// // // Copyright (C) 2018-2020 Greg Landrum and T5 Informatics GmbH // // @@ 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 "catch.hpp" #include #include #include #include #include #include #include #include #include using namespace RDKit; #if 1 TEST_CASE("SMILES Parsing works", "[molops]") { std::unique_ptr mol(SmilesToMol("C1CC1")); REQUIRE(mol); REQUIRE(mol->getNumAtoms() == 3); } TEST_CASE("Sanitization tests", "[molops]") { std::unique_ptr mol(SmilesToMol("C1=CC=CC=C1Cc2ccccc2", false, false)); REQUIRE(mol); REQUIRE(mol->getNumAtoms() == 13); SECTION("properties") { mol->updatePropertyCache(); CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 1); CHECK(!mol->getAtomWithIdx(0)->getIsAromatic()); CHECK(mol->getAtomWithIdx(10)->getIsAromatic()); SECTION("aromaticity") { unsigned int opThatFailed; MolOps::sanitizeMol(*mol, opThatFailed, MolOps::SANITIZE_SETAROMATICITY); // mol->debugMol(std::cerr); CHECK(mol->getAtomWithIdx(10)->getIsAromatic()); // blocked by #1730 // CHECK(mol->getAtomWithIdx(0)->getIsAromatic()); } SECTION("kekulize") { unsigned int opThatFailed; MolOps::sanitizeMol(*mol, opThatFailed, MolOps::SANITIZE_KEKULIZE); CHECK(!mol->getAtomWithIdx(0)->getIsAromatic()); CHECK(!mol->getAtomWithIdx(10)->getIsAromatic()); } } } TEST_CASE("Github #2062", "[bug][molops]") { SmilesParserParams ps; ps.removeHs = false; ps.sanitize = true; std::unique_ptr mol(SmilesToMol("[C:1][C:2]([H:3])([H])[O:4][H]", ps)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 6); mol->getAtomWithIdx(1)->setProp("intProp", 42); MolOps::mergeQueryHs(*mol); CHECK(mol->getNumAtoms() == 3); SECTION("basics") { CHECK(mol->getAtomWithIdx(1)->getAtomMapNum() == 2); } SECTION("other props") { REQUIRE(mol->getAtomWithIdx(1)->hasProp("intProp")); CHECK(mol->getAtomWithIdx(1)->getProp("intProp") == 42); } } TEST_CASE("Github #2086", "[bug][molops]") { SECTION("reported version") { auto mol = "C1CCCC1"_smiles; REQUIRE(mol); MolOps::addHs(*mol); REQUIRE(mol->getNumAtoms() == 15); mol->removeBond(4, 13); MolOps::removeHs(*mol); REQUIRE(mol->getNumAtoms() == 6); } } TEST_CASE("github #299", "[bug][molops][SSSR]") { SECTION("simplified") { auto mol = "C13%13%14.C124%18.C25%13%15.C368%17.C4679.C75%10%17.C8%11%14%16.C9%11%12%18.C%10%12%15%16"_smiles; REQUIRE(mol); REQUIRE(mol->getNumAtoms() == 9); } SECTION("old example from molopstest") { auto mol = "C123C45C11C44C55C22C33C14C523"_smiles; REQUIRE(mol); REQUIRE(mol->getNumAtoms() == 9); } SECTION("carborane") { std::unique_ptr mol( SmilesToMol("[B]1234[B]567[B]118[B]229[B]33%10[B]454[B]656[B]711[B]822[" "C]933[B]%1045[C]6123", 0, false)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 12); mol->updatePropertyCache(false); MolOps::findSSSR(*mol); REQUIRE(mol->getRingInfo()->isInitialized()); } SECTION("original report from ChEbI") { std::string pathName = getenv("RDBASE"); pathName += "/Code/GraphMol/test_data/"; std::unique_ptr mol( MolFileToMol(pathName + "ChEBI_50252.mol", false)); REQUIRE(mol); CHECK(mol->getNumAtoms() == 80); mol->updatePropertyCache(false); MolOps::findSSSR(*mol); REQUIRE(mol->getRingInfo()->isInitialized()); } } TEST_CASE("github #2224", "[bug][molops][removeHs][query]") { SECTION("the original report") { std::string pathName = getenv("RDBASE"); pathName += "/Code/GraphMol/test_data/"; std::unique_ptr mol(MolFileToMol(pathName + "github2224_1.mol")); REQUIRE(mol); REQUIRE(mol->getNumAtoms() == 7); } SECTION("basics") { SmilesParserParams ps; ps.removeHs = false; ps.sanitize = true; std::unique_ptr mol(SmilesToMol("C[H]", ps)); REQUIRE(mol); REQUIRE(mol->getNumAtoms() == 2); { // The H without a query is removed std::unique_ptr m2(MolOps::removeHs(*mol)); CHECK(m2->getNumAtoms() == 1); } { // but if we add a query feature it's not removed RWMol m2(*mol); auto *qa = new QueryAtom(1); m2.replaceAtom(1, qa); m2.getAtomWithIdx(1)->setAtomicNum(1); MolOps::removeHs(m2); CHECK(m2.getNumAtoms() == 2); delete qa; } } } TEST_CASE( "github #2268: Recognize N in three-membered rings as potentially chiral", "[bug][stereo]") { SECTION("basics: N in a 3 ring") { const auto mol = "C[N@]1CC1C"_smiles; REQUIRE(mol); CHECK(mol->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED); } SECTION("basics: N in a 4 ring") { const auto mol = "C[N@]1CCC1C"_smiles; REQUIRE(mol); CHECK(mol->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED); } SECTION("the original molecule") { std::string mb = R"CTAB( Mrv1810 02131915062D 18 20 0 0 1 0 999 V2000 -0.7207 -1.3415 0.0000 N 0 0 1 0 0 0 0 0 0 0 0 0 -0.0583 -0.8416 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0083 -1.7540 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3956 -0.8666 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3250 -0.0667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1955 -0.6499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1499 -0.0792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6541 -0.4292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7830 -1.2291 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6081 -1.6623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4080 0.1500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3665 -0.8374 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6416 0.3958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1996 0.3708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4121 1.1624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3498 0.8207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0790 -0.4167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0665 0.4083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 0 0 0 0 1 3 1 1 0 0 0 4 1 1 0 0 0 0 5 2 1 0 0 0 0 4 6 1 0 0 0 0 7 4 1 0 0 0 0 2 8 1 6 0 0 0 9 6 2 0 0 0 0 4 10 1 1 0 0 0 11 6 1 0 0 0 0 12 8 2 0 0 0 0 13 8 1 0 0 0 0 14 11 1 0 0 0 0 15 14 1 0 0 0 0 16 13 2 0 0 0 0 17 12 1 0 0 0 0 18 16 1 0 0 0 0 2 3 1 0 0 0 0 5 7 1 0 0 0 0 17 18 2 0 0 0 0 M END )CTAB"; std::unique_ptr mol(MolBlockToMol(mb)); REQUIRE(mol); CHECK(mol->getAtomWithIdx(0)->getChiralTag() != Atom::CHI_UNSPECIFIED); } } TEST_CASE("github #2244", "[bug][molops][stereo]") { SECTION("the original report") { auto mol = "CC=CC=CC"_smiles; REQUIRE(mol); MolOps::findPotentialStereoBonds(*mol, true); CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOANY); CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY); mol->getBondWithIdx(3)->setStereo(Bond::STEREONONE); MolOps::findPotentialStereoBonds(*mol, true); CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOANY); CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY); } } TEST_CASE( "github #2258: heterocycles with exocyclic bonds not failing valence check", "[bug][molops]") { SECTION("the original report") { std::vector smiles = {"C=n1ccnc1", "C#n1ccnc1"}; for (auto smi : smiles) { CHECK_THROWS_AS(SmilesToMol(smi), MolSanitizeException); } } } TEST_CASE("github #908: AddHs() using 3D coordinates with 2D conformations", "[bug][molops]") { SECTION("basics: single atom mols") { std::vector smiles = {"Cl", "O", "N", "C"}; for (auto smi : smiles) { // std::cerr << smi << std::endl; std::unique_ptr mol(SmilesToMol(smi)); REQUIRE(mol); auto conf = new Conformer(1); conf->set3D(false); conf->setAtomPos(0, RDGeom::Point3D(0, 0, 0)); mol->addConformer(conf, true); bool explicitOnly = false; bool addCoords = true; MolOps::addHs(*mol, explicitOnly, addCoords); for (size_t i = 0; i < mol->getNumAtoms(); ++i) { // std::cerr << " " << i << " " << conf->getAtomPos(i) << std::endl; CHECK(conf->getAtomPos(i).z == 0.0); } } } } TEST_CASE( "github #2437: Canon::rankMolAtoms results in crossed double bonds in " "rings", "[bug][molops]") { SECTION("underlying problem") { std::string molb = R"CTAB(testmol Mrv1824 05081910082D 4 4 0 0 0 0 999 V2000 6.9312 -8.6277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9312 -9.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7562 -8.6277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7562 -9.4527 0.0000 C 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 3 4 1 0 0 0 0 2 4 2 0 0 0 0 M END )CTAB"; bool sanitize = false; bool removeHs = false; std::unique_ptr mol(MolBlockToMol(molb, sanitize, removeHs)); REQUIRE(mol); mol->updatePropertyCache(); CHECK(mol->getBondWithIdx(3)->getBondType() == Bond::BondType::DOUBLE); CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::BondDir::NONE); std::vector ranks; CHECK(!mol->getRingInfo()->isInitialized()); Canon::rankMolAtoms(*mol, ranks); } SECTION("as discovered") { std::string molb = R"CTAB(testmol Mrv1824 05081910082D 4 4 0 0 0 0 999 V2000 6.9312 -9.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7562 -8.6277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7562 -9.4527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9312 -8.6277 0.0000 C 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 3 4 1 0 0 0 0 2 4 2 0 0 0 0 M END )CTAB"; bool sanitize = false; bool removeHs = false; std::unique_ptr mol(MolBlockToMol(molb, sanitize, removeHs)); REQUIRE(mol); mol->updatePropertyCache(); CHECK(mol->getBondWithIdx(3)->getBondType() == Bond::BondType::DOUBLE); CHECK(mol->getBondWithIdx(3)->getBondDir() == Bond::BondDir::NONE); auto nmb = MolToMolBlock(*mol); CHECK(nmb.find("2 4 2 3") == std::string::npos); CHECK(nmb.find("2 4 2 0") != std::string::npos); std::vector ranks; Canon::rankMolAtoms(*mol, ranks); nmb = MolToMolBlock(*mol); CHECK(nmb.find("2 4 2 3") == std::string::npos); CHECK(nmb.find("2 4 2 0") != std::string::npos); } } TEST_CASE( "github #2423: Incorrect assignment of explicit Hs to Al+3 read from mol " "block", "[bug][molops]") { SECTION("basics: single atom mols") { std::string mb = R"CTAB(2300 -OEChem-01301907122D 1 0 0 0 0 0 0 