 4 * -2.6656 8.3533 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 3 4 M V30 END BOND M V30 BEGIN SGROUP M V30 1 SRU 0 ATOMS=(2 2 3) XBONDS=(20 1 3) BRKXYZ=(9 -3.9121 8.7006 0 - M V30 -2.9881 7.1002 0 0 0 0) BRKXYZ=(9 -5.4201 7.2361 0 -6.3441 8.8365 0 0 - M V30 0 0) CONNECT=HT LABEL=n M V30 END SGROUP M V30 END CTAB M END )CTAB"; std::unique_ptr mol; REQUIRE_THROWS_AS(mol.reset(MolBlockToMol(mb)), FileParseException); } SECTION("ATOMS") { auto mb = R"CTAB( Mrv2108 01202214292D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 4 3 1 0 0 M V30 BEGIN ATOM M V30 1 * -6.6667 7.5833 0 0 M V30 2 C -5.333 8.3533 0 0 M V30 3 C -3.9993 7.5833 0 0 M V30 4 * -2.6656 8.3533 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 3 4 M V30 END BOND M V30 BEGIN SGROUP M V30 1 SRU 0 ATOMS=(12 2 3) XBONDS=(2 1 3) BRKXYZ=(9 -3.9121 8.7006 0 - M V30 -2.9881 7.1002 0 0 0 0) BRKXYZ=(9 -5.4201 7.2361 0 -6.3441 8.8365 0 0 - M V30 0 0) CONNECT=HT LABEL=n M V30 END SGROUP M V30 END CTAB M END )CTAB"; std::unique_ptr mol; REQUIRE_THROWS_AS(mol.reset(MolBlockToMol(mb)), FileParseException); } } TEST_CASE("Github #5108: Wiggly bonds don't override wedged bonds") { SECTION("as reported") { auto m = R"CTAB( Mrv2102 03212207042D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 4 0 0 1 M V30 BEGIN ATOM M V30 1 C 1.54 -1.54 0 0 M V30 2 C 1.54 0 0 0 M V30 3 O 1.54 1.54 0 0 M V30 4 F 3.08 -0 0 0 M V30 5 Cl 0 0 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 2 1 M V30 2 1 2 3 CFG=2 M V30 3 1 2 4 CFG=1 M V30 4 1 2 5 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_UNSPECIFIED); } SECTION("as reported, bond ordering changed") { auto m = R"CTAB( Mrv2102 03212207042D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 4 0 0 1 M V30 BEGIN ATOM M V30 1 C 1.54 -1.54 0 0 M V30 2 C 1.54 0 0 0 M V30 3 O 1.54 1.54 0 0 M V30 4 F 3.08 -0 0 0 M V30 5 Cl 0 0 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 2 1 M V30 2 1 2 4 CFG=1 M V30 3 1 2 3 CFG=2 M V30 4 1 2 5 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_UNSPECIFIED); } SECTION("assignChiralTypesFromBondDirs details") { auto m = R"CTAB( Mrv2102 03212207042D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 4 0 0 1 M V30 BEGIN ATOM M V30 1 C 1.54 -1.54 0 0 M V30 2 C 1.54 0 0 0 M V30 3 O 1.54 1.54 0 0 M V30 4 F 3.08 -0 0 0 M V30 5 Cl 0 0 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 2 1 M V30 2 1 2 4 CFG=1 M V30 3 1 2 3 M V30 4 1 2 5 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); CHECK(m->getAtomWithIdx(1)->getChiralTag() != Atom::ChiralType::CHI_UNSPECIFIED); m->getBondBetweenAtoms(1, 2)->setBondDir(Bond::BondDir::UNKNOWN); bool replaceExistingTags = false; MolOps::assignChiralTypesFromBondDirs(*m, -1, replaceExistingTags); CHECK(m->getAtomWithIdx(1)->getChiralTag() != Atom::ChiralType::CHI_UNSPECIFIED); replaceExistingTags = true; MolOps::assignChiralTypesFromBondDirs(*m, -1, replaceExistingTags); CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_UNSPECIFIED); } } TEST_CASE( "Github #5152: presence of exocyclic query bonds in CTAB prevents " "aromaticity perception") { SECTION("as reported") { auto m = R"CTAB( RDKit 2D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 8 8 0 0 1 M V30 BEGIN ATOM M V30 1 C -2.229300 0.915100 0.000000 0 M V30 2 C -3.562800 0.145100 0.000000 0 M V30 3 C -3.562800 -1.395100 0.000000 0 M V30 4 C -2.229300 -2.165100 0.000000 0 M V30 5 C -0.895500 -1.395100 0.000000 0 M V30 6 C -0.895500 0.145100 0.000000 0 M V30 7 A 0.438100 0.915100 0.000000 0 M V30 8 A 0.438100 -2.165100 0.000000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 2 1 2 M V30 2 1 2 3 M V30 3 2 3 4 M V30 4 1 4 5 M V30 5 2 5 6 M V30 6 1 6 1 M V30 7 6 6 7 M V30 8 6 5 8 M V30 END BOND M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); CHECK(m->getAtomWithIdx(0)->getIsAromatic()); CHECK(m->getBondWithIdx(0)->getIsAromatic()); } SECTION("more detailed") { std::string molb = R"CTAB( RDKit 2D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 8 8 0 0 1 M V30 BEGIN ATOM M V30 1 C -2.229300 0.915100 0.000000 0 M V30 2 C -3.562800 0.145100 0.000000 0 M V30 3 C -3.562800 -1.395100 0.000000 0 M V30 4 C -2.229300 -2.165100 0.000000 0 M V30 5 C -0.895500 -1.395100 0.000000 0 M V30 6 C -0.895500 0.145100 0.000000 0 M V30 7 A 0.438100 0.915100 0.000000 0 M V30 8 A 0.438100 -2.165100 0.000000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 2 1 2 M V30 2 1 2 3 M V30 3 2 3 4 M V30 4 1 4 5 M V30 5 2 5 6 M V30 6 1 6 1 M V30 7 6 6 7 M V30 8 6 5 8 M V30 END BOND M V30 END CTAB M END)CTAB"; std::string ptrn = "7 6 6 7"; std::vector alternatives = { "7 5 6 7", // S/D "7 7 6 7", // D/A "7 8 6 7", // any }; auto pos = molb.find(ptrn); REQUIRE(pos != std::string::npos); for (auto alternative : alternatives) { auto mb2 = molb.replace(pos, ptrn.size(), alternative); std::unique_ptr m(MolBlockToMol(mb2)); REQUIRE(m); CHECK(m->getAtomWithIdx(0)->getIsAromatic()); CHECK(m->getBondWithIdx(0)->getIsAromatic()); } } } TEST_CASE( "Github #5165: issue with V3000 SD files containing enhanced " "stereochemistry information") { SECTION("as reported") { std::string rdbase = getenv("RDBASE"); std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/" "mol_with_enhanced_stereo_2_And_groups.sdf"; SDMolSupplier suppl(fName); std::unique_ptr mol{suppl.next()}; REQUIRE(mol); auto groups = mol->getStereoGroups(); REQUIRE(groups.size() == 2); CHECK(groups[0].getGroupType() == RDKit::StereoGroupType::STEREO_AND); CHECK(groups[1].getGroupType() == RDKit::StereoGroupType::STEREO_AND); } SECTION("as reported, less whitespace") { std::string rdbase = getenv("RDBASE"); std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/m_with_enh_stereo.sdf"; SDMolSupplier suppl(fName); std::unique_ptr mol{suppl.next()}; REQUIRE(mol); auto groups = mol->getStereoGroups(); REQUIRE(groups.size() == 2); CHECK(groups[0].getGroupType() == RDKit::StereoGroupType::STEREO_AND); CHECK(groups[1].getGroupType() == RDKit::StereoGroupType::STEREO_AND); } } TEST_CASE("POL atoms in CTABS") { SECTION("V3000") { auto mol = R"CTAB( Mrv2102 05042219282D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 3 2 0 0 0 M V30 BEGIN ATOM M V30 1 Pol -6.25 3.375 0 0 M V30 2 C -4.9163 4.145 0 0 M V30 3 C -3.5826 3.375 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); std::string val; CHECK(mol->getAtomWithIdx(0)->getPropIfPresent( common_properties::dummyLabel, val)); CHECK(val == "Pol"); auto mb = MolToV3KMolBlock(*mol); CHECK(mb.find("1 Pol") != std::string::npos); mol->clearConformers(); auto smi = MolToCXSmiles(*mol); CHECK(smi == "*CC |$Pol_p;;$|"); } SECTION("V2000") { auto mol = R"CTAB( Mrv2102 05042219412D 3 2 0 0 0 0 999 V2000 -3.3482 1.8080 0.0000 Mod 0 0 0 0 0 0 0 0 0 0 0 0 -2.6337 2.2205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9193 1.8080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 M END )CTAB"_ctab; REQUIRE(mol); std::string val; CHECK(mol->getAtomWithIdx(0)->getPropIfPresent( common_properties::dummyLabel, val)); CHECK(val == "Mod"); auto mb = MolToMolBlock(*mol); CHECK(mb.find("0 Mod 0") != std::string::npos); mol->clearConformers(); auto smi = MolToCXSmiles(*mol); CHECK(smi == "*CC |$Mod_p;;$|"); } } TEST_CASE("PDB ACE caps bond order") { auto mol = R"DATA(HEADER TEST ATOM 1 H1 ACE 1 25.950 25.179 24.582 1.00 0.00 H ATOM 2 CH3 ACE 1 25.986 26.176 24.145 1.00 0.00 C ATOM 3 H2 ACE 1 25.332 26.843 24.703 1.00 0.00 H ATOM 4 H3 ACE 1 25.673 26.131 23.104 1.00 0.00 H ATOM 5 C ACE 1 27.405 26.691 24.218 1.00 0.00 C ATOM 6 O ACE 1 28.285 25.999 24.713 1.00 0.00 O ATOM 7 N ALA 2 27.621 27.909 23.728 1.00 0.00 N ATOM 8 H ALA 2 26.838 28.435 23.370 1.00 0.00 H ATOM 9 CA ALA 2 28.916 28.589 23.730 1.00 0.00 C ATOM 10 HA ALA 2 29.471 28.288 24.620 1.00 0.00 H ATOM 11 CB ALA 2 29.710 28.153 22.489 1.00 0.00 C ATOM 12 HB1 ALA 2 29.172 28.440 21.584 1.00 0.00 H ATOM 13 HB2 ALA 2 30.691 28.627 22.488 1.00 0.00 H ATOM 14 HB3 ALA 2 29.844 27.070 22.499 1.00 0.00 H ATOM 15 C ALA 2 28.737 30.119 23.778 1.00 0.00 C ATOM 16 O ALA 2 27.675 30.634 23.429 1.00 0.00 O ATOM 17 N NME 3 29.784 30.841 24.197 1.00 0.00 N ATOM 18 H NME 3 30.622 30.348 24.461 1.00 0.00 H ATOM 19 CH3 NME 3 29.784 32.300 24.293 1.00 0.00 C ATOM 20 HH31 NME 3 28.951 32.628 24.918 1.00 0.00 H ATOM 21 HH32 NME 3 30.720 32.652 24.729 1.00 0.00 H ATOM 22 HH33 NME 3 29.663 32.734 23.299 1.00 0.00 H TER 23 NME 3 END )DATA"_pdb; REQUIRE(mol); // Oxygen in ACE (3rd heavy atom in mol) should be C=O, i.e. not OH CHECK(mol->getAtomWithIdx(2)->getTotalNumHs() == 0); CHECK(mol->getAtomWithIdx(2)->getTotalDegree() == 1); auto bond = mol->getBondBetweenAtoms(1, 2); REQUIRE(bond); CHECK(bond->getBondType() == Bond::BondType::DOUBLE); } TEST_CASE( "github #5327: MolFromMolBlock should correctly assign stereochemistry " "to 3D molecules") { SECTION("basics") { auto m = R"CTAB( RDKit 3D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 4 0 0 0 M V30 BEGIN ATOM M V30 1 C 0.900794 -0.086835 0.009340 0 M V30 2 C -0.552652 0.319534 0.077502 0 M V30 3 F -0.861497 0.413307 1.437370 0 M V30 4 Cl -0.784572 1.925710 -0.672698 0 M V30 5 O -1.402227 -0.583223 -0.509512 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 2 4 M V30 4 1 2 5 M V30 END BOND M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); CHECK(m->getConformer().is3D()); CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CW); } SECTION("wiggly bond") { auto m = R"CTAB( RDKit 3D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 4 0 0 0 M V30 BEGIN ATOM M V30 1 C 0.900794 -0.086835 0.009340 0 M V30 2 C -0.552652 0.319534 0.077502 0 M V30 3 F -0.861497 0.413307 1.437370 0 M V30 4 Cl -0.784572 1.925710 -0.672698 0 M V30 5 O -1.402227 -0.583223 -0.509512 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 2 4 CFG=2 M V30 4 1 2 5 M V30 END BOND M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); CHECK(m->getConformer().is3D()); CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_UNSPECIFIED); } SECTION("3D as 2D") { // here we lie to the RDKit and tell it that a 3D conformer is 2D, // the code detects that and still sets the conformer to be 3D and // assigns stereo: auto m = R"CTAB( RDKit 2D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 4 0 0 0 M V30 BEGIN ATOM M V30 1 C 0.900794 -0.086835 0.009340 0 M V30 2 C -0.552652 0.319534 0.077502 0 M V30 3 F -0.861497 0.413307 1.437370 0 M V30 4 Cl -0.784572 1.925710 -0.672698 0 M V30 5 O -1.402227 -0.583223 -0.509512 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 2 4 M V30 4 1 2 5 M V30 END BOND M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); CHECK(m->getConformer().is3D()); CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CW); } SECTION("2D as 3D") { // here we lie to the RDKit and tell it that a 2D