// // Copyright (C) 2018 Greg Landrum // @@ 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. // #define CATCH_CONFIG_MAIN // This tells Catch to provide a main() - only do // this in one cpp file #include "RDGeneral/test.h" #include "catch.hpp" #include #include #include #include #include using namespace RDKit; TEST_CASE("Basic SVG Parsing", "[SVG,parser]") { SECTION("basics") { std::string svg = R"SVG( )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,parser]") { 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", "[parser,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", "[parser,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("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 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") == "MRV_IMPLICIT_H"); } }