0 0999 V2000 -66.7000 999.0000 0.0000 Al 0 1 0 0 0 0 0 0 0 0 0 0 M CHG 1 1 3 M END)CTAB"; std::unique_ptr mol(MolBlockToMol(mb)); REQUIRE(mol); CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 3); CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0); } } TEST_CASE("Specialized exceptions for sanitization errors", "[molops]") { SECTION("AtomValenceException") { std::vector> smiles = { {"C=n1ccnc1", 1}, {"CCO(C)C", 2}}; for (auto pr : smiles) { CHECK_THROWS_AS(SmilesToMol(pr.first), AtomValenceException); try { auto m = SmilesToMol(pr.first); RDUNUSED_PARAM(m); } catch (const AtomValenceException &e) { CHECK(e.getType() == "AtomValenceException"); CHECK(e.getAtomIdx() == pr.second); } } } SECTION("AtomKekulizeException") { std::vector> smiles = { {"CCcc", 2}, {"C1:c:CC1", 0}}; for (auto pr : smiles) { CHECK_THROWS_AS(SmilesToMol(pr.first), AtomKekulizeException); try { auto m = SmilesToMol(pr.first); RDUNUSED_PARAM(m); } catch (const AtomKekulizeException &e) { CHECK(e.getType() == "AtomKekulizeException"); CHECK(e.getAtomIdx() == pr.second); } } } SECTION("KekulizeException") { std::vector>> smiles = { {"c1cccc1", {0, 1, 2, 3, 4}}, {"Cc1cc1", {1, 2, 3}}}; for (auto pr : smiles) { CHECK_THROWS_AS(SmilesToMol(pr.first), KekulizeException); try { auto m = SmilesToMol(pr.first); RDUNUSED_PARAM(m); } catch (const KekulizeException &e) { CHECK(e.getType() == "KekulizeException"); CHECK(e.getAtomIndices() == pr.second); } } } } TEST_CASE("detectChemistryProblems", "[molops]") { SECTION("Basics") { SmilesParserParams ps; ps.sanitize = false; auto m = std::unique_ptr(SmilesToMol("CO(C)CFCc1cc1", ps)); REQUIRE(m); auto res = MolOps::detectChemistryProblems(*m); REQUIRE(res.size() == 3); CHECK(res[0]->getType() == "AtomValenceException"); REQUIRE(dynamic_cast(res[0].get())); CHECK(dynamic_cast(res[0].get())->getAtomIdx() == 1); CHECK(res[1]->getType() == "AtomValenceException"); REQUIRE(dynamic_cast(res[1].get())); CHECK(dynamic_cast(res[1].get())->getAtomIdx() == 4); CHECK(res[2]->getType() == "KekulizeException"); REQUIRE(dynamic_cast(res[2].get())); CHECK(dynamic_cast(res[2].get())->getAtomIndices() == std::vector({6, 7, 8})); } SECTION("No problems") { SmilesParserParams ps; ps.sanitize = false; auto m = std::unique_ptr(SmilesToMol("c1ccccc1", ps)); REQUIRE(m); auto res = MolOps::detectChemistryProblems(*m); REQUIRE(res.size() == 0); } } TEST_CASE( "github #2606: Bad valence corrections on Pb, Sn" "[bug][molops]") { SECTION("basics-Pb") { std::string mb = R"CTAB( Mrv1810 08141905562D 5 0 0 0 0 0 999 V2000 -3.6316 -0.4737 0.0000 Pb 0 0 0 0 0 0 0 0 0 0 0 0 -3.6541 0.3609 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -2.4586 -0.5188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -3.6992 -1.5338 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -4.5789 -0.4286 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 M CHG 5 1 4 2 -1 3 -1 4 -1 5 -1 M END )CTAB"; std::unique_ptr mol(MolBlockToMol(mb)); REQUIRE(mol); CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 4); CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0); } SECTION("basics-Sn") { std::string mb = R"CTAB( Mrv1810 08141905562D 5 0 0 0 0 0 999 V2000 -3.6316 -0.4737 0.0000 Sn 0 0 0 0 0 0 0 0 0 0 0 0 -3.6541 0.3609 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -2.4586 -0.5188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -3.6992 -1.5338 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -4.5789 -0.4286 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 M CHG 5 1 4 2 -1 3 -1 4 -1 5 -1 M END )CTAB"; std::unique_ptr mol(MolBlockToMol(mb)); REQUIRE(mol); CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 4); CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0); } SECTION("basics-Ge") { std::string mb = R"CTAB( Mrv1810 08141905562D 5 0 0 0 0 0 999 V2000 -3.6316 -0.4737 0.0000 Ge 0 0 0 0 0 0 0 0 0 0 0 0 -3.6541 0.3609 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -2.4586 -0.5188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -3.6992 -1.5338 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -4.5789 -0.4286 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 M CHG 5 1 4 2 -1 3 -1 4 -1 5 -1 M END )CTAB"; std::unique_ptr mol(MolBlockToMol(mb)); REQUIRE(mol); CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 4); CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0); } } TEST_CASE( "github #2607: Pb, Sn should support valence 2" "[bug][molops]") { SECTION("basics-Pb") { std::string mb = R"CTAB( Mrv1810 08141905562D 3 0 0 0 0 0 999 V2000 -3.6316 -0.4737 0.0000 Pb 0 0 0 0 0 0 0 0 0 0 0 0 -3.6541 0.3609 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -2.4586 -0.5188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 M CHG 3 1 2 2 -1 3 -1 M END )CTAB"; std::unique_ptr mol(MolBlockToMol(mb)); REQUIRE(mol); CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 2); CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0); } SECTION("basics-Sn") { std::string mb = R"CTAB( Mrv1810 08141905562D 3 0 0 0 0 0 999 V2000 -3.6316 -0.4737 0.0000 Sn 0 0 0 0 0 0 0 0 0 0 0 0 -3.6541 0.3609 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -2.4586 -0.5188 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 M CHG 3 1 2 2 -1 3 -1 M END )CTAB"; std::unique_ptr mol(MolBlockToMol(mb)); REQUIRE(mol); CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 2); CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0); } } TEST_CASE( "github #2649: Allenes read from mol blocks have crossed bonds assigned" "[bug][stereochemistry]") { SECTION("basics") { std::string mb = R"CTAB(mol Mrv1824 09191901002D 6 5 0 0 0 0 999 V2000 -1.6986 -7.4294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2522 -6.8245 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1438 -8.0357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8095 -6.2156 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3374 -7.8470 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6162 -6.3886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 3 2 0 0 0 0 2 1 2 0 0 0 0 3 5 1 0 0 0 0 4 2 2 0 0 0 0 6 4 1 0 0 0 0 M END)CTAB"; std::unique_ptr mol(MolBlockToMol(mb)); REQUIRE(mol); CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE); CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREONONE); CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREONONE); auto outmolb = MolToMolBlock(*mol); // std::cerr< mol(MolBlockToMol(mb, sanitize)); REQUIRE(mol); CHECK(mol->getBondWithIdx(0)->getBondType() == Bond::DOUBLE); CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE); MolOps::setBondStereoFromDirections(*mol); CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOTRANS); } SECTION("basics 1b") { std::string mb = R"CTAB( Mrv1810 10141909562D 4 3 0 0 0 0 999 V2000 3.3412 -2.9968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5162 -2.9968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1037 -3.7112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7537 -2.2823 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 4 1 1 0 0 0 0 M END )CTAB"; bool sanitize = false; std::unique_ptr mol(MolBlockToMol(mb, sanitize)); REQUIRE(mol); CHECK(mol->getBondWithIdx(0)->getBondType() == Bond::DOUBLE); CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE); MolOps::setBondStereoFromDirections(*mol); CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOTRANS); } SECTION("basics 2a") { std::string mb = R"CTAB( Mrv1810 10141909582D 4 3 0 0 0 0 999 V2000 3.4745 -5.2424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6495 -5.2424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2370 -5.9569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8870 -5.9569 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 1 4 1 0 0 0 0 M END )CTAB"; bool sanitize = false; std::unique_ptr mol(MolBlockToMol(mb, sanitize)); REQUIRE(mol); CHECK(mol->getBondWithIdx(0)->getBondType() == Bond::DOUBLE); CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE); MolOps::setBondStereoFromDirections(*mol); CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOCIS); } SECTION("basics 2b") { std::string mb = R"CTAB( Mrv1810 10141909582D 4 3 0 0 0 0 999 V2000 3.4745 -5.2424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6495 -5.2424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2370 -5.9569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8870 -5.9569 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 4 1 1 0 0 0 0 M END )CTAB"; bool sanitize = false; std::unique_ptr mol(MolBlockToMol(mb, sanitize)); REQUIRE(mol); CHECK(mol->getBondWithIdx(0)->getBondType() == Bond::DOUBLE); CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREONONE); MolOps::setBondStereoFromDirections(*mol); CHECK(mol->getBondWithIdx(0)->getStereo() == Bond::STEREOCIS); } } TEST_CASE("removeHs screwing up double bond stereo", "[bug][removeHs]") { SECTION("example1") { std::string molblock = R"CTAB(molblock = """ SciTegic12221702182D 47 51 0 0 0 0 999 V2000 0.2962 6.2611 0.0000 C 0 0 -3.9004 4.4820 0.0000 C 0 0 1.4195 5.2670 0.0000 C 0 0 -3.8201 -7.4431 0.0000 C 0 0 -4.9433 -6.4490 0.0000 C 0 0 -2.3975 -6.9674 0.0000 C 0 0 3.5921 -3.5947 0.0000 C 0 0 -3.1475 2.3700 0.0000 C 0 0 2.1695 -4.0705 0.0000 C 0 0 -2.0242 1.3759 0.0000 C 0 0 -4.6440 -4.9792 0.0000 C 0 0 2.7681 -1.1308 0.0000 C 0 0 -5.8626 1.1332 0.0000 C 0 0 3.0674 0.3391 0.0000 C 0 0 3.6660 3.2787 0.0000 C 0 0 8.1591 -0.6978 0.0000 C 0 0 7.3351 1.7662 0.0000 C 0 0 -6.3876 3.5028 0.0000 C 0 0 -0.6756 -5.0219 0.0000 C 0 0 7.0358 0.2964 0.0000 C 0 0 3.8914 -2.1249 0.0000 C 0 0 -2.0982 -5.4976 0.0000 C 0 0 -4.5701 1.8943 0.0000 C 0 0 1 0 0 0 -6.9859 2.1273 0.0000 C 0 0 1 0 0 0 4.4900 0.8148 0.0000 C 0 0 1.3455 -1.6065 0.0000 