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9055646b54
* fix scsr parsing for non-template SUP groups * Rempoved two tests not related to this PR * Update Code/GraphMol/FileParsers/SCSRMolFileParser.cpp added the constexpr as suggested Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * changed constrexpr to const for std:string --------- Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
361 lines
14 KiB
C++
361 lines
14 KiB
C++
//
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// Copyright (C) 2025 Tad Hurst 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 <algorithm>
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#include <fstream>
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#include <string>
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#include <sstream>
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#include <streambuf>
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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/Atropisomers.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <RDGeneral/BoostStartInclude.h>
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#include <boost/lexical_cast.hpp>
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#include <RDGeneral/BoostEndInclude.h>
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#include <filesystem>
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using namespace RDKit;
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using namespace v2::FileParsers;
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using namespace RDKit;
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class ScsiMolTest {
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public:
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public:
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bool generateExpectedFiles = false;
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ScsiMolTest() {}
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class ScsiTest {
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public:
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std::string fileName;
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unsigned int totalAtomCount;
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unsigned int totalBondCount;
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unsigned int sgroupCount;
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unsigned int totalQueryAtomCount;
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unsigned int totalQueryBondCount;
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unsigned int querySgroupCount;
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bool scsrExpandResult;
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SCSRBaseHbondOptions scsrBaseHbondOptions;
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ScsiTest(std::string fileNameInit, bool scsrExpandResult,
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SCSRBaseHbondOptions scsrBaseHbondOptions,
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unsigned int totalAtomCountInit, unsigned int totalBondCountInit,
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unsigned int sgroupCountInit, unsigned int totalQueryAtomCountInit,
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unsigned int totalQueryBondCountInit,
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unsigned int querySgroupCountInit = 0)
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: fileName(fileNameInit),
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totalAtomCount(totalAtomCountInit),
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totalBondCount(totalBondCountInit),
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sgroupCount(sgroupCountInit),
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totalQueryAtomCount(totalQueryAtomCountInit),
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totalQueryBondCount(totalQueryBondCountInit),
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querySgroupCount(querySgroupCountInit),
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scsrExpandResult(scsrExpandResult),
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scsrBaseHbondOptions(scsrBaseHbondOptions) {};
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};
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void testScsiFiles(const ScsiTest *scsiTest) {
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BOOST_LOG(rdInfoLog) << "testing scsr files" << std::endl;
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INFO(scsiTest->fileName);
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std::string rdbase = getenv("RDBASE");
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std::string fName = rdbase +
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"/Code/GraphMol/FileParsers/test_data/macromols/" +
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scsiTest->fileName;
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RDKit::v2::FileParsers::MolFileParserParams pp;
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pp.sanitize = true;
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pp.removeHs = false;
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pp.strictParsing = true;
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RDKit::v2::FileParsers::MolFromSCSRParams molFromSCSRParams;
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molFromSCSRParams.includeLeavingGroups = true;
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molFromSCSRParams.scsrBaseHbondOptions = scsiTest->scsrBaseHbondOptions;
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std::unique_ptr<RDKit::RWMol> mol;
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if (scsiTest->scsrExpandResult) {
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REQUIRE_NOTHROW(mol = MolFromSCSRFile(fName, pp, molFromSCSRParams));
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} else {
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REQUIRE_THROWS(mol = MolFromSCSRFile(fName, pp, molFromSCSRParams));
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return;
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}
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RDKit::Chirality::removeNonExplicit3DChirality(*(mol.get()));
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CHECK(mol != nullptr);
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CHECK(mol->getNumAtoms() == scsiTest->totalAtomCount);
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CHECK(mol->getNumBonds() == scsiTest->totalBondCount);
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CHECK(getSubstanceGroups(*mol).size() == scsiTest->sgroupCount);
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// now make the expanded mol in "query" mode - not including any leaving
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// groups
