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* run clang-format-18 across Code/*.cpp and Code/*.h * run clang-format-18 across External
129 lines
3.5 KiB
C++
129 lines
3.5 KiB
C++
//
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// Copyright (C) 2002-2021 Greg Landrum and other RDKit contributors
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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 "RDGeneral/test.h"
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#include <catch2/catch_all.hpp>
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#include <RDGeneral/Invariant.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/SmilesParse/SmartsWrite.h>
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#include <RDGeneral/FileParseException.h>
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#include <boost/algorithm/string.hpp>
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#include <RDGeneral/BadFileException.h>
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#include <GraphMol/Chirality.h>
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#include <RDGeneral/RDLog.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/FileParsers/MolFileStereochem.h>
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#include <GraphMol/ChemReactions/Reaction.h>
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#include <GraphMol/ChemReactions/ReactionParser.h>
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#include <string>
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using namespace RDKit;
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class MolTest {
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public:
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std::string fileName;
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bool expectedResult;
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unsigned int atomCount;
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unsigned int bondCount;
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MolTest(std::string fileNameInit, bool expectedResultInit, int atomCountInit,
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int bondCountInit)
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: fileName(fileNameInit),
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expectedResult(expectedResultInit),
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atomCount(atomCountInit),
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bondCount(bondCountInit) {};
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};
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void testMolFiles(const MolTest *molFileTest) {
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BOOST_LOG(rdInfoLog) << "testing marvin writing" << std::endl;
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std::string rdbase = getenv("RDBASE");
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std::string fName =
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rdbase + "/Code/GraphMol/FileParsers/test_data/" + molFileTest->fileName;
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try {
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std::unique_ptr<RWMol> mol(MolFileToMol(fName, true, false, false));
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RDKit::Chirality::reapplyMolBlockWedging(*mol);
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CHECK(mol != nullptr);
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CHECK(mol->getNumAtoms() == molFileTest->atomCount);
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CHECK(mol->getNumBonds() == molFileTest->bondCount);
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{
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std::string expectedMrvName = fName + ".expected.sdf";
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std::string outMolStr = "";
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try {
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outMolStr = MolToMolBlock(*mol, true, 0, true, true);
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} catch (const RDKit::KekulizeException &e) {
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outMolStr = "";
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} catch (...) {
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throw; // re-trhow the error if not a kekule error
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}
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if (outMolStr == "") {
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outMolStr = MolToMolBlock(*mol, true, 0, false,
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true); // try without kekule'ing
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}
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// code to create the expected files for new or changed tests
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// {
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// std::ofstream out;
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// out.open(fName + ".NEW.sdf");
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// out << outMolStr;
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// }
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std::stringstream expectedMolStr;
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std::ifstream in;
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in.open(expectedMrvName);
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expectedMolStr << in.rdbuf();
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std::string expectedStr = expectedMolStr.str();
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CHECK(expectedStr == outMolStr);
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}
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BOOST_LOG(rdInfoLog) << "done" << std::endl;
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} catch (const std::exception &e) {
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if (molFileTest->expectedResult != false) {
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throw;
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}
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return;
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}
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CHECK(molFileTest->expectedResult == true);
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return;
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}
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TEST_CASE("CrossedDoubleBondWithChiralNbr") {
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SECTION("SIMPLE") {
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MolTest molTest("CrossedDoubleBondWithChiralNbr.sdf", true, 10, 9);
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testMolFiles(&molTest);
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}
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}
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TEST_CASE("CrossedDoubleBondWithChiralNbr2") {
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SECTION("SIMPLE") {
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MolTest molTest("CrossedDoubleBondWithChiralNbr2.sdf", true, 10, 9);
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testMolFiles(&molTest);
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}
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}
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TEST_CASE("SimpleWiggleDoubleBond") {
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SECTION("SIMPLE") {
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MolTest molTest("SimpleWiggleDoubleBond.sdf", true, 6, 5);
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testMolFiles(&molTest);
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}
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}
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