C 0 0 4.7893 2.2846 0.0000 C 0 0 1.9442 1.3332 0.0000 C 0 0 1.0462 -3.0763 0.0000 C 0 0 2.2435 2.8030 0.0000 C 0 0 -0.6017 1.8516 0.0000 C 0 0 5.6132 -0.1794 0.0000 C 0 0 0.2223 -0.6124 0.0000 Cl 0 0 9.2823 -1.6919 0.0000 N 0 0 -3.2215 -4.5035 0.0000 N 0 0 6.2119 2.7603 0.0000 N 0 0 5.3139 -1.6492 0.0000 N 0 0 0.5216 0.8575 0.0000 N 0 0 -4.8945 3.3588 0.0000 N 0 0 -8.2913 2.8662 0.0000 O 0 0 -0.3024 3.3214 0.0000 O 0 0 1.1202 3.7971 0.0000 O 0 0 -0.3763 -3.5520 0.0000 O 0 0 -2.8482 3.8398 0.0000 H 0 0 -2.3235 -0.0940 0.0000 H 0 0 -3.9483 0.5292 0.0000 H 0 0 -7.8572 0.9063 0.0000 H 0 0 1 3 1 0 2 39 1 0 3 42 1 0 4 5 2 0 4 6 1 0 5 11 1 0 6 22 2 0 7 9 2 0 7 21 1 0 8 44 1 0 8 10 2 0 8 23 1 0 9 29 1 0 10 45 1 0 10 31 1 0 11 35 2 0 12 21 2 0 12 26 1 0 13 23 1 0 13 24 1 0 14 25 2 0 14 28 1 0 15 27 2 0 15 30 1 0 16 20 1 0 16 34 3 0 17 20 2 0 17 36 1 0 18 24 1 0 18 39 1 0 19 22 1 0 19 43 1 0 20 32 1 0 21 37 1 0 22 35 1 0 23 46 1 6 23 39 1 0 24 47 1 1 24 40 1 0 25 27 1 0 25 32 1 0 26 29 2 0 26 33 1 0 27 36 1 0 28 30 2 0 28 38 1 0 29 43 1 0 30 42 1 0 31 38 2 0 31 41 1 0 32 37 2 3 M END """ )CTAB"; bool sanitize = false; bool removeHs = false; std::unique_ptr m(MolBlockToMol(molblock, sanitize, removeHs)); REQUIRE(m); m->updatePropertyCache(); MolOps::setBondStereoFromDirections(*m); CHECK(m->getBondWithIdx(10)->getBondType() == Bond::DOUBLE); CHECK(m->getBondWithIdx(10)->getStereo() == Bond::STEREOTRANS); REQUIRE(m->getBondWithIdx(10)->getStereoAtoms().size() == 2); CHECK(m->getBondWithIdx(10)->getStereoAtoms()[0] == 43); CHECK(m->getBondWithIdx(10)->getStereoAtoms()[1] == 44); MolOps::removeHs(*m); // implicitOnly,updateExplicitCount,sanitize); // m->debugMol(std::cerr); CHECK(m->getBondWithIdx(9)->getBondType() == Bond::DOUBLE); CHECK(m->getBondWithIdx(9)->getStereo() == Bond::STEREOTRANS); REQUIRE(m->getBondWithIdx(9)->getStereoAtoms().size() == 2); CHECK(m->getBondWithIdx(9)->getStereoAtoms()[0] == 22); CHECK(m->getBondWithIdx(9)->getStereoAtoms()[1] == 30); } } TEST_CASE("setDoubleBondNeighborDirections()", "[stereochemistry][bug]") { SECTION("basics cis") { auto m = "CC=CC"_smiles; REQUIRE(m); m->getBondWithIdx(1)->getStereoAtoms() = {0, 3}; m->getBondWithIdx(1)->setStereo(Bond::STEREOCIS); MolOps::setDoubleBondNeighborDirections(*m); CHECK(m->getBondWithIdx(0)->getBondDir() == Bond::ENDUPRIGHT); CHECK(m->getBondWithIdx(2)->getBondDir() == Bond::ENDDOWNRIGHT); CHECK(MolToSmiles(*m) == "C/C=C\\C"); } SECTION("basics trans") { auto m = "CC=CC"_smiles; REQUIRE(m); m->getBondWithIdx(1)->getStereoAtoms() = {0, 3}; m->getBondWithIdx(1)->setStereo(Bond::STEREOTRANS); MolOps::setDoubleBondNeighborDirections(*m); CHECK(m->getBondWithIdx(0)->getBondDir() == Bond::ENDUPRIGHT); CHECK(m->getBondWithIdx(2)->getBondDir() == Bond::ENDUPRIGHT); CHECK(MolToSmiles(*m) == "C/C=C/C"); } SECTION("swap (Github #3322)") { auto m = "CC=CC"_smiles; REQUIRE(m); m->getBondWithIdx(1)->getStereoAtoms() = {0, 3}; m->getBondWithIdx(1)->setStereo(Bond::STEREOTRANS); MolOps::setDoubleBondNeighborDirections(*m); CHECK(m->getBondWithIdx(0)->getBondDir() == Bond::ENDUPRIGHT); CHECK(m->getBondWithIdx(2)->getBondDir() == Bond::ENDUPRIGHT); CHECK(MolToSmiles(*m) == "C/C=C/C"); m->clearComputedProps(); m->getBondWithIdx(1)->getStereoAtoms() = {0, 3}; m->getBondWithIdx(1)->setStereo(Bond::STEREOCIS); MolOps::setDoubleBondNeighborDirections(*m); CHECK(m->getBondWithIdx(0)->getBondDir() == Bond::ENDUPRIGHT); CHECK(m->getBondWithIdx(2)->getBondDir() == Bond::ENDDOWNRIGHT); CHECK(MolToSmiles(*m) == "C/C=C\\C"); } } TEST_CASE("github #2782: addHs() fails on atoms with 'bad' valences", "[bug]") { SECTION("basics") { SmilesParserParams ps; ps.sanitize = false; std::unique_ptr m( static_cast(SmilesToMol("C=C1=CC=CC=C1", ps))); REQUIRE(m); bool strict = false; m->updatePropertyCache(strict); CHECK(m->getNumAtoms() == 7); MolOps::addHs(*m); CHECK(m->getNumAtoms() == 14); // this doesn't change the fact that there's still a bad valence present: CHECK_THROWS_AS(m->updatePropertyCache(), AtomValenceException); } } TEST_CASE( "Github #2784: Element symbol lookup for some transuranics returns " "incorrect results", "[transuranics][bug]") { auto pt = PeriodicTable::getTable(); SECTION("number to symbol") { std::vector> data = { {113, "Nh"}, {114, "Fl"}, {115, "Mc"}, {116, "Lv"}, {117, "Ts"}, {118, "Og"}}; for (const auto &pr : data) { CHECK(pt->getElementSymbol(pr.first) == pr.second); } } SECTION("symbol to number") { std::vector> data = { {113, "Nh"}, {114, "Fl"}, {115, "Mc"}, {116, "Lv"}, {117, "Ts"}, {118, "Og"}, {113, "Uut"}, {115, "Uup"}}; for (const auto &pr : data) { CHECK(pt->getAtomicNumber(pr.second) == pr.first); } } } TEST_CASE("github #2775", "[valence][bug]") { SECTION("basics") { std::string molblock = R"CTAB(bismuth citrate Mrv1810 11111908592D 14 12 0 0 0 0 999 V2000 7.4050 -0.5957 