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molFromSCSRParams.includeLeavingGroups = false;
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std::unique_ptr<RDKit::RWMol> molNoLeavingGroups;
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if (scsiTest->scsrExpandResult) {
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REQUIRE_NOTHROW(molNoLeavingGroups =
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MolFromSCSRFile(fName, pp, molFromSCSRParams));
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} else {
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REQUIRE_THROWS(molNoLeavingGroups =
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MolFromSCSRFile(fName, pp, molFromSCSRParams));
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return;
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}
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CHECK(molNoLeavingGroups != nullptr);
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CHECK(molNoLeavingGroups->getNumAtoms() == scsiTest->totalQueryAtomCount);
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CHECK(molNoLeavingGroups->getNumBonds() == scsiTest->totalQueryBondCount);
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CHECK(getSubstanceGroups(*molNoLeavingGroups).size() ==
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scsiTest->querySgroupCount);
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}
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void threeLetterCodeTest(const ScsiTest *scsiTest) {
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BOOST_LOG(rdInfoLog) << "testing scsr files with three letter codes"
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<< std::endl;
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std::string rdbase = getenv("RDBASE");
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std::string fName = rdbase +
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"/Code/GraphMol/FileParsers/test_data/macromols/" +
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scsiTest->fileName;
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RDKit::v2::FileParsers::MolFileParserParams pp;
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pp.sanitize = false;
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pp.removeHs = false;
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pp.strictParsing = false;
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RDKit::v2::FileParsers::MolFromSCSRParams molFromSCSRParams;
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molFromSCSRParams.includeLeavingGroups = true;
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molFromSCSRParams.scsrTemplateNames =
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RDKit::v2::FileParsers::SCSRTemplateNames::AsEntered;
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molFromSCSRParams.scsrBaseHbondOptions = scsiTest->scsrBaseHbondOptions;
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std::unique_ptr<RDKit::RWMol> mol;
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if (scsiTest->scsrExpandResult) {
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REQUIRE_NOTHROW(mol = MolFromSCSRFile(fName, pp, molFromSCSRParams));
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} else {
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REQUIRE_THROWS(mol = MolFromSCSRFile(fName, pp, molFromSCSRParams));
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return;
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}
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RDKit::Chirality::removeNonExplicit3DChirality(*(mol.get()));
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CHECK(mol);
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CHECK(mol->getNumAtoms() == scsiTest->totalAtomCount);
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CHECK(mol->getNumBonds() == scsiTest->totalBondCount);
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CHECK(getSubstanceGroups(*mol).size() == scsiTest->sgroupCount);
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molFromSCSRParams.includeLeavingGroups = true;
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molFromSCSRParams.scsrTemplateNames =
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RDKit::v2::FileParsers::SCSRTemplateNames::UseFirstName;
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std::unique_ptr<RWMol> mol2;
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if (scsiTest->scsrExpandResult) {
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REQUIRE_NOTHROW(mol2 = MolFromSCSRFile(fName, pp, molFromSCSRParams));
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} else {
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REQUIRE_THROWS(mol2 = MolFromSCSRFile(fName, pp, molFromSCSRParams));
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}
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// const std::unique_ptr<RDKit::RWMol> mol;
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CHECK(mol2);
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CHECK(mol2->getNumAtoms() == scsiTest->totalQueryAtomCount);
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CHECK(mol2->getNumBonds() == scsiTest->totalQueryBondCount);
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CHECK(getSubstanceGroups(*mol2).size() == scsiTest->querySgroupCount);
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};
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};
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TEST_CASE("scsiTests", "scsiTests") {
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SECTION("basics") {
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std::list<ScsiMolTest::ScsiTest> scsiTests{
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ScsiMolTest::ScsiTest("Conjugate.mol", true, SCSRBaseHbondOptions::Auto,
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91, 91, 14, 87, 87, 10),
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ScsiMolTest::ScsiTest("ModifiedPeptide2.mol", true,
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SCSRBaseHbondOptions::Auto, 438, 444, 81, 407,
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413, 50),
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ScsiMolTest::ScsiTest("DnaBadPairs_NoCh.mol", true,
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SCSRBaseHbondOptions::Auto, 84, 94, 14, 80, 90,
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10),
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ScsiMolTest::ScsiTest("DnaBadPairs.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 84, 94, 14, 80,
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90, 10),
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ScsiMolTest::ScsiTest("DnaTest.mol", false,
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SCSRBaseHbondOptions::UseSapAll, 254, 300, 14,
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250, 296, 10),
