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1727ffd538
* allow cleanupOrganometallics to work with carbon * do not use cleanupOrganometallics with mol2 * fix handling of C atoms in cleanupOrganometallics * add test for #8312 * Update Code/GraphMol/MolOps.cpp Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com> --------- Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
418 lines
13 KiB
C++
418 lines
13 KiB
C++
//
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// Copyright (C) 2024 Greg Landrum and other RDKit contributors
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <catch2/catch_all.hpp>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/MolOps.h>
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#include <GraphMol/test_fixtures.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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using namespace RDKit;
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TEST_CASE("github #7556: chiral sulfur in conjugated rings") {
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SECTION("as reported") {
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auto m = "CC1=CC(Cl)=CC2=C1N=[S@](C)N=C2N"_smiles;
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REQUIRE(m);
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CHECK(!m->getBondBetweenAtoms(8, 9)->getIsConjugated());
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CHECK(!m->getBondBetweenAtoms(9, 11)->getIsConjugated());
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REQUIRE(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
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}
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}
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TEST_CASE("getAvgMolWt") {
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SECTION("basics") {
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auto mol = "C"_smiles;
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REQUIRE(mol);
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auto amw = MolOps::getAvgMolWt(*mol);
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CHECK_THAT(amw, Catch::Matchers::WithinAbs(16.043, 0.001));
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amw = MolOps::getAvgMolWt(*mol, true);
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CHECK_THAT(amw, Catch::Matchers::WithinAbs(12.011, 0.001));
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MolOps::addHs(*mol);
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amw = MolOps::getAvgMolWt(*mol);
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CHECK_THAT(amw, Catch::Matchers::WithinAbs(16.043, 0.001));
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amw = MolOps::getAvgMolWt(*mol, true);
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CHECK_THAT(amw, Catch::Matchers::WithinAbs(12.011, 0.001));
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}
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SECTION("Hs in SMILES") {
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auto mol = "[CH4]"_smiles;
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REQUIRE(mol);
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auto amw = MolOps::getAvgMolWt(*mol);
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CHECK_THAT(amw, Catch::Matchers::WithinAbs(16.043, 0.001));
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amw = MolOps::getAvgMolWt(*mol, true);
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CHECK_THAT(amw, Catch::Matchers::WithinAbs(12.011, 0.001));
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}
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SECTION("isotopes") {
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auto mol = "C[2H]"_smiles;
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REQUIRE(mol);
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auto amw = MolOps::getAvgMolWt(*mol);
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CHECK_THAT(amw, Catch::Matchers::WithinAbs(17.0, 0.1));
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}
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}
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TEST_CASE("getExactMolWt") {
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SECTION("basics") {
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auto mol = "C"_smiles;
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REQUIRE(mol);
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auto mw = MolOps::getExactMolWt(*mol);
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CHECK_THAT(mw, Catch::Matchers::WithinAbs(16.031, 0.001));
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mw = MolOps::getExactMolWt(*mol, true);
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CHECK_THAT(mw, Catch::Matchers::WithinAbs(12.000, 0.001));
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MolOps::addHs(*mol);
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mw = MolOps::getExactMolWt(*mol);
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CHECK_THAT(mw, Catch::Matchers::WithinAbs(16.031, 0.001));
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mw = MolOps::getExactMolWt(*mol, true);
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CHECK_THAT(mw, Catch::Matchers::WithinAbs(12.000, 0.001));
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}
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SECTION("Hs in SMILES") {
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auto mol = "[CH4]"_smiles;
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REQUIRE(mol);
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auto mw = MolOps::getExactMolWt(*mol);
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CHECK_THAT(mw, Catch::Matchers::WithinAbs(16.031, 0.001));
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mw = MolOps::getExactMolWt(*mol, true);
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CHECK_THAT(mw, Catch::Matchers::WithinAbs(12.000, 0.001));
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}
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SECTION("isotopes") {
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auto mol = "C[2H]"_smiles;
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REQUIRE(mol);
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auto mw = MolOps::getExactMolWt(*mol);
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CHECK_THAT(mw, Catch::Matchers::WithinAbs(17.037, 0.001));
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mw = MolOps::getExactMolWt(*mol, true);
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CHECK_THAT(mw, Catch::Matchers::WithinAbs(12.000, 0.001));
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}
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SECTION("Cl") {
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auto mol = "Cl"_smiles;
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REQUIRE(mol);
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auto mw = MolOps::getExactMolWt(*mol);
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CHECK_THAT(mw, Catch::Matchers::WithinAbs(34.9688 + 1.0078, 0.001));
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mw = MolOps::getAvgMolWt(*mol);
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CHECK_THAT(mw, Catch::Matchers::WithinAbs(35.453 + 1.008, 0.001));
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mol = "[35ClH]"_smiles;
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REQUIRE(mol);
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mw = MolOps::getExactMolWt(*mol);
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CHECK_THAT(mw, Catch::Matchers::WithinAbs(34.9688 + 1.0078, 0.001));
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mw = MolOps::getAvgMolWt(*mol);
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CHECK_THAT(mw, Catch::Matchers::WithinAbs(34.9688 + 1.008, 0.001));
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mol = "[36ClH]"_smiles;
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REQUIRE(mol);
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mw = MolOps::getExactMolWt(*mol);
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CHECK_THAT(mw, Catch::Matchers::WithinAbs(35.9683 + 1.0078, 0.001));
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mw = MolOps::getAvgMolWt(*mol);
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CHECK_THAT(mw, Catch::Matchers::WithinAbs(35.9683 + 1.008, 0.001));
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}
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}