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6906 -1.0082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9761 -0.5957 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.6906 -1.8332 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 7.4050 0.2293 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5800 0.2293 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1675 0.9438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5800 1.6583 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3425 0.9438 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 8.2300 0.2293 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6425 -0.4851 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6425 0.9438 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 7.4050 1.0543 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5175 0.9438 0.0000 Bi 0 1 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 1 5 1 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 7 9 1 0 0 0 0 5 10 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 5 13 1 0 0 0 0 M CHG 4 4 -1 9 -1 12 -1 14 3 M END )CTAB"; std::unique_ptr m(MolBlockToMol(molblock)); REQUIRE(m); CHECK(m->getAtomWithIdx(13)->getSymbol() == "Bi"); CHECK(m->getAtomWithIdx(13)->getNumImplicitHs() == 0); } } TEST_CASE("RemoveHsParameters", "[molops]") { SmilesParserParams smilesPs; smilesPs.removeHs = false; SECTION("H-H") { std::unique_ptr m{SmilesToMol("[H][H].[H]O[H]", smilesPs)}; REQUIRE(m); CHECK(m->getNumAtoms() == 5); { RWMol cp(*m); MolOps::removeHs(cp); CHECK(cp.getNumAtoms() == 3); } { MolOps::RemoveHsParameters ps; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 3); } { MolOps::RemoveHsParameters ps; ps.removeOnlyHNeighbors = true; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 1); } } SECTION("dummies") { std::unique_ptr m{SmilesToMol("[H][*]O[H]", smilesPs)}; REQUIRE(m); CHECK(m->getNumAtoms() == 4); { RWMol cp(*m); MolOps::removeHs(cp); CHECK(cp.getNumAtoms() == 3); } { MolOps::RemoveHsParameters ps; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 3); } { MolOps::RemoveHsParameters ps; ps.removeDummyNeighbors = true; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 2); } } SECTION("chiralHs") { std::unique_ptr m{SmilesToMol("[C@]12([H])CCC1CO2", smilesPs)}; REQUIRE(m); CHECK(m->getNumAtoms() == 7); // artificial wedging since we don't have a conformer m->getBondBetweenAtoms(0, 1)->setBondDir(Bond::BEGINWEDGE); { RWMol cp(*m); MolOps::removeHs(cp); CHECK(cp.getNumAtoms() == 6); } { MolOps::RemoveHsParameters ps; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 6); } { MolOps::RemoveHsParameters ps; ps.removeWithWedgedBond = false; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 7); } } SECTION("degree zero") { std::unique_ptr m{SmilesToMol("[F-].[H+]", smilesPs)}; REQUIRE(m); CHECK(m->getNumAtoms() == 2); { RWMol cp(*m); MolOps::removeHs(cp); CHECK(cp.getNumAtoms() == 2); } { MolOps::RemoveHsParameters ps; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 2); } { MolOps::RemoveHsParameters ps; ps.removeDegreeZero = true; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 1); } } SECTION("isotopes") { std::unique_ptr m{SmilesToMol("F[2H]", smilesPs)}; REQUIRE(m); CHECK(m->getNumAtoms() == 2); { RWMol cp(*m); MolOps::removeHs(cp); CHECK(cp.getNumAtoms() == 2); } { MolOps::RemoveHsParameters ps; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 2); } { MolOps::RemoveHsParameters ps; ps.removeIsotopes = true; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 1); } } SECTION("defining bond stereo") { std::unique_ptr m{SmilesToMol("F/C=N/[H]", smilesPs)}; REQUIRE(m); CHECK(m->getNumAtoms() == 4); { RWMol cp(*m); MolOps::removeHs(cp); CHECK(cp.getNumAtoms() == 4); } { MolOps::RemoveHsParameters ps; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 4); } { MolOps::RemoveHsParameters ps; ps.removeDefiningBondStereo = true; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 3); } } SECTION("Query atoms") { std::unique_ptr m{SmartsToMol("O[#1]")}; REQUIRE(m); CHECK(m->getNumAtoms() == 2); { RWMol cp(*m); MolOps::removeHs(cp); CHECK(cp.getNumAtoms() == 2); } { MolOps::RemoveHsParameters ps; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 2); } { MolOps::RemoveHsParameters ps; ps.removeWithQuery = true; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 1); } } SECTION("higher degree") { // this is a silly example std::unique_ptr m{SmilesToMol("F[H-]F", smilesPs)}; REQUIRE(m); CHECK(m->getNumAtoms() == 3); { RWMol cp(*m); MolOps::removeHs(cp); CHECK(cp.getNumAtoms() == 3); } { MolOps::RemoveHsParameters ps; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 3); } { MolOps::RemoveHsParameters ps; ps.removeHigherDegrees = true; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 2); } } SECTION("mapped Hs") { std::unique_ptr m{SmilesToMol("[H:1]O[H]", smilesPs)}; REQUIRE(m); CHECK(m->getNumAtoms() == 3); { RWMol cp(*m); MolOps::removeHs(cp); CHECK(cp.getNumAtoms() == 1); } { MolOps::RemoveHsParameters ps; ps.removeMapped = false; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 2); } } SECTION("allHs") { std::unique_ptr m{SmilesToMol( "[C@]12([H])CCC1CO2.