conformer is 3D, // there's no chiral volume, so we don't end up with a chiral center auto m = R"CTAB( RDKit 3D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 4 0 0 0 M V30 BEGIN ATOM M V30 1 C -1.299038 -0.750000 0.000000 0 M V30 2 C 0.000000 -0.000000 0.000000 0 M V30 3 F 0.750000 -1.299038 0.000000 0 M V30 4 Cl -0.750000 1.299038 0.000000 0 M V30 5 O 1.299038 0.750000 0.000000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 2 4 M V30 4 1 2 5 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); CHECK(m->getConformer().is3D()); CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_UNSPECIFIED); } SECTION("double bond") { auto m = R"CTAB( RDKit 3D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 4 3 0 0 0 M V30 BEGIN ATOM M V30 1 C 1.911935 -0.058147 -0.007384 0 M V30 2 C 0.477913 -0.091130 -0.413392 0 M V30 3 C -0.494810 0.079132 0.449979 0 M V30 4 C -1.932350 0.037738 -0.006356 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 2 2 3 M V30 3 1 3 4 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); CHECK(m->getConformer().is3D()); CHECK(Chirality::translateEZLabelToCisTrans( m->getBondWithIdx(1)->getStereo()) == Bond::BondStereo::STEREOTRANS); } SECTION("double bond, crossed") { auto m = R"CTAB( RDKit 3D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 4 3 0 0 0 M V30 BEGIN ATOM M V30 1 C 1.911935 -0.058147 -0.007384 0 M V30 2 C 0.477913 -0.091130 -0.413392 0 M V30 3 C -0.494810 0.079132 0.449979 0 M V30 4 C -1.932350 0.037738 -0.006356 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 2 2 3 CFG=2 M V30 3 1 3 4 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); CHECK(m->getConformer().is3D()); CHECK(Chirality::translateEZLabelToCisTrans( m->getBondWithIdx(1)->getStereo()) == Bond::BondStereo::STEREOANY); } SECTION("double bond, wiggly bond") { auto m = R"CTAB( RDKit 3D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 4 3 0 0 0 M V30 BEGIN ATOM M V30 1 C 1.911935 -0.058147 -0.007384 0 M V30 2 C 0.477913 -0.091130 -0.413392 0 M V30 3 C -0.494810 0.079132 0.449979 0 M V30 4 C -1.932350 0.037738 -0.006356 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 2 2 3 M V30 3 1 3 4 CFG=2 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); CHECK(m->getConformer().is3D()); CHECK(Chirality::translateEZLabelToCisTrans( m->getBondWithIdx(1)->getStereo()) == Bond::BondStereo::STEREOANY); } SECTION("non-tetrahedral") { auto m = R"CTAB( Mrv2108 05252216313D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 6 5 0 0 0 M V30 BEGIN ATOM M V30 1 C -1.7191 0.2488 -3.5085 0 M V30 2 As -1.0558 1.9209 -2.6345 0 M V30 3 F -0.4636 3.422 -1.7567 0 M V30 4 O -2.808 2.4243 -2.1757 0 M V30 5 Cl -0.1145 2.6609 -4.5048 0 M V30 6 Br 0.2255 0.6458 -1.079 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 2 4 M V30 4 1 2 5 M V30 5 1 2 6 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); CHECK(m->getConformer().is3D()); CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_TRIGONALBIPYRAMIDAL); } SECTION("non-tetrahedral, wiggly") { auto m = R"CTAB( Mrv2108 05252216313D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 6 5 0 0 0 M V30 BEGIN ATOM M V30 1 C -1.7191 0.2488 -3.5085 0 M V30 2 As -1.0558 1.9209 -2.6345 0 M V30 3 F -0.4636 3.422 -1.7567 0 M V30 4 O -2.808 2.4243 -2.1757 0 M V30 5 Cl -0.1145 2.6609 -4.5048 0 M V30 6 Br 0.2255 0.6458 -1.079 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 2 4 M V30 4 1 2 5 CFG=2 M V30 5 1 2 6 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); CHECK(m->getConformer().is3D()); CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_UNSPECIFIED); } } TEST_CASE("Force use of MolBlock wedges", "") { SECTION("basics") { auto m = R"CTAB(bad wedging ChemDraw07092209022D 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 7 7 0 0 0 M V30 BEGIN ATOM M V30 1 C -0.714471 0.825000 0.000000 0 M V30 2 C -0.714471 0.000000 0.000000 0 M V30 3 C -0.000000 -0.412500 0.000000 0 M V30 4 C 0.714471 0.000000 0.000000 0 M V30 5 C 0.714471 0.825000 0.000000 0 M V30 6 C -0.000000 1.237500 0.000000 0 M V30 7 C -0.000000 -1.237500 0.000000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 3 4 CFG=1 M V30 4 1 4 5 M V30 5 1 5 6 M V30 6 1 6 1 M V30 7 1 3 7 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); CHECK(m->getBondWithIdx(2)->getBondDir() == Bond::BondDir::NONE); Chirality::reapplyMolBlockWedging(*m); CHECK(m->getBondWithIdx(2)->getBondDir() == Bond::BondDir::BEGINWEDGE); Chirality::invertMolBlockWedgingInfo(*m); Chirality::reapplyMolBlockWedging(*m); CHECK(m->getBondWithIdx(2)->getBondDir() == Bond::BondDir::BEGINDASH); Chirality::invertMolBlockWedgingInfo(*m); Chirality::reapplyMolBlockWedging(*m); CHECK(m->getBondWithIdx(2)->getBondDir() == Bond::BondDir::BEGINWEDGE); Chirality::clearMolBlockWedgingInfo(*m); Chirality::reapplyMolBlockWedging(*m); CHECK(m->getBondWithIdx(2)->getBondDir() == Bond::BondDir::NONE); } SECTION( "Reapply the original wedging, regardless the bond type of wedged bonds") { auto m = R"CTAB( Mrv2311 04232413302D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 4 0 0 0 M V30 BEGIN ATOM M V30 1 S -11.583 11.3533 0 0 M V30 2 C -12.9167 10.5833 0 0 M V30 3 O -11.583 12.8933 0 0 M V30 4 C -10.2493 10.5833 0 0 M V30 5 C -10.2493 9.0433 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 4 5 M V30 2 1 2 1 M V30 3 1 1 4 M V30 4 2 1 3 CFG=1 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); CHECK(m->getBondWithIdx(3)->getBondType() == Bond::BondType::DOUBLE); Chirality::reapplyMolBlockWedging(*m); CHECK(m->getBondWithIdx(3)->getBondDir() == Bond::BondDir::BEGINWEDGE); Chirality::reapplyMolBlockWedging(*m, false); CHECK(m->getBondWithIdx(3)->getBondDir() == Bond::BondDir::NONE); } SECTION("GitHub5448") { { auto m = R"CTAB( ChemDraw07232208492D 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 12 12 0 0 1 M V30 BEGIN ATOM M V30 1 C 1.151421 0.903801 0.000000 0 M V30 2 C 1.151421 0.078801 0.000000 0 M V30 3 N 1.936021 -0.176200 0.000000 0 M V30 4 C 2.420921 0.491301 0.000000 0 M V30 5 N 1.936021 1.158699 0.000000 0 M V30 6 C 0.436921 -0.333699 0.000000 0 M V30 7 C -0.277478 0.078801 0.000000 0 M V30 8 C -0.991978 -0.333699 0.000000 0 M V30 9 C 0.436921 -1.158699 0.000000 0 M V30 10 C -1.706442 0.078813 0.000000 0 M V30 11 C -2.420921 -0.333674 0.000000 0 M V30 12 F -1.706428 0.903813 0.000000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 2 1 2 M V30 2 1 2 3 M V30 3 2 3 4 M V30 4 1 4 5 M V30 5 1 5 1 M V30 6 1 2 6 M V30 7 1 6 7 M V30 8 2 7 8 CFG=2 M V30 9 1 6 9 CFG=2 M V30 10 1 8 10 M V30 11 1 10 11 M V30 12 1 10 12 CFG=1 M V30 END BOND M V30 BEGIN COLLECTION M V30 MDLV30/STEABS ATOMS=(1 10) M V30 END COLLECTION M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); Chirality::wedgeMolBonds(*m, &m->getConformer()); CHECK(m->getBondWithIdx(10)->getBondDir() == Bond::BondDir::BEGINWEDGE); CHECK(m->getBondWithIdx(11)->getBondDir() == Bond::BondDir::NONE); Chirality::reapplyMolBlockWedging(*m); CHECK(m->getBondWithIdx(10)->getBondDir() == Bond::BondDir::NONE); CHECK(m->getBondWithIdx(11)->getBondDir() == Bond::BondDir::BEGINWEDGE); } } } TEST_CASE( "GitHub Issue #5423: Parsing a Mol block/file does not clear the " "\"molTotValence\" property from atoms") { auto m = R"CTAB( RDKit 2D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM M V30 1 N -3.657143 -0.742857 0.000000 0 CHG=1 VAL=4 M V30 END ATOM M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); CHECK(!m->getAtomWithIdx(0)->hasProp(common_properties::molTotValence)); } TEST_CASE("Github #5433: PRECONDITION error with nonsense molecule") { auto m = R"CTAB( SomeFailingMolFile 8 8 0 0 1 0 999 V2000 -0.7145 1.2375 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 0.8250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7145 -1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.6500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7145 -1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 6 0 0 0 2 3 2 0 0 0 0 3 4 1 4 0 0 0 3 8 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 M END)CTAB"_ctab; REQUIRE(m); } TEST_CASE("Github #5765: R label information lost") { SECTION("just R") { auto m = R"CTAB( MJ221900 4 3 0 0 0 0 0 0 0 0999 V2000 2.1433 1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4289 2.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8578 2.0625 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0 2.1433 0.8250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 0 0 0 0 4 1 2 0 0 0 0 M END)CTAB"_ctab; REQUIRE(m); CHECK(m->getAtomWithIdx(2)->hasProp(common_properties::dummyLabel)); CHECK(m->getAtomWithIdx(2)->getProp( common_properties::dummyLabel) == "R"); } SECTION("R with number") { auto m = R"CTAB( MJ221900 4 3 0 0 0 0 0 0 0 0999 V2000 2.1433 1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4289 2.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8578 2.0625 0.0000 R95 0 0 0 0 0 0 0 0 0 0 0 0 2.1433 0.8250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 0 0 0 0 4 1 2 0 0 0 0 M END)CTAB"_ctab; REQUIRE(m); CHECK(m->getAtomWithIdx(2)->hasProp(common_properties::dummyLabel)); CHECK(m->getAtomWithIdx(2)->getProp( common_properties::dummyLabel) == "R95"); } SECTION("V3000") { auto m = R"CTAB( Mrv1810 02111915102D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 3 2 0 0 0 M V30 BEGIN ATOM M V30 1 C -2.9167 3 0 0 M V30 2 C -1.583 3.77 0 0 M V30 3 R -4.2503 3.77 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 3 M V30 2 1 1 2 M V30 END BOND M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); CHECK(m->getAtomWithIdx(2)->hasProp(common_properties::dummyLabel)); CHECK(m->getAtomWithIdx(2)->getProp( common_properties::dummyLabel) == "R"); } SECTION("V3000 with number") { auto m = R"CTAB( Mrv1810 02111915102D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 3 2 0 0 0 M V30 BEGIN ATOM M V30 1 C -2.9167 3 0 0 M V30 2 C -1.583 3.77 0 0 M V30 3 R98 -4.2503 3.77 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 3 M V30 2 1 1 2 M V30 END BOND M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); CHECK(m->getAtomWithIdx(2)->hasProp(common_properties::dummyLabel)); CHECK(m->getAtomWithIdx(2)->getProp( common_properties::dummyLabel) == "R98"); } SECTION("R# also gets the tag (was #5810)") { auto m = R"CTAB( Mrv1810 02111915102D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 3 2 0 0 0 M V30 BEGIN ATOM M V30 1 C -2.9167 3 0 0 M V30 2 C -1.583 3.77 0 0 M V30 3 R# -4.2503 3.77 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 3 M V30 2 1 1 2 M V30 END BOND M V30 END CTAB M END)CTAB"_ctab; REQUIRE(m); CHECK(m->getAtomWithIdx(2)->hasProp(common_properties::dummyLabel)); CHECK(m->getAtomWithIdx(2)->getProp( common_properties::dummyLabel) == "R#"); } SECTION("R# also gets the tag (V2000, #5810)") { auto