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196dde4b04
* fix compilation error * wip * undo change to CMakeLists * add test --------- Co-authored-by: greg landrum <greg.landrum@gmail.com>
286 lines
8.2 KiB
C++
286 lines
8.2 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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