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TEST_CASE("getMolFormula") {
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SECTION("basics") {
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auto mol = "C"_smiles;
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REQUIRE(mol);
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auto formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "CH4");
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MolOps::addHs(*mol);
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formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "CH4");
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mol = "[CH4]"_smiles;
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REQUIRE(mol);
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formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "CH4");
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mol = "CO"_smiles;
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REQUIRE(mol);
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formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "CH4O");
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MolOps::addHs(*mol);
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formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "CH4O");
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mol = "C(=O)N"_smiles;
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REQUIRE(mol);
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formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "CH3NO");
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mol = "C(=O)=O"_smiles;
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REQUIRE(mol);
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formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "CO2");
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mol = "C(=O)[O-]"_smiles;
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REQUIRE(mol);
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formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "CHO2-");
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mol = "C([O-])[O-]"_smiles;
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REQUIRE(mol);
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formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "CH2O2-2");
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mol = "C([NH3+])[O-]"_smiles;
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REQUIRE(mol);
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formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "CH5NO");
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mol = "C([NH3+])O"_smiles;
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REQUIRE(mol);
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formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "CH6NO+");
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mol = "C([NH3+])[NH3+]"_smiles;
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REQUIRE(mol);
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formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "CH8N2+2");
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}
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SECTION("H isotopes") {
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auto mol = "[2H]C([3H])O"_smiles;
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REQUIRE(mol);
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auto formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "CH4O");
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formula = MolOps::getMolFormula(*mol, true);
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CHECK(formula == "CH2DTO");
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formula = MolOps::getMolFormula(*mol, true, false);
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CHECK(formula == "CH2[2H][3H]O");
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}
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SECTION("isotopes") {
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auto mol = "[13CH3]C[13CH2]C"_smiles;
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REQUIRE(mol);
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auto formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "C4H10");
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formula = MolOps::getMolFormula(*mol, true);
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CHECK(formula == "C2[13C]2H10");
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formula = MolOps::getMolFormula(*mol, true, false);
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CHECK(formula == "C2[13C]2H10");
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mol = "[13CH3]C([2H])O"_smiles;
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REQUIRE(mol);
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formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "C2H6O");
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formula = MolOps::getMolFormula(*mol, true);
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CHECK(formula == "C[13C]H5DO");
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formula = MolOps::getMolFormula(*mol, true, false);
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CHECK(formula == "C[13C]H5[2H]O");
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mol = "[13CH3]C[13CH2]CB(O)O[2H]"_smiles;
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REQUIRE(mol);
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formula = MolOps::getMolFormula(*mol);
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CHECK(formula == "C4H11BO2");
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formula = MolOps::getMolFormula(*mol, true);
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CHECK(formula == "C2[13C]2H10DBO2");
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formula = MolOps::getMolFormula(*mol, true, false);
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CHECK(formula == "C2[13C]2H10[2H]BO2");
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}
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}
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TEST_CASE(
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"github #8121: symmetric ring finding not returning correct results for molecules with fragments") {
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auto twoCubanes = "C12C3C4C1C5C2C3C45.C12C3C4C1C5C2C3C45"_smiles;
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REQUIRE(twoCubanes);
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auto rinfo = twoCubanes->getRingInfo();
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CHECK(rinfo->numRings() == 12);
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}
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TEST_CASE("check division by zero in setTerminalAtomCoords") {
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SECTION("degree 4") {
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auto m = R"CTAB(
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Mrv2311 11162401483D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 5 4 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C 0 0 0 0
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M V30 2 F -0.7971 -0.9945 1.275 0
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M V30 3 F 0.7971 0.9945 -1.275 0
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M V30 4 F -1.2069 -0.1568 -0.8768 0
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M V30 5 Cl 1.1223 1.1513 0.8154 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 1 1 3
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M V30 3 1 1 4
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M V30 4 1 1 5
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M V30 END BOND
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M V30 END CTAB
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M END
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)CTAB"_ctab;
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REQUIRE(m);
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CHECK_NOTHROW(MolOps::setTerminalAtomCoords(*m, 4, 0));
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}
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SECTION("degree 2, aligned 2nd neighbors") {
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// This looks like a weird mol, but it's an intermediate
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// state in AddHs.