m = R"CTAB( RDKit 2D 3 2 0 0 0 0 0 0 0 0999 V2000 -2.9167 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5830 3.7700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2503 3.7700 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 1 2 1 0 M END)CTAB"_ctab; REQUIRE(m); CHECK(m->getAtomWithIdx(2)->hasProp(common_properties::dummyLabel)); CHECK(m->getAtomWithIdx(2)->getProp( common_properties::dummyLabel) == "R#"); } } TEST_CASE("github #5718: ") { SECTION("as reported") { auto m = R"CTAB( Mrv2108 07152116012D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 1 0 0 M V30 BEGIN ATOM M V30 1 C -0.8333 4.5421 0 0 M V30 2 C 0.5003 5.3121 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(1 2) - M V30 FIELDDISP=" 0.0000 0.0000 DR ALL 0 0" - M V30 QUERYTYPE=SMARTSQ QUERYOP== FIELDDATA=[#6;R] M V30 END SGROUP M V30 END CTAB M END")CTAB"_ctab; REQUIRE(m); CHECK(!m->getAtomWithIdx(0)->hasQuery()); CHECK(m->getAtomWithIdx(1)->hasQuery()); auto ctab = MolToV3KMolBlock(*m); CHECK(ctab.find("SMARTSQ") != std::string::npos); CHECK(ctab.find("[#6;R]") != std::string::npos); } } TEST_CASE("github #5827: do not write properties with new lines to SDF") { auto m = R"CTAB( Mrv2211 12152210292D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 2 1 0 0 0 M V30 BEGIN ATOM M V30 1 C 0.5 6.0833 0 0 M V30 2 O 1.8337 6.8533 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); SECTION("basics") { m->setProp("foo", "fooprop"); m->setProp("bar", "foo\n\nprop"); m->setProp("baz", "foo\r\n\r\nprop"); m->setProp("bletch\nnope", "fooprop"); m->setProp("bletch\r\nnope2", "fooprop"); std::ostringstream oss; SDWriter sdw(&oss); sdw.write(*m); sdw.flush(); auto sdf = oss.str(); CHECK(sdf.find("") != std::string::npos); CHECK(sdf.find("") == std::string::npos); CHECK(sdf.find("") == std::string::npos); CHECK(sdf.find(" m; CHECK_THROWS_AS(m.reset(MolBlockToMol(mb)), FileParseException); bool sanitize = true; bool removeHs = true; bool strictParsing = false; m.reset(MolBlockToMol(mb, sanitize, removeHs, strictParsing)); REQUIRE(m); CHECK(m->getAtomWithIdx(1)->getAtomicNum() == 0); CHECK(m->getAtomWithIdx(1)->hasProp(common_properties::dummyLabel)); } SECTION("V2000") { std::string mb = R"CTAB( Mrv1810 02111915042D 2 1 0 0 0 0 999 V2000 -1.5625 1.6071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8480 2.0196 0.0000 QQQ 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 M END )CTAB"; std::unique_ptr m; CHECK_THROWS_AS(m.reset(MolBlockToMol(mb)), FileParseException); bool sanitize = true; bool removeHs = true; bool strictParsing = false; m.reset(MolBlockToMol(mb, sanitize, removeHs, strictParsing)); REQUIRE(m); CHECK(m->getAtomWithIdx(1)->getAtomicNum() == 0); CHECK(m->getAtomWithIdx(1)->hasProp(common_properties::dummyLabel)); } } TEST_CASE( "Github #5930: single-element atom list queries not output to mol blocks") { SECTION("as reported") { auto m = R"CTAB( Mrv2211 01052305042D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM M V30 1 "NOT [N]" -3.0413 6.2283 0 0 M V30 END ATOM M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); REQUIRE(m->getAtomWithIdx(0)->hasQuery()); CHECK(m->getAtomWithIdx(0)->getQuery()->getNegation()); auto mb = MolToV3KMolBlock(*m); { INFO(mb); CHECK(mb.find("NOT [N]") != std::string::npos); } } SECTION("output the query even if it's not negated") { auto m = R"CTAB( Mrv2211 01052305042D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 1 0 0 0 0 M V30 BEGIN ATOM M V30 1 "[N]" -3.0413 6.2283 0 0 M V30 END ATOM M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); REQUIRE(m->getAtomWithIdx(0)->hasQuery()); CHECK(!m->getAtomWithIdx(0)->getQuery()->getNegation()); auto mb = MolToV3KMolBlock(*m); { INFO(mb); CHECK(mb.find("V30 1 [N]") != std::string::npos); } } SECTION("v2000") { auto m = R"CTAB( Mrv2211 01052305142D 1 0 1 0 0 0 999 V2000 -1.6293 3.3366 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0 1 T 1 7 M ALS 1 1 T N M END )CTAB"_ctab; REQUIRE(m); REQUIRE(m->getAtomWithIdx(0)->hasQuery()); CHECK(m->getAtomWithIdx(0)->getQuery()->getNegation()); auto mb = MolToMolBlock(*m); { INFO(mb); CHECK(mb.find("M ALS 1 1 T N") != std::string::npos); } } SECTION("broader consequences") { std::vector smas{"[!N]", "[!#7]", "[!n]"}; for (const auto &sma : smas) { INFO(sma); std::unique_ptr m(SmartsToMol(sma)); REQUIRE(m); REQUIRE(m->getAtomWithIdx(0)->hasQuery()); CHECK(m->getAtomWithIdx(0)->getQuery()->getNegation()); auto mb = MolToV3KMolBlock(*m); CHECK(mb.find("NOT [N]") != std::string::npos); } } } TEST_CASE("Github #6395: Mol Unsaturated Query Not Parsed Correctly") { SECTION("as reported") { auto m = R"CTAB( MOESketch 2D 5 5 0 0 1 0 999 V2000 13.5413 2.8394 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0 14.0120 1.4152 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 15.5120 1.4227 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 15.9683 2.8516 0.0000 N 0 0 0 0 0 0 0 0 0 2 0 0 14.7504 3.7272 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0 1 2 8 0 0 0 4 2 3 8 0 0 0 0 3 4 8 0 0 0 4 4 5 8 0 0 0 9 5 1 1 0 0 0 0 M SUB 4 1 2 2 2 3 2 4 2 M UNS 4 2 1 3 1 4 1 5 1 M END )CTAB"_ctab; REQUIRE(m); } SECTION("test that queries exist for only nonzero unsaturated values") { auto m = R"CTAB( MOESketch 2D 5 5 0 0 1 0 999 V2000 13.5413 2.8394 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0 14.0120 1.4152 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 15.5120 1.4227 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 15.9683 2.8516 0.0000 N 0 0 0 0 0 0 0 0 0 2 0 0 14.7504 3.7272 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0 1 2 8 0 0 0 4 2 3 8 0 0 0 0 3 4 8 0 0 0 4 4 5 8 0 0 0 9 5 1 1 0 0 0 0 M UNS 4 2 1 3 0 4 1 5 0 M END )CTAB"_ctab; REQUIRE(m); REQUIRE(m->getAtomWithIdx(1)->hasQuery()); REQUIRE(!m->getAtomWithIdx(2)->hasQuery()); REQUIRE(m->getAtomWithIdx(3)->hasQuery()); REQUIRE(!m->getAtomWithIdx(4)->hasQuery()); } SECTION("test that isotope properties parse correctly") { auto m = R"CTAB( MOESketch 2D 5 5 0 0 1 0 999 V2000 13.5413 2.8394 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0 14.0120 1.4152 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 15.5120 1.4227 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 15.9683 2.8516 0.0000 N 0 0 0 0 0 0 0 0 0 2 0 0 14.7504 3.7272 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0 1 2 8 0 0 0 4 2 3 8 0 0 0 0 3 4 8 0 0 0 4 4 5 8 0 0 0 9 5 1 1 0 0 0 0 M ISO 3 2 15 3 -1 5 14 M END )CTAB"_ctab; REQUIRE(m); REQUIRE(m->getAtomWithIdx(1)->getIsotope() == 15); REQUIRE(m->getAtomWithIdx(2)->getIsotope() == 0); REQUIRE(m->getAtomWithIdx(4)->getIsotope() == 14); } SECTION("test that substitution properties parse correctly") { auto m = R"CTAB( MOESketch 2D 5 5 0 0 1 0 999 V2000 13.5413 2.8394 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0 14.0120 1.4152 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 15.5120 1.4227 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 15.9683 2.8516 0.0000 N 0 0 0 0 0 0 0 0 0 2 0 0 14.7504 3.7272 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0 1 2 8 0 0 0 4 2 3 8 0 0 0 0 3 4 8 0 0 0 4 4 5 8 0 0 0 9 5 1 1 0 0 0 0 M SUB 4 2 1 3 0 4 -1 5 0 M END )CTAB"_ctab; REQUIRE(m); REQUIRE(m->getAtomWithIdx(1)->hasQuery()); REQUIRE(!m->getAtomWithIdx(2)->hasQuery()); REQUIRE(m->getAtomWithIdx(3)->hasQuery()); REQUIRE(!m->getAtomWithIdx(4)->hasQuery()); } SECTION("test that ring bond count properties parse correctly") { auto m = R"CTAB( MOESketch 2D 5 5 0 0 1 0 999 V2000 13.5413 2.8394 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0 14.0120 1.4152 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 15.5120 1.4227 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 15.9683 2.8516 0.0000 N 0 0 0 0 0 0 0 0 0 2 0 0 14.7504 3.7272 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0 1 2 8 0 0 0 4 2 3 8 0 0 0 0 3 4 8 0 0 0 4 4 5 8 0 0 0 9 5 1 1 0 0 0 0 M RBC 4 2 1 3 0 4 -1 5 0 M END )CTAB"_ctab; REQUIRE(m); REQUIRE(m->getAtomWithIdx(1)->hasQuery()); REQUIRE(!m->getAtomWithIdx(2)->hasQuery()); REQUIRE(m->getAtomWithIdx(3)->hasQuery()); REQUIRE(!m->getAtomWithIdx(4)->hasQuery()); } } TEST_CASE("Github #3246: O.co2 types around P not correctly handled") { SECTION("as reported") { std::string mol2 = R"MOL2(# Name: temp # Creating user name: baliuste # Creation time: 12. 03. 2021 13:50 # Modifying user name: baliuste # Modification time: 12. 03. 2021 13:50 # Program: corina 4.3.0 0026 30.10.2019 # @ENERGY # 0.00 # @FOOTER # DeltaE 0.0 @MOLECULE temp 20 21 0 0 0 SMALL NO_CHARGES @ATOM 1 C1 -1.2321 -0.8688 0.0096 C.3 2 C2 0.0021 -0.0041 0.0020 C.2 3 N3 1.1984 -0.4572 -0.0118 N.2 4 C4 2.2083 0.4335 -0.0167 C.ar 5 C5 3.6010 0.2154 -0.0311 C.ar 6 C6 4.4640 1.2688 -0.0342 C.ar 7 C7 3.9918 2.5739 -0.0227 C.ar 8 C8 2.6369 2.8170 -0.0080 C.ar 9 C9 1.7390 1.7516 -0.0051 C.ar 10 S10 -0.0211 1.7022 0.0114 S.3 11 P11 5.1612 3.9606 -0.0264 P.3 12 O12 6.4827 3.5313 0.6973 O.co2 13 O13 5.4837 4.3678 -1.5044 O.co2 14 O14 4.5270 5.1805 0.7248 O.co2 15 H15 -1.5398 -1.0718 -1.0162 H 16 H16 -1.0139 -1.8089 0.5163 H 17 H17 -2.0352 -0.3512 0.5342 H 18 H18 3.9859 -0.7936 -0.0402 H 19 H19 5.5284 1.0865 -0.0460 H 20 H20 2.2703 3.8328 0.0010 H @BOND 1 1 2 1 2 1 15 1 3 1 16 1 4 1 17 1 5 2 10 1 6 2 3 2 7 3 4 1 8 4 9 ar 9 4 5 ar 10 5 6 ar 11 5 18 1 12 6 7 ar 13 6 19 1 14 7 8 ar 15 7 11 1 16 8 9 ar 17 8 20 1 18 9 10 1 19 11 12 ar 20 11 13 ar 21 11 14 ar # End of record)MOL2"; std::unique_ptr m(Mol2BlockToMol(mol2)); REQUIRE(m); CHECK(m->getAtomWithIdx(10)->getAtomicNum() == 15); CHECK(m->getAtomWithIdx(10)->getFormalCharge() == 0); CHECK(m->getAtomWithIdx(11)->getFormalCharge() == 0); CHECK(m->getBondBetweenAtoms(10, 11)->getBondType() == Bond::DOUBLE); CHECK(m->getAtomWithIdx(12)->getFormalCharge() == -1); CHECK(m->getBondBetweenAtoms(10, 12)->getBondType() == Bond::SINGLE); // CHECK: is this correct? Should both of the Os be negative or just one? CHECK(m->getAtomWithIdx(13)->getFormalCharge() == -1); CHECK(m->getBondBetweenAtoms(10, 13)->getBondType() == Bond::SINGLE); } } std::string read_file(const std::string &fname) { std::ifstream ifs(fname); return std::string(std::istreambuf_iterator(ifs), std::istreambuf_iterator()); } #ifdef RDK_BUILD_MAEPARSER_SUPPORT TEST_CASE("MaeMolSupplier setData and reset methods", "[mae][MaeMolSupplier][reader]") { std::string rdbase = getenv("RDBASE"); MaeMolSupplier supplier; std::vector mol_names1 = { "48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213", "220", "229", "256"}; std::string fname1 = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.mae"; auto data1 = read_file(fname1); supplier.setData(data1); // Test the reset method by iterating the same input twice for (unsigned i = 0; i < 2; ++i) { unsigned j = 0; while (!supplier.atEnd()) { INFO("First input, lap " + std::to_string(i) + ", mol " + std::to_string(j)); std::unique_ptr mol(supplier.next()); REQUIRE(mol != nullptr); std::string mol_name; REQUIRE(mol->getPropIfPresent("_Name", mol_name) == true); REQUIRE(j < mol_names1.size()); CHECK(mol_name == mol_names1[j]); ++j; } INFO("First input, mol count"); CHECK(j == 16); supplier.reset(); } // Now reuse the supplier with some different input std::string fname2 = rdbase + "/Code/GraphMol/FileParsers/test_data/stereochem.mae"; auto data2 = read_file(fname2); supplier.setData(data2); unsigned i = 0; while (!supplier.atEnd()) { INFO("Second input, mol " + std::to_string(i)); std::unique_ptr molptr(supplier.next()); ++i; } INFO("Second input, mol count"); CHECK(i == 5); // Reset throws if called after close INFO("Reset after close"); supplier.close(); REQUIRE_THROWS_AS(supplier.reset(), Invar::Invariant); } TEST_CASE("MaeMolSupplier length", "[mae][MaeMolSupplier][reader]") { std::string rdbase = getenv("RDBASE"); std::string fname1 = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.mae"; std::vector mol_names = { "48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213", "220", "229", "256"}; auto mols_in_file = mol_names.size(); MaeMolSupplier supplier(fname1); CHECK(supplier.length() == mols_in_file); unsigned i = 0; for (; i < 2; ++i) { std::unique_ptr mol(supplier.next()); std::string mol_name; REQUIRE(mol->getPropIfPresent("_Name", mol_name) == true); CHECK(mol_name == mol_names[i]); } CHECK(supplier.length() == mols_in_file); while (!supplier.atEnd()) { std::unique_ptr mol(supplier.next()); std::string mol_name; REQUIRE(mol->getPropIfPresent("_Name", mol_name) == true); CHECK(mol_name == mol_names[i]); ++i; } CHECK(i == mols_in_file); CHECK(supplier.length() == mols_in_file); CHECK(supplier.atEnd()); } TEST_CASE("MaeMolSupplier and operator[]", "[mae][MaeMolSupplier][reader]") { std::string rdbase = getenv("RDBASE"); std::string fname1 = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.mae"; std::vector mol_names = { "48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213", "220", "229", "256"}; auto mols_in_file = mol_names.size(); MaeMolSupplier supplier(fname1); std::string mol_name; for (unsigned i = 0; i < mols_in_file; ++i) { std::unique_ptr mol(supplier[i]); REQUIRE(mol->getPropIfPresent("_Name", mol_name) == true); CHECK(mol_name == mol_names[i]); auto j = mols_in_file - (i + 1); mol.reset(supplier[j]); REQUIRE(mol->getPropIfPresent("_Name", mol_name) == true); CHECK(mol_name == mol_names[j]); } CHECK_THROWS_AS(supplier[mols_in_file], FileParseException); CHECK_THROWS_AS(supplier[-1], FileParseException); } TEST_CASE("MaeMolSupplier is3D flag", "[mae][MaeMolSupplier][reader]") { std::string rdbase = getenv("RDBASE"); std::string fname1 = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.mae"; MaeMolSupplier supplier(fname1); std::unique_ptr mol(supplier[0]); std::string mol_name; REQUIRE(mol->getPropIfPresent("_Name", mol_name) == true); CHECK(mol_name == "48"); CHECK(mol->getConformer().is3D() == true); std::string fname2 = rdbase + "/Code/GraphMol/FileParsers/test_data/benzene.mae"; supplier.setData(read_file(fname2)); mol.reset(supplier[0]); REQUIRE(mol->getPropIfPresent("_Name", mol_name) == true); CHECK(mol_name == "Structure1"); CHECK(mol->getConformer().is3D() == false); } void check_roundtripped_properties(RDProps &original, RDProps &roundtrip) { // We don't care about the computed or private props original.clearComputedProps(); auto includePrivate = false; auto originalPropNames = original.getPropList(includePrivate); auto roundtripPropNames = roundtrip.getPropList(includePrivate); // We allow the roundtrip to add extra info, but the original // properties must be present REQUIRE(roundtripPropNames.size() >= originalPropNames.size()); std::sort(originalPropNames.begin(), originalPropNames.end()); std::sort(roundtripPropNames.begin(), roundtripPropNames.end()); REQUIRE(std::includes(roundtripPropNames.begin(), roundtripPropNames.end(), originalPropNames.begin(), originalPropNames.end())); for (const auto &o : original.getDict()) { if (o.key == detail::computedPropName) { continue; } UNSCOPED_INFO("Checking property = " << o.key); switch (o.val.getTag()) { case RDTypeTag::BoolTag: CHECK(rdvalue_cast(o.val) == roundtrip.getProp(o.key)); break; case RDTypeTag::IntTag: case RDTypeTag::UnsignedIntTag: CHECK(rdvalue_cast(o.val) == roundtrip.getProp(o.key)); break; case RDTypeTag::DoubleTag: case RDTypeTag::FloatTag: CHECK(rdvalue_cast(o.val) == roundtrip.getProp(o.key)); break; case RDTypeTag::StringTag: CHECK(rdvalue_cast(o.val) == roundtrip.getProp(o.key)); break; default: throw std::runtime_error("Unexpected property type"); } } } TEST_CASE("MaeWriter atom numbering chirality", "[mae][MaeWriter][writer]") { SECTION("R") { auto mol = "C/C=C/[C@@H](CO)C(C)C"_smiles; auto oss = new std::ostringstream; MaeWriter w(oss); w.write(*mol); w.flush(); auto iss = new std::istringstream(oss->str()); auto roundtrip = MaeMolSupplier(iss).next(); CHECK(roundtrip->getAtomWithIdx(3)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW); delete roundtrip; } SECTION("S") { auto mol = "C/C=C/[C@H](CO)C(C)C"_smiles; auto oss = new std::ostringstream; MaeWriter w(oss); w.write(*mol); w.flush(); auto iss = new std::istringstream(oss->str()); auto roundtrip = MaeMolSupplier(iss).next(); CHECK(roundtrip->getAtomWithIdx(3)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW); delete roundtrip; } } TEST_CASE("MaeWriter any stereo", "[mae][MaeWriter][writer]") { auto m = R"CTAB( RDKit 2D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 6 5 0 0 0 M V30 BEGIN ATOM M V30 1 C -2.942857 -0.857143 0.000000 0 M V30 2 C -1.514286 -0.857143 0.000000 0 M V30 3 H -3.657143 0.380036 0.000000 0 M V30 4 Br -3.657143 -2.094322 0.000000 0 M V30 5 F -0.800000 -2.094322 0.000000 0 M V30 6 Cl -0.800000 0.380036 0.000000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 2 1 2 CFG=2 M V30 2 1 1 3 M V30 3 1 1 4 M V30 4 1 2 5 M V30 5 1 2 6 M V30 END BOND M V30 END CTAB M END $$$$ )CTAB"_ctab; REQUIRE(m); // Currently, MaeMolSupplier does not recognize "either" double bonds, this // just tests that the bond will be recognizable by schrodinger software auto oss = new std::ostringstream; MaeWriter w(oss); w.write(*m); w.flush(); auto maeblock = oss->str(); CHECK(maeblock.find("i_sd_original_parity") != std::string::npos); // expected bond line -- include RDKit cfg properties CHECK(maeblock.find("1 1 2 2 2 2 2") != std::string::npos); } TEST_CASE("MaeWriter basic testing", "[mae][MaeWriter][writer]") { auto mol = "C1CCC(*)CC1"_smiles; REQUIRE(mol); auto add_some_props = [](RDProps &obj, const std::string &prefix) { obj.setProp(prefix + "_bool_prop", false); obj.setProp(prefix + "_int_prop", 42); obj.setProp(prefix + "_real_prop", 3.141592); obj.setProp(prefix + "_string_prop", "this is just a dummy property"); }; add_some_props(*mol, "mol"); add_some_props(*mol->getAtomWithIdx(0), "atom"); add_some_props(*mol->getBondWithIdx(0), "bond"); setAtomRLabel(mol->getAtomWithIdx(4), 3); SECTION("Check output") { mol->setProp(common_properties::_Name, "test mol 1"); // The writer always takes ownership of the stream! auto oss = new std::ostringstream; MaeWriter w(oss); w.write(*mol); w.flush(); auto mae = oss->str(); // Check for the Maestro file header REQUIRE(mae.find("s_m_m2io_version") != std::string::npos); // Check the CT header and Structure properties auto ctBlockStart = mae.find("f_m_ct"); REQUIRE(ctBlockStart != std::string::npos); auto atomBlockStart = mae.find("m_atom[7]"); REQUIRE(atomBlockStart != std::string::npos); auto bondBlockStart = mae.find("m_bond[7]"); REQUIRE(bondBlockStart != std::string::npos); std::string ctBlock(&mae[ctBlockStart], atomBlockStart - ctBlockStart); std::string atomBlock(&mae[atomBlockStart], bondBlockStart - atomBlockStart); std::string bondBlock(&mae[bondBlockStart]); // Check mol properties CHECK(ctBlock.find("s_m_title") != std::string::npos); CHECK(ctBlock.find("b_rdkit_mol_bool_prop") != std::string::npos); CHECK(ctBlock.find("i_rdkit_mol_int_prop") != std::string::npos); CHECK(ctBlock.find("r_rdkit_mol_real_prop") != std::string::npos); CHECK(ctBlock.find("s_rdkit_mol_string_prop") != std::string::npos); // Check Atom properties CHECK(atomBlock.find("r_m_x_coord") != std::string::npos); CHECK(atomBlock.find("r_m_y_coord") != std::string::npos); CHECK(atomBlock.find("r_m_z_coord") != std::string::npos); CHECK(atomBlock.find("i_m_atomic_number") != std::string::npos); CHECK(atomBlock.find("i_m_formal_charge") != std::string::npos); CHECK(atomBlock.find("b_rdkit_atom_bool_prop") != std::string::npos); CHECK(atomBlock.find("i_rdkit_atom_int_prop") != std::string::npos); CHECK(atomBlock.find("r_rdkit_atom_real_prop") != std::string::npos); CHECK(atomBlock.find("s_rdkit_atom_string_prop") != std::string::npos); // Check Bond properties CHECK(bondBlock.find("i_m_from") != std::string::npos); CHECK(bondBlock.find("i_m_to") != std::string::npos); CHECK(bondBlock.find("i_m_order") != std::string::npos); CHECK(bondBlock.find("b_rdkit_bond_bool_prop") != std::string::npos); CHECK(bondBlock.find("i_rdkit_bond_int_prop") != std::string::npos); CHECK(bondBlock.find("r_rdkit_bond_real_prop") != std::string::npos); CHECK(bondBlock.find("s_rdkit_bond_string_prop") != std::string::npos); } SECTION("Check bond ends indices order") { // in the bonds block, 'from' index must be lower than 'to' index // As usual, the writer takes ownership of the stream auto oss = new std::stringstream; MaeWriter w(oss); w.write(*mol); w.flush(); std::string line; while (std::getline(*oss, line) && line.find("m_bond[7]") == std::string::npos) { // Discard data until we reach the bond block } unsigned from_pos = -1; // offset comment unsigned to_pos = -1; // offset comment bool from_seen = false; bool to_seen = false; while (std::getline(*oss, line) && line.find(":::") == std::string::npos) { // Skip lines (comment, property names, separator) // until we reach the actual data. // Also, find position of 'to' and 'from' indices in the property list if (!from_seen) { ++from_pos; if (line.find("i_m_from") != std::string::npos) { from_seen = true; } } if (!to_seen) { ++to_pos; if (line.find("i_m_to") != std::string::npos) { to_seen = true; } } } REQUIRE(from_pos > 0); REQUIRE(to_pos > 0); int from = -1; int to = -1; std::string prop; unsigned tokens = 1 + std::max(from_pos, to_pos); for (unsigned i = 0; i < mol->getNumAtoms(); ++i) { std::getline(*oss, line); std::stringstream ss(line); for (unsigned j = 0; j < tokens; ++j) { if (j == from_pos) { ss >> from; } else if (j == to_pos) { ss >> to; } else { ss >> prop; } } REQUIRE(from != -1); REQUIRE(to != -1); CHECK(from < to); } } SECTION("Check Property filtering") { std::vector keptProps{ "mol_bool_prop", "atom_int_prop", "bond_real_prop", "non_existent_property", }; mol->setProp(common_properties::_Name, "test mol 2"); // The writer always takes ownership of the stream! auto oss = new std::ostringstream; MaeWriter w(oss); w.setProps(keptProps); w.write(*mol); w.flush(); auto mae = oss->str(); // Check for the Maestro file header REQUIRE(mae.find("s_m_m2io_version") != std::string::npos); // Check the CT header and Structure properties auto ctBlockStart = mae.find("f_m_ct"); REQUIRE(ctBlockStart != std::string::npos); auto atomBlockStart = mae.find("m_atom[7]"); REQUIRE(atomBlockStart != std::string::npos); auto bondBlockStart = mae.find("m_bond[7]"); REQUIRE(bondBlockStart != std::string::npos); std::string_view ctBlock(&mae[ctBlockStart], atomBlockStart - ctBlockStart); std::string atomBlock(&mae[atomBlockStart], bondBlockStart - atomBlockStart); std::string bondBlock(&mae[bondBlockStart]); // Check mol properties CHECK(ctBlock.find("s_m_title") != std::string::npos); CHECK(ctBlock.find("b_rdkit_mol_bool_prop") != std::string::npos); CHECK(ctBlock.find("i_rdkit_mol_int_prop") == std::string::npos); CHECK(ctBlock.find("r_rdkit_mol_real_prop") == std::string::npos); CHECK(ctBlock.find("s_rdkit_mol_string_prop") == std::string::npos); // Check Atom properties CHECK(atomBlock.find("r_m_x_coord") != std::string::npos); CHECK(atomBlock.find("r_m_y_coord") != std::string::npos); CHECK(atomBlock.find("r_m_z_coord") != std::string::npos); CHECK(atomBlock.find("i_m_atomic_number") != std::string::npos); CHECK(atomBlock.find("i_m_formal_charge") != std::string::npos); CHECK(atomBlock.find("i_rdkit_atom_int_prop") != std::string::npos); CHECK(atomBlock.find("b_rdkit_atom_bool_prop") == std::string::npos); CHECK(atomBlock.find("r_rdkit_atom_real_prop") == std::string::npos); CHECK(atomBlock.find("s_rdkit_atom_string_prop") == std::string::npos); // Check Bond properties CHECK(bondBlock.find("i_m_from") != std::string::npos); CHECK(bondBlock.find("i_m_to") != std::string::npos); CHECK(bondBlock.find("i_m_order") != std::string::npos); CHECK(bondBlock.find("r_rdkit_bond_real_prop") != std::string::npos); CHECK(bondBlock.find("b_rdkit_bond_bool_prop") == std::string::npos); CHECK(bondBlock.find("i_rdkit_bond_int_prop") == std::string::npos); CHECK(bondBlock.find("s_rdkit_bond_string_prop") == std::string::npos); // The "i_rdkit_atom_int_prop" prop should only be set on the first atom, // and unset on the other six auto count_occurrences = [&atomBlock](const char *needle) { size_t pos = 0; unsigned counter = 0; while (pos < std::string::npos) { pos = atomBlock.find(needle, pos + 1); counter += (pos != std::string::npos); } return counter; }; CHECK(count_occurrences(" 42") == 1); CHECK(count_occurrences(" <>") == 6); } SECTION("Check roundtrip") { mol->setProp(common_properties::_Name, "test mol 3"); // The writer always takes ownership of the stream! auto oss = new std::ostringstream; MaeWriter w(oss); w.write(*mol); w.flush(); auto iss = new std::istringstream(oss->str()); MaeMolSupplier r(iss); std::unique_ptr roundtrip_mol(r.next()); REQUIRE(roundtrip_mol); REQUIRE(MolToSmiles(*roundtrip_mol) == "*C1CCCCC1"); { INFO("Checking mol properties"); check_roundtripped_properties(*mol, *roundtrip_mol); } { INFO("Checking atom properties"); for (unsigned i = 0; i < mol->getNumAtoms(); ++i) { check_roundtripped_properties(*mol->getAtomWithIdx(i), *roundtrip_mol->getAtomWithIdx(i)); } } // Maeparser does not parse bond properties, so don't check them. } SECTION("Check reverse roundtrip") { std::string maeBlock = R"MAE(f_m_ct { s_m_title ::: "" m_atom[1] { # First column is Index # r_m_x_coord r_m_y_coord r_m_z_coord i_m_atomic_number i_m_formal_charge ::: 1 -2.542857 2.171429 0.000000 6 0 ::: } })MAE"; auto iss = new std::istringstream(maeBlock.data()); MaeMolSupplier r(iss); std::unique_ptr mol(r.next()); REQUIRE(mol); // The writer always takes ownership of the stream! auto oss = new std::stringstream; MaeWriter w(oss); w.write(*mol); w.flush(); std::string line; while (std::getline(*oss, line) && line != "f_m_ct {") { // Skip ahead to the ct block } // The only ct level property should be the title and stereo status std::getline(*oss, line); CHECK(line.find("i_m_ct_stereo_status") != std::string::npos); std::getline(*oss, line); CHECK(line.find("s_m_title") != std::string::npos); // End block marker std::getline(*oss, line); CHECK(line.find(":::") != std::string::npos); while (std::getline(*oss, line) && line.find("m_atom[1]") == std::string::npos) { // Skip ahead to the atom block } // Only the atom properties in the initial mae block should be present std::getline(*oss, line); // Chomp the comment line CAPTURE(line); REQUIRE(line.find("# First column is Index #") != std::string::npos); std::getline(*oss, line); CAPTURE(line); CHECK(line.find("r_m_x_coord") != std::string::npos); std::getline(*oss, line); CHECK(line.find("r_m_y_coord") != std::string::npos); std::getline(*oss, line); CHECK(line.find("r_m_z_coord") != std::string::npos); std::getline(*oss, line); CHECK(line.find("i_m_atomic_number") != std::string::npos); std::getline(*oss, line); CHECK(line.find("i_m_formal_charge") != std::string::npos); // End block marker std::getline(*oss, line); CHECK(line.find(":::") != std::string::npos); } SECTION("getText()") { mol->setProp(common_properties::_Name, "test mol 4"); // The writer always takes ownership of the stream! auto oss = new std::ostringstream; std::string mae; { MaeWriter w(oss); w.write(*mol); mae = oss->str(); } // Check for the Maestro file header REQUIRE(mae.find("s_m_m2io_version") != std::string::npos); // Check the CT header and Structure properties auto ctBlockStart = mae.find("f_m_ct"); REQUIRE(ctBlockStart != std::string::npos); std::string_view ctBlock(&mae[ctBlockStart]); CHECK((ctBlock == MaeWriter::getText(*mol))); } } TEST_CASE("MaeWriter edge case testing", "[mae][MaeWriter][writer][bug]") { SECTION("No atoms") { ROMol m; CHECK_THROWS_AS(RDKit::MaeWriter::getText(m), ValueErrorException); } SECTION("No bonds") { auto m = "C"_smiles; REQUIRE(m); auto oss = new std::ostringstream; MaeWriter w(oss); w.write(*m); w.flush(); auto mae = oss->str(); REQUIRE(!mae.empty()); CHECK(mae.find("m_atom[1]") != std::string::npos); CHECK(mae.find("m_bond[") == std::string::npos); } SECTION("Not kekulizable mols") { v2::SmilesParse::SmilesParserParams p; p.sanitize = false; auto mol = v2::SmilesParse::MolFromSmiles("c1ccnc1", p); REQUIRE(mol); CHECK_THROWS_AS(RDKit::MaeWriter::getText(*mol), KekulizeException); } SECTION("Unsupported bonds") { auto m = "CC"_smiles; REQUIRE(m); m->getBondWithIdx(0)->setBondType(Bond::DATIVEONE); CHECK_THROWS_AS(RDKit::MaeWriter::getText(*m), ValueErrorException); } } TEST_CASE("GitHub issue #6153: MaeMolSupplier requires bond block", "[mae][MaeMolSupplier][reader]") { SECTION("Reported issue: allow structure blocks without bond block") { std::string maeBlock = R"MAE(f_m_ct { s_m_title ::: "" m_atom[1] { # First column is Index # r_m_x_coord r_m_y_coord r_m_z_coord i_m_atomic_number i_m_formal_charge ::: 1 -2.542857 2.171429 0.000000 6 0 ::: } })MAE"; MaeMolSupplier supplier; supplier.setData(maeBlock); std::unique_ptr mol{supplier.next()}; CHECK(mol); CHECK(mol->getNumAtoms() == 1); } SECTION("Fail on ct block without atom block") { std::string maeBlock = R"MAE(f_m_ct { s_m_title ::: "" } })MAE"; MaeMolSupplier supplier; supplier.setData(maeBlock); CHECK_THROWS_AS(supplier.next(), FileParseException); } SECTION("Fail on atom block without atoms #1") { // Note that the number of elements in the block is not // read from the block header! std::string maeBlock = R"MAE(f_m_ct { s_m_title ::: "" m_atom[1] { # First column is Index # r_m_x_coord r_m_y_coord r_m_z_coord i_m_atomic_number i_m_formal_charge ::: ::: } })MAE"; MaeMolSupplier supplier; CHECK_THROWS_AS(supplier.setData(maeBlock), FileParseException); } SECTION("Fail on atom block without atoms #2") { // Note that the number of elements in the block is not // read from the block header! std::string maeBlock = R"MAE(f_m_ct { s_m_title ::: "" m_atom[1] { # First column is Index # r_m_x_coord r_m_y_coord r_m_z_coord i_m_atomic_number i_m_formal_charge ::: 1 -2.542857 2.171429 0.000000 6 0 ::: } } f_m_ct { s_m_title ::: "" m_atom[1] { # First column is Index # r_m_x_coord r_m_y_coord r_m_z_coord i_m_atomic_number i_m_formal_charge ::: ::: } })MAE"; MaeMolSupplier supplier; supplier.setData(maeBlock); // The first structure is ok std::unique_ptr mol{supplier.next()}; CHECK(mol); CHECK(mol->getNumAtoms() == 1); CHECK_THROWS_AS(supplier.next(), FileParseException); } } TEST_CASE( "GitHub issue #6153: MaeMolSupplier cannot read dummy atoms from Maestro files", "[mae][MaeMolSupplier][MaeWriter]") { std::string maeBlock = R"MAE(f_m_ct { s_m_title i_m_ct_stereo_status i_m_ct_format ::: COCH3 1 2 m_atom[7] { # First column is atom index # i_m_mmod_type r_m_x_coord r_m_y_coord r_m_z_coord i_m_color i_m_atomic_number s_m_color_rgb s_m_atom_name i_m_mass_number ::: 1 61 -0.536336 0.931891 -0.000000 10 -2 1EE11E DU1 1 2 2 0.000000 0.000000 0.000000 2 6 A0A0A0 C2 <> 3 3 1.500000 0.000000 0.000000 2 6 A0A0A0 C3 <> 4 15 -0.623038 -1.078345 -0.000420 70 8 FF2F2F O4 <> 5 41 1.863333 -1.027662 -0.000000 21 1 FFFFFF H5 <> 6 41 1.863333 0.513831 -0.889981 21 1 FFFFFF H6 <> 7 41 1.863333 0.513831 0.889981 21 1 FFFFFF H7 <> ::: } m_bond[6] { # First column is bond index # i_m_from i_m_to i_m_order ::: 1 1 2 1 2 2 3 1 3 2 4 2 4 3 5 1 5 3 6 1 6 3 7 1 ::: } })MAE"; SECTION("Read dummy atoms") { MaeMolSupplier supplier; supplier.setData(maeBlock); std::unique_ptr mol{supplier.next()}; CHECK(mol); CHECK(mol->getNumAtoms() == 4); CHECK(mol->getAtomWithIdx(0)->getAtomicNum() == 0); } SECTION("Read Mol with reserved atom type") { const std::string dummyAtomicNum = " -2 "; const std::string reservedAtomicNum = " 0 "; size_t pos = maeBlock.find(dummyAtomicNum); maeBlock.replace(pos, dummyAtomicNum.size(), reservedAtomicNum); MaeMolSupplier supplier; supplier.setData(maeBlock); std::unique_ptr mol{supplier.next()}; CHECK(mol); CHECK(mol->getNumAtoms() == 3); CHECK(mol->getNumBonds() == 2); CHECK(mol->getAtomWithIdx(0)->getAtomicNum() == 6); } SECTION("Write dummy atoms") { auto m = "*CC"_smiles; REQUIRE(m); REQUIRE(m->getNumAtoms() == 3); REQUIRE(m->getAtomWithIdx(0)->getAtomicNum() == 0); auto oss = new std::ostringstream; MaeWriter w(oss); w.write(*m); w.flush(); const auto mae = oss->str(); REQUIRE(!mae.empty()); auto atomBlockStart = mae.find("m_atom[3]"); REQUIRE(atomBlockStart != std::string::npos); auto bondBlockStart = mae.find("m_bond[2]"); REQUIRE(bondBlockStart != std::string::npos); const std::string atomBlock(&mae[atomBlockStart], bondBlockStart - atomBlockStart); CHECK(atomBlock.find(" -2 ") != std::string::npos); } } TEST_CASE("MaeWriter should not prefix Maestro-formatted properties") { std::string rdbase = getenv("RDBASE"); std::string fname1 = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.mae"; v2::FileParsers::MaeMolSupplier supplier(fname1); auto mol = supplier.next(); REQUIRE(mol); // MaeMolSupplier should ignore the i_m_ct_enhanced_stereo_status property // (it's meaningless to the RDKit) CHECK(mol->hasProp("i_m_ct_enhanced_stereo_status") == false); std::string mae_block; { auto oss = new std::ostringstream; MaeWriter w(oss); w.write(*mol); w.flush(); mae_block = oss->str(); } // properties that already match the Maestro format should not be prefixed // with "[birs]_rdkit_" CHECK(mae_block.find("b_rdkit_b_m_subgroup_collapsed") == std::string::npos); CHECK(mae_block.find("b_m_subgroup_collapsed") != std::string::npos); CHECK(mae_block.find("b_rdkit_b_sd_chiral_flag") == std::string::npos); CHECK(mae_block.find("b_sd_chiral_flag") != std::string::npos); CHECK(mae_block.find("i_rdkit_i_m_Source_File_Index") == std::string::npos); CHECK(mae_block.find("i_m_Source_File_Index") != std::string::npos); CHECK(mae_block.find("i_rdkit_i_m_ct_format") == std::string::npos); CHECK(mae_block.find("i_m_ct_format") != std::string::npos); CHECK(mae_block.find("s_rdkit_s_m_entry_name") == std::string::npos); CHECK(mae_block.find("s_m_entry_name") != std::string::npos); } #endif TEST_CASE("Chained bond stereo and wiggly bonds") { SECTION("github6434") { std::string molblock = R"CTAB( Mrv2004 07102311132D 10 9 0 0 0 0 999 V2000 -4.7714 -0.0130 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4839 -0.4255 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2152 -0.0130 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9277 -0.4255 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4839 -1.2693 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -6.2152 0.8120 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5007 1.2245 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9277 1.2433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6422 0.8308 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9192 2.0683 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 0 0 0 0 3 2 2 0 0 0 0 2 5 1 4 0 0 0 4 3 1 0 0 0 0 6 3 1 0 0 0 0 8 6 2 0 0 0 0 6 7 1 4 0 0 0 8 9 1 4 0 0 0 8 10 1 0 0 0 0 M END )CTAB"; std::unique_ptr m; m.reset(MolBlockToMol(molblock)); REQUIRE(m); CHECK(m->getNumAtoms() == 8); } } TEST_CASE("StereoGroup id forwarding", "[StereoGroup][ctab]") { auto m = "C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)O |&7:3,o1:7,&8:1,&9:5|"_smiles; REQUIRE(m); CHECK(m->getStereoGroups().size() == 4); SECTION("ids reassigned by default") { const auto mb_out = MolToMolBlock(*m); CHECK(mb_out.find("M V30 MDLV30/STERAC1") != std::string::npos); CHECK(mb_out.find("M V30 MDLV30/STERAC2") != std::string::npos); CHECK(mb_out.find("M V30 MDLV30/STERAC3") != std::string::npos); CHECK(mb_out.find("M V30 MDLV30/STEREL1") != std::string::npos); } SECTION("forward input ids") { forwardStereoGroupIds(*m); const auto mb_out = MolToMolBlock(*m); CHECK(mb_out.find("M V30 MDLV30/STERAC7") != std::string::npos); CHECK(mb_out.find("M V30 MDLV30/STERAC8") != std::string::npos); CHECK(mb_out.find("M V30 MDLV30/STERAC9") != std::string::npos); CHECK(mb_out.find("M V30 MDLV30/STEREL1") != std::string::npos); } } TEST_CASE( "GitHub issue #6664: Mol file parser strips stereogenic H from imine bonds", "[reader]") { auto useLegacy = GENERATE(true, false); UseLegacyStereoPerceptionFixture fx(useLegacy); SECTION("mol file") { auto mol = R"CTAB( 2D 7 7 0 0 0 0 0 0 0 0999 V2000 -5.6250 1.1481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2924 0.6631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0375 -0.1214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2125 -0.1214 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9576 0.6631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1729 0.9181 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.0014 1.7250 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 1 5 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 M END )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getNumAtoms() == 7); auto dblBond = mol->getBondWithIdx(3); REQUIRE(dblBond->getBondType() == Bond::DOUBLE); if (useLegacy) { CHECK(dblBond->getStereo() == Bond::STEREOE); } else { CHECK(dblBond->getStereo() == Bond::STEREOCIS); CHECK(dblBond->getStereoAtoms()[0] == 0); CHECK(dblBond->getStereoAtoms()[1] == 6); } } SECTION("mol2 file") { auto mol = R"MOL2( @MOLECULE title: molecule 1 7 7 1 SMALL USER_CHARGES @ATOM 1 C1 -5.6250 1.1481 0.0000 C.3 1 UNK 0.0000 2 C2 -6.2924 0.6631 0.0000 C.3 1 UNK 0.0000 3 C3 -6.0375 -0.1214 0.0000 C.3 1 UNK 0.0000 4 O4 -5.2125 -0.1214 0.0000 O.3 1 UNK 0.0000 5 C5 -4.9576 0.6631 0.0000 C.2 1 UNK 0.0000 6 N6 -4.1729 0.9181 0.0000 N.2 1 UNK 0.0000 7 H7 -4.0014 1.7250 0.0000 H 1 UNK 0.0000 @BOND 1 1 2 1 2 1 5 1 3 2 3 1 4 3 4 1 5 4 5 1 6 5 6 2 7 6 7 1 )MOL2"_mol2; REQUIRE(mol); CHECK(mol->getNumAtoms() == 7); auto dblBond = mol->getBondWithIdx(5); REQUIRE(dblBond->getBondType() == Bond::DOUBLE); if (useLegacy) { CHECK(dblBond->getStereo() == Bond::STEREOE); } else { CHECK(dblBond->getStereo() == Bond::STEREOCIS); CHECK(dblBond->getStereoAtoms()[0] == 0); CHECK(dblBond->getStereoAtoms()[1] == 6); } } } TEST_CASE( "z coordinate tolerance in flat structures" "[bug][molblock]") { const auto mol = R"CTAB( RDKit 2D 4 3 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0010 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2990 2.2500 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 2 3 1 0 2 4 1 0 M END )CTAB"_ctab; REQUIRE(mol); REQUIRE(mol->getNumConformers() == 1); auto conf = mol->getConformer(); CHECK(!conf.is3D()); CHECK(mol->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CCW); } TEST_CASE("Calculate 2D/3D from coordinates", "[molblock]") { SECTION("v2000, 2D structure marked as 3D without 2D stereo marks") { const auto mol = R"CTAB( RDKit 3D 4 3 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2990 2.2500 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 2 3 1 2 4 1 M END )CTAB"_ctab; REQUIRE(mol); REQUIRE(mol->getNumConformers() == 1); auto conf = mol->getConformer(); CHECK(conf.is3D()); CHECK(mol->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_UNSPECIFIED); } SECTION("v2000, 2D structure marked as 3D with 2D stereo marks") { const auto mol = R"CTAB( RDKit 3D 4 3 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2990 2.2500 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 2 3 1 0 2 4 1 0 M END )CTAB"_ctab; REQUIRE(mol); REQUIRE(mol->getNumConformers() == 1); auto conf = mol->getConformer(); CHECK(!conf.is3D()); CHECK(mol->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CCW); } SECTION("v2000, 3D structure marked as 2D") { const auto mol = R"CTAB( RDKit 2D 4 3 0 0 0 0 0 0 0 0999 V2000 -0.0017 0.0135 0.0027 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8238 0.0150 0.0040 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0881 -0.3228 0.6346 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1772 0.9156 -0.0296 S 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 2 3 1 2 4 1 M END )CTAB"_ctab; REQUIRE(mol); REQUIRE(mol->getNumConformers() == 1); auto conf = mol->getConformer(); CHECK(conf.is3D()); CHECK(mol->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CCW); } SECTION("v3000, 2D structure marked as 3D without 2D stereo marks") { const auto mol = R"CTAB( RDKit 3D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 4 3 0 0 0 M V30 BEGIN ATOM M V30 1 C 1.0912 0.945 0 0 M V30 2 C 2.4248 1.715 0 0 M V30 3 O 3.7586 0.945 0 0 M V30 4 S 2.4248 3.255 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 2 1 M V30 2 1 2 3 M V30 3 1 2 4 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); REQUIRE(mol->getNumConformers() == 1); auto conf = mol->getConformer(); CHECK(conf.is3D()); CHECK(mol->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_UNSPECIFIED); } SECTION("v3000, 2D structure marked as 3D with 2D stereo marks") { const auto mol = R"CTAB( RDKit 3D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 4 3 0 0 0 M V30 BEGIN ATOM M V30 1 C 1.0912 0.945 0 0 M V30 2 C 2.4248 1.715 0 0 CFG=2 M V30 3 O 3.7586 0.945 0 0 M V30 4 S 2.4248 3.255 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 2 1 CFG=1 M V30 2 1 2 3 M V30 3 1 2 4 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); REQUIRE(mol->getNumConformers() == 1); auto conf = mol->getConformer(); CHECK(!conf.is3D()); CHECK(mol->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CCW); } SECTION("v3000, 3D structure marked as 2D") { const auto mol = R"CTAB( RDKit 2D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 4 3 0 0 0 M V30 BEGIN ATOM M V30 1 C -0.0033 0.0252 0.0052 0 M V30 2 C 1.5379 0.028 0.0075 0 CFG=2 M V30 3 O 2.0313 -0.6027 1.1846 0 M V30 4 S 2.1975 1.7092 -0.0554 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 2 1 M V30 2 1 2 3 M V30 3 1 2 4 M V30 END BOND M V30 END CTAB M END )CTAB"_ctab; REQUIRE(mol); REQUIRE(mol->getNumConformers() == 1); auto conf = mol->getConformer(); CHECK(conf.is3D()); CHECK(mol->getAtomWithIdx(1)->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CCW); } } TEST_CASE( "GitHub Issue #6703: Exporting to mol marks imine bonds EITHERDOUBLE when imine H is implicit", "[bug][writer][stereo]") { auto m = "NC(O)=N"_smiles; REQUIRE(m); REQUIRE(m->getNumAtoms() == 4); auto bond = m->getBondWithIdx(2); REQUIRE(bond->getBondType() == Bond::DOUBLE); REQUIRE(bond->getStereo() == Bond::BondStereo::STEREONONE); REQUIRE(bond->getBondDir() == Bond::BondDir::NONE); std::string molblock; SECTION("v2000") { molblock = MolToMolBlock(*m); REQUIRE(molblock.find(" 4 3 0 0 0 0 0 0 0 0999 V2000") != std::string::npos); // There must be a double bond, but it must not be marked as either REQUIRE(molblock.find(" 2 4 2") != std::string::npos); CHECK(molblock.find(" 2 4 2 3") == std::string::npos); } SECTION("v3000") { molblock = MolToV3KMolBlock(*m); REQUIRE(molblock.find("M V30 COUNTS 4 3 0 0 0") != std::string::npos); // There must be a double bond, but it must not be marked as either REQUIRE(molblock.find("M V30 3 2 2 4") != std::string::npos); CHECK(molblock.find("CFG=2") == std::string::npos); } std::unique_ptr m2{MolBlockToMol(molblock)}; REQUIRE(m2); REQUIRE(m2->getNumAtoms() == 4); auto bond2 = m2->getBondWithIdx(2); REQUIRE(bond2->getBondType() == Bond::DOUBLE); CHECK(bond2->getStereo() == Bond::BondStereo::STEREONONE); CHECK(bond2->getBondDir() == Bond::BondDir::NONE); } TEST_CASE( "github #5819: Support writing detailed SMARTS queries to CTABs using the SMARTSQ mechanism") { SECTION("as reported") { auto m = "[C,N,O]C[#6]*[$(C(=O)O)]"_smarts; REQUIRE(m); auto ctab = MolToV3KMolBlock(*m); // std::cerr << ctab << std::endl; // make sure we still do list queries correctly CHECK(ctab.find("V30 1 [C,N,O]") != std::string::npos); CHECK(ctab.find("FIELDDATA=\"[C,N,O]") == std::string::npos); CHECK(ctab.find("FIELDDATA=\"C\"") == std::string::npos); CHECK(ctab.find("FIELDDATA=\"[#6]\"") == std::string::npos); CHECK(ctab.find("FIELDDATA=\"*\"") == std::string::npos); CHECK(ctab.find("SMARTSQ") != std::string::npos); CHECK(ctab.find("[$(C(=O)O)]") != std::string::npos); // make sure we can properly parse that std::unique_ptr nm{MolBlockToMol(ctab)}; REQUIRE(nm); CHECK(MolToSmarts(*nm) == "[#6,#7,#8][#6][#6]*[$(C(=O)O)]"); } } void testFragmentation(const std::string &fileName, unsigned int origSgroupCount, unsigned int newSgroupCount) { INFO(fileName); std::string rdbase = getenv("RDBASE"); std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/sgroupFragments/" + fileName; std::unique_ptr mol(MolFileToMol(fName, false)); // don't sanitize yet REQUIRE(mol); CHECK(getSubstanceGroups(*mol).size() == origSgroupCount); auto frags = MolOps::getMolFrags(*mol, true); CHECK(frags.size() > 1); // get the largest fragment unsigned int largestFragSize = 0; ROMol *largestFrag = nullptr; for (auto frag : frags) { if (frag->getNumAtoms() > largestFragSize) { largestFragSize = frag->getNumAtoms(); largestFrag = frag.get(); } } CHECK(largestFrag); CHECK(getSubstanceGroups(*largestFrag).size() == newSgroupCount); if (origSgroupCount == newSgroupCount) { // if the number of sgroups is the same, then the sgroups should be the // same for (unsigned int sgIndex = 0; sgIndex < getSubstanceGroups(*largestFrag).size(); ++sgIndex) { CHECK(getSubstanceGroups(*largestFrag)[sgIndex].getProp( "TYPE") == getSubstanceGroups(*mol)[sgIndex].getProp("TYPE")); } } } TEST_CASE("FragmentSgroupTest", "[bug][reader]") { SECTION("basics") { std::vector> tests = { {"polymerSalt.mol", 1, 1}, {"copolymer_sgroup.sdf", 1, 0}, // fragmntation does not keep the sgroup for this one {"DataSgroup.sdf", 2, 2}, {"DataSgroupMissingUnitsDisplayed.sdf", 1, 1}, {"EmbeddedSGroupSUP_MUL.sdf", 2, 2}, {"EmbeddedSgroupCOP_SUP.sdf", 2, 2}, {"EmbeddedSgroupDAT_SUP.sdf", 2, 2}, {"EmbeddedSgroupMUL_MUL.sdf", 3, 3}, {"EmbeddedSgroupMUL_SUP.sdf", 2, 2}, {"EmbeddedSgroupSRU_SUP.sdf", 2, 2}, {"EmbeddedSgroupSUPEXP_SUP.sdf", 2, 2}, {"EmbeddedSgroupSUPEXP_SUP2.sdf", 2, 2}, {"EmbeddedSgroupSUP_SUP.sdf", 2, 2}, {"EmbeddedSgroupSUP_SUP2.sdf", 2, 2}, {"GenericSgroup.sdf", 1, 1}, {"MarvinOldSuperGroupTest.sdf", 9, 5}, {"MonomerSgroup.sdf", 1, 1}, {"MultipleSgroup.sdf", 1, 1}, {"MultipleSgroupParentInMiddleOfAtomBlock.sdf", 1, 1}, {"SgroupExpanded.sdf", 1, 1}, {"SgroupMultAttach.sdf", 4, 4}, {"Sgroup_MUL_ParentInMiddle.sdf", 1, 1}, {"modification_sgroup.sdf", 2, 1}, }; for (const auto &[fileName, origSgroupCount, newSgroupCount] : tests) { testFragmentation(fileName, origSgroupCount, newSgroupCount); } }; } void testWedges(const std::string &fileName, unsigned int origWedgeCount, unsigned int newWedgeCount) { INFO(fileName); UseLegacyStereoPerceptionFixture reset_stereo_perception{false}; std::string rdbase = getenv("RDBASE"); std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/wedgeTests/" + fileName; std::unique_ptr mol(MolFileToMol(fName, true)); // REQUIRE(mol); RDKit::Chirality::reapplyMolBlockWedging(*mol, true, false); unsigned int wedgeCount = 0; for (const auto bond : mol->bonds()) { if (bond->getBondDir() == Bond::BEGINWEDGE || bond->getBondDir() == Bond::BEGINDASH) { ++wedgeCount; } } CHECK(wedgeCount == origWedgeCount); RDKit::Chirality::reapplyMolBlockWedging(*mol, true, true); wedgeCount = 0; for (const auto bond : mol->bonds()) { if (bond->getBondDir() == Bond::BEGINWEDGE || bond->getBondDir() == Bond::BEGINDASH) { ++wedgeCount; } } CHECK(wedgeCount == newWedgeCount); } TEST_CASE("WedgeTest", "[bug][reader]") { SECTION("basics") { std::vector> tests = { {"JDQ443_atropBad1.sdf", 2, 0}, {"badWedgeError.sdf", 1, 0}, {"StereoGroupError.mol", 2, 1}, }; for (const auto &[fileName, origWedgeCount, newWedgeCount] : tests) { testWedges(fileName, origWedgeCount, newWedgeCount); } }; } TEST_CASE( "GitHub Issue #7259: Writing StereoGroups to Mol files should break lines at 80 characters", "[bug]") { auto run_checks = [](const auto &mol) { REQUIRE(mol); REQUIRE(mol->getNumAtoms() == 77); const auto stgs = mol->getStereoGroups(); REQUIRE(stgs.size() == 1); CHECK(stgs[0].getAtoms().size() == 35); }; // Just some long chain with (a lot of) random up and down side branches const auto m = ("CC(C)[C@@H](C)[C@H](C)[C@@H](C)[C@H](C)[C@@H](C)[C@H](C)[C@@H](C)[C@H](C)[C@@H](C)[C@H]" "(C)[C@@H](C)[C@H](C)[C@@H](C)[C@H](C)[C@H](C)[C@H](C)[C@@H](C)[C@H](C)[C@H]1C[C@@H]([C@H]" "(C)[C@@H](C)[C@H](C)[C@@H](C)[C@H](C)[C@@H](C)[C@H](C)[C@@H](C)[C@H](C)[C@@H](C)[C@H](C)" "[C@@H](C)[C@H](C)[C@@H](C)C(C)C)[C@@H](C)[C@H]1C |a:1,3,5,7,9,11,13,15,17,19,21,23,25,27," "29,31,33,35,39,41,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,73,75|"_smiles); run_checks(m); const auto mb = MolToMolBlock(*m); const auto steAbsPos = mb.find("M V30 MDLV30/STEABS ATOMS=(35 "); REQUIRE(steAbsPos != std::string::npos); const auto endOfLine = mb.find("\nM V30 ", steAbsPos + 1); REQUIRE(endOfLine != std::string::npos); CHECK(mb[endOfLine - 1] == '-'); run_checks(v2::FileParsers::MolFromMolBlock(mb)); } TEST_CASE( "GitHub Issue #7256: RDKit fails to parse \"M RAD\" lines where radical is 0", "[bug]") { const auto mb = R"CTAB( RDKit 2D 1 0 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 M RAD 1 1 0 M END )CTAB"; std::unique_ptr mol(MolBlockToMol(mb)); REQUIRE(mol); REQUIRE(mol->getNumAtoms() == 1); const auto at = mol->getAtomWithIdx(0); CHECK(at->getNumRadicalElectrons() == 0); } TEST_CASE("ZBOs in V3K blocks") { std::string rdbase = getenv("RDBASE"); rdbase += "/Code/GraphMol/FileParsers/test_data/"; SECTION("basics") { auto run_tests = [](auto &m) { CHECK(m->getNumAtoms() == 2); CHECK(m->getNumBonds() == 1); CHECK(m->getBondWithIdx(0)->getBondType() == Bond::ZERO); CHECK(m->getAtomWithIdx(0)->getFormalCharge() == 0); CHECK(m->getAtomWithIdx(1)->getFormalCharge() == 0); CHECK(m->getAtomWithIdx(0)->getTotalNumHs() == 3); CHECK(m->getAtomWithIdx(1)->getTotalNumHs() == 3); CHECK(m->getAtomWithIdx(0)->hasProp("_ZBO_H")); }; std::string fName; fName = rdbase + "H3BNH3.mol"; auto m = v2::FileParsers::MolFromMolFile(fName); REQUIRE(m); { INFO("v2000"); run_tests(m); } auto mb = MolToV3KMolBlock(*m); CHECK(mb.find("M V30 1 0 1 2") == std::string::npos); CHECK(mb.find("M V30 1 1 1 2") != std::string::npos); CHECK(mb.find("ZBO") != std::string::npos); CHECK(mb.find("HYD") != std::string::npos); CHECK(mb.find("ZCH") != std::string::npos); auto m2 = v2::FileParsers::MolFromMolBlock(mb); REQUIRE(m2); { INFO("v3000"); run_tests(m2); } } SECTION("example") { // from SI of Alex Clark's ZBO paper auto m = R"CTAB( RDKit 2D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 8 8 1 0 0 M V30 BEGIN ATOM M V30 1 Cl 2.121320 1.060660 0.000000 0 M V30 2 I 1.060660 0.000000 0.000000 0 M V30 3 Cl 2.121320 -1.060660 0.000000 0 M V30 4 Cl -0.000000 -1.060660 0.000000 0 M V30 5 Cl 0.000000 1.060660 0.000000 0 M V30 6 I -1.060660 0.000000 0.000000 0 M V30 7 Cl -2.121320 -1.060660 0.000000 0 M V30 8 Cl -2.121320 1.060660 0.000000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 2 4 M V30 4 1 2 5 M V30 5 1 5 6 M V30 6 1 6 7 M V30 7 1 6 8 M V30 8 1 6 4 M V30 END BOND M V30 BEGIN SGROUP M V30 1 DAT 0 ATOMS=(4 2 5 6 4) CBONDS=(2 4 8) FIELDNAME=ZBO M V30 END SGROUP M V30 END CTAB M END )CTAB"_ctab; REQUIRE(m); CHECK(m->getNumAtoms() == 8); CHECK(m->getNumBonds() == 8); CHECK(m->getBondWithIdx(3)->getBondType() == Bond::ZERO); CHECK(m->getBondWithIdx(7)->getBondType() == Bond::ZERO); auto mb = MolToV3KMolBlock(*m); CHECK(mb.find("ZBO") != std::string::npos); CHECK(mb.find("HYD") != std::string::npos); CHECK(mb.find("ZCH") != std::string::npos); auto m2 = v2::FileParsers::MolFromMolBlock(mb); REQUIRE(m2); CHECK(m2->getNumAtoms() == 8); CHECK(m2->getNumBonds() == 8); CHECK(m2->getBondWithIdx(3)->getBondType() == Bond::ZERO); CHECK(m2->getBondWithIdx(7)->getBondType() == Bond::ZERO); } } TEST_CASE("MolToV2KMolBlock") { SECTION("basics") { auto m = "[NH3]->[Pt]"_smiles; REQUIRE(m); // by default we get a V3K block since there is a dative bond present auto mb = MolToMolBlock(*m); CHECK(mb.find("V3000") != std::string::npos); CHECK(mb.find("V30 1 9 1 2") != std::string::npos); // but we can ask for a V2K block mb = MolToV2KMolBlock(*m); CHECK(mb.find("V2000") != std::string::npos); CHECK(mb.find(" 1 2 9 0") != std::string::npos); } SECTION("limits") { // we won't test SGroups since creating 1000 of them is a bit much std::vector smileses = { std::string(1000, 'C'), "C1CC2" + std::string(996, 'C') + "12", }; for (const auto &smi : smileses) { INFO(smi); auto m = v2::SmilesParse::MolFromSmiles(smi); REQUIRE(m); CHECK_THROWS_AS(MolToV2KMolBlock(*m), ValueErrorException); } } } TEST_CASE("Github #7306: bad crossed bonds in large aromatic rings") { std::string rdbase = getenv("RDBASE"); rdbase += "/Code/GraphMol/FileParsers/test_data/"; SECTION("as reported") { auto m = v2::FileParsers::MolFromMolFile(rdbase + "github7306.mol"); REQUIRE(m); auto ctab = MolToV3KMolBlock(*m); CHECK(ctab.find("CFG=2") == std::string::npos); ctab = MolToMolBlock(*m); CHECK(ctab.find("2 3\n") == std::string::npos); } } TEST_CASE( "Github #8023: explicit valence for charged organic atoms in mol block") { SECTION("as reported 1") { auto m = "C[NH3+]"_smiles; REQUIRE(m); auto ctab = MolToMolBlock(*m); CHECK(ctab.find("N 0 0 0 0 0 0 0") != std::string::npos); ctab = MolToV3KMolBlock(*m); CHECK(ctab.find("CHG=1") != std::string::npos); CHECK(ctab.find("VAL=4") == std::string::npos); } SECTION("nitro-type") { auto m = "C[N+](=S)[O-]"_smiles; REQUIRE(m); auto ctab = MolToMolBlock(*m); CHECK(ctab.find("N 0 0 0 0 0 0 0") != std::string::npos); CHECK(ctab.find("O 0 0 0 0 0 0 0") != std::string::npos); ctab = MolToV3KMolBlock(*m); CHECK(ctab.find("CHG=1") != std::string::npos); CHECK(ctab.find("VAL=4") == std::string::npos); CHECK(ctab.find("CHG=-1") != std::string::npos); CHECK(ctab.find("VAL=1") == std::string::npos); } } TEST_CASE("Github #8060: crash with a bad mol block") { SECTION("as reported") { std::string molblock = R"CTAB( 11 20 0 0 0 0 0 0 0 0999 V2000 0.7752 1.4699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0024 0.9086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2976 