[H+].F[H-]F.[H][H].[H]*.F/C=C/[H]", smilesPs)}; REQUIRE(m); // artificial wedging since we don't have a conformer m->getBondBetweenAtoms(0, 1)->setBondDir(Bond::BEGINWEDGE); RWMol cp(*m); MolOps::removeAllHs(cp); for (auto atom : cp.atoms()) { CHECK(atom->getAtomicNum() != 1); } } SECTION("allHs2") { std::unique_ptr m{SmilesToMol( "[C@]12([H])CCC1CO2.[H+].F[H-]F.[H][H].[H]*.F/C=C/[H]", smilesPs)}; REQUIRE(m); // artificial wedging since we don't have a conformer m->getBondBetweenAtoms(0, 1)->setBondDir(Bond::BEGINWEDGE); std::unique_ptr cp{MolOps::removeAllHs(*m)}; for (auto atom : cp->atoms()) { CHECK(atom->getAtomicNum() != 1); } } } #endif TEST_CASE("github #2895: acepentalene aromaticity perception ", "[molops][bug][aromaticity]") { SECTION("acepentalene") { std::unique_ptr m{SmilesToMol("C1=CC2=CC=C3C2=C1C=C3")}; REQUIRE(m); auto smi = MolToSmiles(*m); CHECK(smi == "C1=CC2=C3C1=CC=C3C=C2"); } } TEST_CASE("github #3256: fused ring aromaticity perception", "[molops][bug][aromaticity]") { SECTION("nitrogen only central ring") { auto mol = "C1=CN2C3=CC=CN3C3=CC=CN3C2=C1"_smiles; REQUIRE(mol); for (const auto b : mol->bonds()) { CHECK(b->getBondType() == Bond::AROMATIC); } auto smi = MolToSmiles(*mol); CHECK(smi == "c1cc2n(c1)c1cccn1c1cccn21"); } } TEST_CASE("phosphine and arsine chirality", "[Chirality]") { SECTION("chiral center recognized") { auto mol1 = "C[P@](C1CCCC1)C1=CC=CC=C1"_smiles; auto mol2 = "C[As@](C1CCCC1)C1=CC=CC=C1"_smiles; REQUIRE(mol1); REQUIRE(mol2); CHECK(mol1->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED); CHECK(mol2->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED); } SECTION("chiral center selective") { auto mol1 = "C[P@](C)C1CCCCC1"_smiles; auto mol2 = "C[As@](C)C1CCCCC1"_smiles; REQUIRE(mol1); REQUIRE(mol2); CHECK(mol1->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED); CHECK(mol2->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED); } SECTION("chiral center specific: P") { auto mol1 = "C[P@](C1CCCC1)C1=CC=CC=C1"_smiles; auto mol2 = "C[P@@](C1CCCC1)C1=CC=CC=C1"_smiles; REQUIRE(mol1); REQUIRE(mol2); CHECK(MolToSmiles(*mol1) != MolToSmiles(*mol2)); } SECTION("chiral center specific: As") { auto mol1 = "C[As@](C1CCCC1)C1=CC=CC=C1"_smiles; auto mol2 = "C[As@@](C1CCCC1)C1=CC=CC=C1"_smiles; REQUIRE(mol1); REQUIRE(mol2); CHECK(MolToSmiles(*mol1) != MolToSmiles(*mol2)); } SECTION("chiral center, implicit H: P") { auto mol1 = "C[P@H]C1CCCCC1"_smiles; auto mol2 = "C[P@@H]C1CCCCC1"_smiles; REQUIRE(mol1); REQUIRE(mol2); CHECK(mol1->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED); CHECK(mol1->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED); } SECTION("chiral center, implicit H: As") { auto mol1 = "C[As@H]C1CCCCC1"_smiles; auto mol2 = "C[As@@H]C1CCCCC1"_smiles; REQUIRE(mol1); REQUIRE(mol2); CHECK(mol1->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED); CHECK(mol1->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED); } SECTION("chiral center specific, implicit H: P") { auto mol1 = "C[P@H]C1CCCCC1"_smiles; auto mol2 = "C[P@@H]C1CCCCC1"_smiles; REQUIRE(mol1); REQUIRE(mol2); CHECK(MolToSmiles(*mol1) != MolToSmiles(*mol2)); } SECTION("chiral center specific, implicit H: As") { auto mol1 = "C[As@H]C1CCCCC1"_smiles; auto mol2 = "C[As@@H]C1CCCCC1"_smiles; REQUIRE(mol1); REQUIRE(mol2); CHECK(MolToSmiles(*mol1) != MolToSmiles(*mol2)); } } TEST_CASE("github #2890", "[bug][molops][stereo]") { auto mol = "CC=CC"_smiles; REQUIRE(mol); auto bond = mol->getBondWithIdx(1); bond->setStereo(Bond::STEREOANY); REQUIRE(bond->getStereoAtoms().empty()); MolOps::findPotentialStereoBonds(*mol); CHECK(bond->getStereo() == Bond::STEREOANY); CHECK(bond->getStereoAtoms().size() == 2); } TEST_CASE("github #3150 MolOps::removeHs removes hydrides", "[bug][molops]") { SmilesParserParams smilesPs; smilesPs.removeHs = false; SECTION("Hydride ion remove Hydrides false") { std::unique_ptr m{SmilesToMol("[H-]", smilesPs)}; REQUIRE(m); MolOps::RemoveHsParameters ps; ps.removeHydrides = false; RWMol cp(*m); MolOps::removeHs(cp, ps); // H atom not removed in this case because by default H atoms with degree 0 // are not removed CHECK(cp.getNumAtoms() == 1); CHECK(MolOps::getFormalCharge(cp) == -1); } SECTION("Hydride ion remove Hydrides true") { std::unique_ptr m{SmilesToMol("[H-]", smilesPs)}; REQUIRE(m); MolOps::RemoveHsParameters ps; ps.removeHydrides = true; RWMol cp(*m); MolOps::removeHs(cp, ps); // H atom not removed in this case because by default H atoms with degree 0 // are not removed CHECK(cp.getNumAtoms() == 