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auto mb = R"CTAB(
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Mrv1908 06032010402D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 4 3 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -19.8317 16.5 0 1 CHG=-1
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M V30 2 N -18.2917 16.5 0 2 CHG=1
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M V30 3 N -16.7517 16.5 0 3
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M V30 4 H 0 0 0 3
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 3 2 3
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M V30 3 1 1 4
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M V30 END BOND
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M V30 END CTAB
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M END
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)CTAB";
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v2::FileParsers::MolFileParserParams p;
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p.removeHs = false;
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auto m = v2::FileParsers::MolFromMolBlock(mb, p);
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REQUIRE(m);
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REQUIRE(m->getNumAtoms() == 4);
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CHECK_NOTHROW(MolOps::setTerminalAtomCoords(*m, 3, 0));
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}
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}
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TEST_CASE("cleanuporganometallics and carbon") {
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SECTION("basics") {
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std::vector<std::pair<std::string,
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std::vector<std::pair<unsigned int, unsigned int>>>>
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data = {
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{"C=[CH2][Fe]", {{1, 2}}}, // this is a silly example, but it's the
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// simplest one I could think of
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{"[CH2]1=[CH2]2.[Fe]12", {{1, 2}, {0, 2}}},
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{"[CH2]1=[CH]2-[CH2-]3.[Fe]123", {{1, 3}, {0, 3}, {2, 3}}},
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{"[CH]12=[CH]3[CH]4=[CH]5[CH-]16.[Fe]23456",
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{{0, 5}, {1, 5}, {2, 5}, {3, 5}, {4, 5}}},
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{"[Fe]12.[CH2]1=[CH2]2",
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{{1, 0}, {2, 0}}}, // reverse the original atom order
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{"[CH]12=[CH]3[CH]4=[CH]5[CH]6=[CH]17.[Fe]234567",
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{{0, 6}, {1, 6}, {2, 6}, {3, 6}, {4, 6}, {5, 6}}},
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{"[cH]12[cH]3[cH]4[cH]5[cH]6[cH]17.[Fe]234567",
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{{0, 6}, {1, 6}, {2, 6}, {3, 6}, {4, 6}, {5, 6}}},
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{"[cH]12[cH]3[cH]4[cH]5[nH]16.[Fe]23456",
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{{0, 5}, {1, 5}, {2, 5}, {3, 5}, {4, 5}}},
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{"[CH]12=[CH]3[CH]4=[CH]5[NH]16.[Fe]23456",
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{{0, 5}, {1, 5}, {2, 5}, {3, 5}, {4, 5}}},
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};
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for (const auto &pr : data) {
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INFO(pr.first);
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auto mol = v2::SmilesParse::MolFromSmiles(pr.first);
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REQUIRE(mol);
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for (const auto &pair : pr.second) {
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REQUIRE(mol->getBondBetweenAtoms(pair.first, pair.second) != nullptr);
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CHECK(mol->getBondBetweenAtoms(pair.first, pair.second)
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->getBeginAtomIdx() == pair.first);
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CHECK(
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mol->getBondBetweenAtoms(pair.first, pair.second)->getBondType() ==
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Bond::BondType::DATIVE);
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}
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}
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}
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SECTION("no dative bonds") {
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std::vector<std::string> smileses = {
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"C=[CH][Fe]",
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"[CH]1=[CH]2.[Fe]12",
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"[CH]1=[C]2-[CH-]3.[Fe]123",
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"[C]12=[C]3[C]4=[C]5[C-]16.[Fe]23456",
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};
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for (const auto &smiles : smileses) {
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INFO(smiles);
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auto mol = v2::SmilesParse::MolFromSmiles(smiles);
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REQUIRE(mol);
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for (const auto bond : mol->bonds()) {
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CHECK(bond->getBondType() != Bond::BondType::DATIVE);
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}
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}