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2528 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5479 0.9086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.9085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2952 4.8170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2504 4.8170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5455 3.9085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7728 3.3471 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7752 2.4009 0.0000 Fe 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 1 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 6 1 0 0 0 0 11 1 1 0 0 0 0 11 2 1 0 0 0 0 11 3 1 0 0 0 0 11 4 1 0 0 0 0 11 5 1 0 0 0 0 11 6 1 0 0 0 0 11 7 1 0 0 0 0 11 8 1 0 0 0 0 11 9 1 0 0 0 0 11 10 1 0 0 0 0 M END)CTAB"; auto m = v2::FileParsers::MolFromMolBlock(molblock); REQUIRE(m); { UseLegacyStereoPerceptionFixture reset_stereo_perception{false}; auto m = v2::FileParsers::MolFromMolBlock(molblock); REQUIRE(m); } } SECTION("catch expected exception") { // the molecule is really stupid std::string molblock = R"CTAB( 21 40 0 0 0 0 0 0 0 0999 V2000 0.7752 1.4699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0024 0.9086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2976 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2528 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5479 0.9086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.9085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2952 4.8170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2504 4.8170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5455 3.9085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7728 3.3471 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7752 1.4699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0024 0.9086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2976 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2528 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5479 0.9086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.9085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2952 4.8170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2504 4.8170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5455 3.9085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7728 3.3471 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7752 2.4009 0.0000 Fe 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 1 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 6 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 11 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 16 1 0 0 0 0 21 1 1 0 0 0 0 21 2 1 0 0 0 0 21 3 1 0 0 0 0 21 4 1 0 0 0 0 21 5 1 0 0 0 0 21 6 1 0 0 0 0 21 7 1 0 0 0 0 21 8 1 0 0 0 0 21 9 1 0 0 0 0 21 10 1 0 0 0 0 21 11 1 0 0 0 0 21 12 1 0 0 0 0 21 13 1 0 0 0 0 21 14 1 0 0 0 0 21 15 1 0 0 0 0 21 16 1 0 0 0 0 21 17 1 0 0 0 0 21 18 1 0 0 0 0 21 19 1 0 0 0 0 21 20 1 0 0 0 0 M END)CTAB"; REQUIRE_THROWS_AS(v2::FileParsers::MolFromMolBlock(molblock), std::out_of_range); { UseLegacyStereoPerceptionFixture reset_stereo_perception{false}; auto m = v2::FileParsers::MolFromMolBlock(molblock); REQUIRE(m); } } } TEST_CASE("Github #8820: allowed list atoms should be read as dummy atoms") { SECTION("v3k basics") { auto mol = R"CTAB( RDKit 2D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 3 2 0 0 0 M V30 BEGIN ATOM M V30 1 C -14.969697 7.242424 0.000000 0 M V30 2 [C,N] -13.670659 7.992424 0.000000 0 M V30 3 C -12.371621 7.242424 0.000000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 END BOND M V30 END CTAB M END $$$$ )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getNumAtoms() == 3); CHECK(mol->getAtomWithIdx(1)->getAtomicNum() == 0); auto ctab = MolToV3KMolBlock(*mol); CHECK(ctab.find("V30 2 [C,N]") != std::string::npos); } SECTION("v3k not") { auto mol = R"CTAB( RDKit 2D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 3 2 0 0 0 M V30 BEGIN ATOM M V30 1 C -14.969697 7.242424 0.000000 0 M V30 2 "NOT [C,N]" -13.670659 7.992424 0.000000 0 M V30 3 C -12.371621 7.242424 0.000000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 END BOND M V30 END CTAB M END $$$$ )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getNumAtoms() == 3); CHECK(mol->getAtomWithIdx(1)->getAtomicNum() == 0); auto ctab = MolToV3KMolBlock(*mol); CHECK(ctab.find("V30 2 \"NOT [C,N]\"") != std::string::npos); } SECTION("v3k single atom") { auto mol = R"CTAB( RDKit 2D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 3 2 0 0 0 M V30 BEGIN ATOM M V30 1 C -14.969697 7.242424 0.000000 0 M V30 2 [C] -13.670659 7.992424 0.000000 0 M V30 3 C -12.371621 7.242424 0.000000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 END BOND M V30 END CTAB M END $$$$ )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getNumAtoms() == 3); CHECK(mol->getAtomWithIdx(1)->getAtomicNum() == 0); auto ctab = MolToV3KMolBlock(*mol); CHECK(ctab.find("V30 2 [C]") != std::string::npos); } SECTION("v3k not single atom") { auto mol = R"CTAB( RDKit 2D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 3 2 0 0 0 M V30 BEGIN ATOM M V30 1 C -14.969697 7.242424 0.000000 0 M V30 2 "NOT [C]" -13.670659 7.992424 0.000000 0 M V30 3 C -12.371621 7.242424 0.000000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 END BOND M V30 END CTAB M END $$$$ )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getNumAtoms() == 3); CHECK(mol->getAtomWithIdx(1)->getAtomicNum() == 0); auto ctab = MolToV3KMolBlock(*mol); // this now ends up being a NOT list query on output: CHECK(ctab.find("V30 2 \"NOT [C]\"") != std::string::npos); } SECTION("v2k") { auto mol = R"CTAB( RDKit 2D 3 2 0 0 0 0 0 0 0 0999 V2000 -14.9697 7.2424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.6707 7.9924 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.3716 7.2424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 M ALS 2 2 F C N M END )CTAB"_ctab; REQUIRE(mol); CHECK(mol->getNumAtoms() == 3); CHECK(mol->getAtomWithIdx(1)->getAtomicNum() == 0); auto ctab = MolToMolBlock(*mol); CHECK(ctab.find("ALS") != std::string::npos); } } TEST_CASE( "Github #8823: aromaticity perception with list queries depends on ordering of atoms") { std::string rdbase = getenv("RDBASE"); std::string fName = rdbase + "/Code/GraphMol/FileParsers/test_data/github8823.sdf"; auto suppl = v2::FileParsers::SDMolSupplier(fName); REQUIRE(suppl.length() == 3); for (auto i = 0u; i < suppl.length(); ++i) { auto m = suppl[i]; REQUIRE(m); REQUIRE(m->getNumAtoms() == 5); CHECK(m->getBondWithIdx(0)->getBondType() == Bond::AROMATIC); } } TEST_CASE("GitHub Issue #8873: Warn/fail on multiple ABS stereo groups") { // This is illegal, according to the spec (ABS groups must be unique) auto mb = R"CTAB( RDKit 2D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 7 6 0 0 0 M V30 BEGIN ATOM M V30 1 N -3.696970 2.121212 0.000000 0 M V30 2 C -2.397932 2.871212 0.000000 0 M V30 3 C -1.098893 2.121212 0.000000 0 M V30 4 C 0.200145 2.871212 0.000000 0 M V30 5 O 1.499183 2.121212 0.000000 0 M V30 6 C -2.397932 4.371212 0.000000 0 M V30 7 C 0.200145 4.371212 0.000000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 3 4 M V30 4 1 4 5 M V30 5 1 2 6 CFG=1 M V30 6 1 4 7 CFG=1 M V30 END BOND M V30 BEGIN COLLECTION M V30 MDLV30/STEABS ATOMS=(1 2) M V30 MDLV30/STEABS ATOMS=(1 4) M V30 END COLLECTION M V30 END CTAB M END $$$$ )CTAB"; constexpr bool removeHs = true; constexpr bool sanitize = true; SECTION("strict parsing disabled: warn and collapse") { bool strictParsing = false; std::unique_ptr m{ MolBlockToMol(mb, sanitize, removeHs, strictParsing)}; REQUIRE(m); const auto &stgs = m->getStereoGroups(); REQUIRE(stgs.size() == 1); const auto &stg = stgs.front(); CHECK(stg.getGroupType() == StereoGroupType::STEREO_ABSOLUTE); CHECK(stg.getAtoms().size() == 2); } SECTION("strict parsing disabled: throw") { bool strictParsing = true; REQUIRE_THROWS_AS(MolBlockToMol(mb, sanitize, removeHs, strictParsing), FileParseException); } } TEST_CASE( "V3000 aromatic bonds with explicit H: kekulization after H removal") { // The V3000 parser sets aromatic flags on bonds but not atoms. // When removeHs strips an explicit H from aromatic N, molRemoveH must // still recognise the atom as aromatic (via its bond flags) so that // numExplicitHs is incremented. Without that, the kekuliser cannot // distinguish pyrrole N from pyridine N and kekulization fails. auto molblock = R"MOL( ChemDraw03022611582D 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 7 7 0 0 0 M V30 BEGIN ATOM M V30 1 C 1.452059 0.404789 0.000000 0 M V30 2 C 0.667439 0.149850 0.000000 0 M V30 3 N 0.412500 -0.634772 0.000000 0 M V30 4 C -0.412500 -0.634772 0.000000 0 M V30 5 N -0.667438 0.149850 0.000000 0 M V30 6 C -0.000000 0.634772 0.000000 0 M V30 7 H -1.452059 0.404790 0.000000 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 4 2 3 M V30 3 4 3 4 M V30 4 4 4 5 M V30 5 4 5 6 M V30 6 4 2 6 M V30 7 1 5 7 M V30 END BOND M V30 END CTAB M END )MOL"; SECTION("default sanitize + removeHs") { std::unique_ptr mol(MolBlockToMol(molblock)); REQUIRE(mol); CHECK(MolToSmiles(*mol) == "Cc1c[nH]cn1"); } SECTION("pyrrole N has correct explicit H count after H removal") { std::unique_ptr mol(MolBlockToMol(molblock)); REQUIRE(mol); // Atom 4 in the original block is the [nH] nitrogen (index 4 after // H removal and reindexing — find it by checking for aromatic N with H). bool foundPyrroleN = false; for (const auto atom : mol->atoms()) { if (atom->getAtomicNum() == 7 && atom->getIsAromatic() && atom->getTotalNumHs() == 1) { CHECK(atom->getNumExplicitHs() == 1); foundPyrroleN = true; } } CHECK(foundPyrroleN); } } TEST_CASE("duplicates in stereo groups") { auto ctab = R"CTAB( Mrv1642508181718102D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 8 7 0 0 0 M V30 BEGIN ATOM M V30 1 C -5.2222 4.7778 0 0 CFG=2 M V30 2 Br -6.9685 5.5478 0 0 M V30 3 C -5.0557 3.2468 0 0 M V30 4 C -3.9796 5.6874 0 0 CFG=2 M V30 5 C -2.5705 5.0661 0 0 CFG=1 M V30 6 F -1.3279 5.9758 0 0 M V30 7 C -4.1461 7.2184 0 0 M V30 8 C -2.404 3.5352 0 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 1 4 M V30 3 1 4 5 M V30 4 1 5 6 M V30 5 1 4 7 CFG=1 M V30 6 1 5 8 CFG=1 M V30 7 1 1 3 CFG=1 M V30 END BOND M V30 BEGIN COLLECTION M V30 MDLV30/STEREL1 ATOMS=(2 4 4) M V30 END COLLECTION M V30 END CTAB M END )CTAB"; // CHECK_THROWS_AS(v2::FileParsers::MolFromMolBlock(ctab), // FileParseException); v2::FileParsers::MolFileParserParams params; params.strictParsing = false; auto m = v2::FileParsers::MolFromMolBlock(ctab, params); REQUIRE(m); const auto &stgs = m->getStereoGroups(); REQUIRE(stgs.size() == 1); CHECK(stgs.front().getGroupType() == StereoGroupType::STEREO_OR); CHECK(stgs.front().getAtoms().size() == 1); }