1); CHECK(MolOps::getFormalCharge(cp) == -1); } SECTION("Water") { std::unique_ptr m{SmilesToMol("[OH+][H-]", smilesPs)}; REQUIRE(m); MolOps::RemoveHsParameters ps; ps.removeHydrides = false; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 2); CHECK(MolOps::getFormalCharge(cp) == 0); } SECTION("Water remove Hydrides true") { std::unique_ptr m{SmilesToMol("[OH+][H-]", smilesPs)}; REQUIRE(m); MolOps::RemoveHsParameters ps; ps.removeHydrides = true; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 1); CHECK(MolOps::getFormalCharge(cp) == 1); } SECTION("Iron Hydride") { std::unique_ptr m{SmilesToMol("[Fe+2]<-[H-]", smilesPs)}; REQUIRE(m); MolOps::RemoveHsParameters ps; ps.removeHydrides = false; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 2); CHECK(MolOps::getFormalCharge(cp) == 1); } SECTION("Iron Hydride remove Hydrides") { std::unique_ptr m{SmilesToMol("[Fe+2]<-[H-]", smilesPs)}; REQUIRE(m); MolOps::RemoveHsParameters ps; ps.removeHydrides = true; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 1); CHECK(MolOps::getFormalCharge(cp) == 2); } SECTION("Ferrous Hydroxide") { std::unique_ptr m{SmilesToMol("[Fe+2]<-[OH-]", smilesPs)}; REQUIRE(m); MolOps::RemoveHsParameters ps; ps.removeHydrides = false; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 2); CHECK(MolOps::getFormalCharge(cp) == 1); } SECTION("Ferrous Hydroxide remove Hydrides") { std::unique_ptr m{SmilesToMol("[Fe+2]<-[OH-]", smilesPs)}; REQUIRE(m); MolOps::RemoveHsParameters ps; ps.removeHydrides = true; RWMol cp(*m); MolOps::removeHs(cp, ps); CHECK(cp.getNumAtoms() == 2); CHECK(MolOps::getFormalCharge(cp) == 1); } SECTION("Remove All Hs in Hydrides Ferrous Hydride") { std::unique_ptr m{SmilesToMol("[Fe+2]<-[H-]", smilesPs)}; REQUIRE(m); RWMol cp(*m); MolOps::removeAllHs(cp); CHECK(cp.getNumAtoms() == 1); CHECK(MolOps::getFormalCharge(cp) == 2); } SECTION("Remove All Hs in Hydrides Water") { std::unique_ptr m{SmilesToMol("[OH+][H-]", smilesPs)}; REQUIRE(m); RWMol cp(*m); MolOps::removeAllHs(cp); CHECK(cp.getNumAtoms() == 1); CHECK(MolOps::getFormalCharge(cp) == 1); } } TEST_CASE("hybridization of unknown atom types", "[bug][molops]") { SECTION("Basics") { auto m = "[U][U][U]"_smiles; REQUIRE(m); for (const auto atom : m->atoms()) { CHECK(atom->getHybridization() == Atom::HybridizationType::S); } } SECTION("comprehensive") { std::string smiles = ""; for (unsigned int i = 89; i <= 118; ++i) { smiles += (boost::format("[#%d]") % i).str(); } std::unique_ptr m(SmilesToMol(smiles)); REQUIRE(m); for (const auto atom : m->atoms()) { CHECK(atom->getHybridization() == Atom::HybridizationType::S); } } } TEST_CASE("Github #3470: Hydrogen is incorrectly identified as an early atom", "[bug][chemistry]") { SECTION("Basics") { RWMol m; m.addAtom(new Atom(1)); m.getAtomWithIdx(0)->setFormalCharge(-1); m.updatePropertyCache(); CHECK(m.getAtomWithIdx(0)->getNumImplicitHs() == 0); m.getAtomWithIdx(0)->setFormalCharge(1); m.updatePropertyCache(); CHECK(m.getAtomWithIdx(0)->getNumImplicitHs() == 0); m.getAtomWithIdx(0)->setFormalCharge(0); m.updatePropertyCache(); CHECK(m.getAtomWithIdx(0)->getNumImplicitHs() == 1); // make sure we still generate errors for stupid stuff m.getAtomWithIdx(0)->setFormalCharge(-2); CHECK_THROWS_AS(m.updatePropertyCache(), AtomValenceException); CHECK(m.getAtomWithIdx(0)->getNumImplicitHs() == 1); } SECTION("confirm with SMILES") { RWMol m; m.addAtom(new Atom(1)); m.getAtomWithIdx(0)->setFormalCharge(-1); m.updatePropertyCache(); CHECK(MolToSmiles(m) == "[H-]"); m.getAtomWithIdx(0)->setFormalCharge(+1); m.updatePropertyCache(); CHECK(MolToSmiles(m) == "[H+]"); m.getAtomWithIdx(0)->setFormalCharge(0); m.updatePropertyCache(); CHECK(MolToSmiles(m) == "[HH]"); // ugly, but I think [H] would be worse } } TEST_CASE("Additional oxidation states", "[chemistry]") { SECTION("Basics") { std::vector smiles = {"F[Po](F)(F)(F)", "F[Po](F)(F)(F)(F)F", "F[Xe](F)(F)(F)", "F[Xe](F)(F)(F)(F)F", "F[I](F)F", "F[I](F)(F)(F)F", "F[At](F)F", "F[At](F)(F)(F)F"}; for (const auto &smi : smiles) { std::unique_ptr m(SmilesToMol(smi)); REQUIRE(m); CHECK(m->getAtomWithIdx(1)->getNumRadicalElectrons() == 0); } } } TEST_CASE("Github #3805: radicals on [He]", "[chemistry]") { SECTION("Basics") { { auto m = "[He]"_smiles; REQUIRE(m); CHECK(m->getAtomWithIdx(0)->getNumRadicalElectrons() == 0); CHECK(m->getAtomWithIdx(0)->getTotalNumHs() == 0); } { auto m = "[Ne]"_smiles; REQUIRE(m); CHECK(m->getAtomWithIdx(0)->getNumRadicalElectrons() == 0); CHECK(m->getAtomWithIdx(0)->getTotalNumHs() == 0); } } SECTION("Basics") { { auto m = "[He+]"_smiles; REQUIRE(m); CHECK(m->getAtomWithIdx(0)->getNumRadicalElectrons() == 1); CHECK(m->getAtomWithIdx(0)->getTotalNumHs() == 0); } { auto m = "[Ne+]"_smiles; REQUIRE(m); CHECK(m->getAtomWithIdx(0)->getNumRadicalElectrons() == 1); CHECK(m->getAtomWithIdx(0)->getTotalNumHs() == 0); } } }