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}
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SECTION("github #8312") {
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std::string mb = R"CTAB(
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ChemDraw03012503262D
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0 0 0 0 0 0 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 21 24 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -1.822529 0.405221 0.000000 0 VAL=5
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M V30 2 C -1.822529 -0.419779 0.000000 0 VAL=5
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M V30 3 C -1.239167 -1.003142 0.000000 0
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M V30 4 C -0.414167 -1.003142 0.000000 0
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M V30 5 C 0.169196 -0.419779 0.000000 0 VAL=5
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M V30 6 C 0.169196 0.405221 0.000000 0 VAL=5
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M V30 7 C -0.414167 0.988584 0.000000 0
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M V30 8 C -1.239167 0.988584 0.000000 0
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M V30 9 Pt 1.335541 -0.028481 0.000000 0 VAL=6
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M V30 10 C 1.697726 0.712766 0.000000 0
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M V30 11 C 1.796387 -0.712766 0.000000 0
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M V30 12 H 2.520757 0.769729 0.000000 0
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M V30 13 H 1.236879 1.397051 0.000000 0
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M V30 14 H 2.059910 1.454013 0.000000 0
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M V30 15 H 2.619419 -0.655803 0.000000 0
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M V30 16 H 1.434203 -1.454013 0.000000 0
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M V30 17 H 2.257234 -1.397051 0.000000 0
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M V30 18 H -2.619419 0.618747 0.000000 0
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M V30 19 H -2.619419 -0.633305 0.000000 0
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M V30 20 H 0.382722 1.202110 0.000000 0
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M V30 21 H 0.581696 -1.134250 0.000000 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 2 1 2
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M V30 2 1 2 3
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M V30 3 1 3 4
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M V30 4 1 4 5
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M V30 5 2 5 6
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M V30 6 1 6 7
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M V30 7 1 7 8
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M V30 8 1 8 1
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M V30 9 1 9 10
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M V30 10 1 9 11
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M V30 11 1 10 12
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M V30 12 1 10 13
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M V30 13 1 10 14
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M V30 14 1 11 15
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M V30 15 1 11 16
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M V30 16 1 11 17
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M V30 17 1 9 6
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M V30 18 1 9 5
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M V30 19 1 9 1
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M V30 20 1 9 2
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M V30 21 1 1 18
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M V30 22 1 2 19
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M V30 23 1 6 20
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M V30 24 1 5 21
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M V30 END BOND
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M V30 END CTAB
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M END)CTAB";
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auto mol = v2::FileParsers::MolFromMolBlock(mb);
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REQUIRE(mol);
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REQUIRE(mol->getBondBetweenAtoms(5, 8));
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CHECK(mol->getBondBetweenAtoms(5, 8)->getBondType() ==
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Bond::BondType::DATIVE);
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REQUIRE(mol->getBondBetweenAtoms(4, 8));
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CHECK(mol->getBondBetweenAtoms(4, 8)->getBondType() ==
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Bond::BondType::DATIVE);
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REQUIRE(mol->getBondBetweenAtoms(0, 8));
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CHECK(mol->getBondBetweenAtoms(0, 8)->getBondType() ==
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Bond::BondType::DATIVE);
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REQUIRE(mol->getBondBetweenAtoms(1, 8));
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CHECK(mol->getBondBetweenAtoms(1, 8)->getBondType() ==
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Bond::BondType::DATIVE);
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REQUIRE(mol->getBondBetweenAtoms(9, 8));
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CHECK(mol->getBondBetweenAtoms(9, 8)->getBondType() ==
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Bond::BondType::SINGLE);
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REQUIRE(mol->getBondBetweenAtoms(10, 8));
|
|
CHECK(mol->getBondBetweenAtoms(10, 8)->getBondType() ==
|
|
Bond::BondType::SINGLE);
|
|
}
|
|
} |