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ScsiMolTest::ScsiTest("wobblePairs2.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 169, 196, 26,
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165, 192, 22),
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ScsiMolTest::ScsiTest("wobblePairs.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 169, 196, 26,
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165, 192, 22),
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ScsiMolTest::ScsiTest("KellanRNA.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 299, 353, 44,
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295, 349, 40),
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ScsiMolTest::ScsiTest("DnaTest2.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 83, 97, 14, 79,
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93, 10),
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ScsiMolTest::ScsiTest("DnaTest3.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 165, 194, 26,
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161, 190, 22),
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ScsiMolTest::ScsiTest("KellanError.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 244, 263, 39,
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236, 255, 31),
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ScsiMolTest::ScsiTest("TestRNA2_fixed.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 106, 117, 17,
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104, 115, 15),
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ScsiMolTest::ScsiTest("DnaTest.mol", true, SCSRBaseHbondOptions::Auto,
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254, 300, 38, 250, 296, 34),
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ScsiMolTest::ScsiTest("wobblePairs2.mol", true,
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SCSRBaseHbondOptions::Auto, 169, 196, 26, 165,
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192, 22),
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ScsiMolTest::ScsiTest("wobblePairs.mol", true,
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SCSRBaseHbondOptions::Auto, 169, 196, 26, 165,
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192, 22),
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ScsiMolTest::ScsiTest("DnaBadPairs.mol", true,
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SCSRBaseHbondOptions::Auto, 84, 94, 14, 80, 90,
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10),
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ScsiMolTest::ScsiTest("DnaTest2.mol", true, SCSRBaseHbondOptions::Auto,
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83, 97, 14, 79, 93, 10),
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ScsiMolTest::ScsiTest("DnaTest3.mol", true, SCSRBaseHbondOptions::Auto,
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165, 194, 26, 161, 190, 22),
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ScsiMolTest::ScsiTest("KellanError.mol", true,
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SCSRBaseHbondOptions::Auto, 244, 263, 39, 236,
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255, 31),
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ScsiMolTest::ScsiTest("TestRNA2_fixed.mol", true,
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SCSRBaseHbondOptions::Auto, 106, 117, 17, 104,
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115, 15),
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ScsiMolTest::ScsiTest("TrastuzumabMaxPlus3Register.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 7606, 7793, 1451,
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7080, 7267, 925),
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ScsiMolTest::ScsiTest("TrastuzumabMaxRegister.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 7576, 7763, 1445,
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7053, 7240, 922),
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ScsiMolTest::ScsiTest("Mixed.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 51, 54, 8, 51,
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54, 8),
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ScsiMolTest::ScsiTest("CrossLink.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 47, 48, 10, 45,
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46, 8),
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ScsiMolTest::ScsiTest("cyclic.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 45, 47, 8, 45,
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47, 8),
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ScsiMolTest::ScsiTest("Triplet.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 30, 30, 6, 27,
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27, 3),
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ScsiMolTest::ScsiTest("FromBioviaDoc.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 27, 26, 7, 25,
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24, 5),
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ScsiMolTest::ScsiTest("testSCSR.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 64, 66, 15, 57,
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59, 8),
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ScsiMolTest::ScsiTest("badAtomName.mol", false,
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SCSRBaseHbondOptions::UseSapAll, 0, 0, 0, 0, 0,
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0),
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ScsiMolTest::ScsiTest("badClass.mol", false,
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SCSRBaseHbondOptions::UseSapAll, 0, 0, 0, 0, 0,
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0),
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ScsiMolTest::ScsiTest("badClassTemplate.mol", false,
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SCSRBaseHbondOptions::UseSapAll, 0, 0, 0, 0, 0,
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0),
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ScsiMolTest::ScsiTest("badMissingTemplate.mol", false,
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SCSRBaseHbondOptions::UseSapAll, 0, 0, 0, 0, 0,
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0),
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ScsiMolTest::ScsiTest("obj3dTest.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 27, 26, 7, 25,
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24, 5),
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ScsiMolTest::ScsiTest("obj3dTest2.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 27, 26, 7, 25,
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24, 5),
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ScsiMolTest::ScsiTest("obj3dFoundTwice.mol", false,
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SCSRBaseHbondOptions::UseSapAll, 27, 26, 0, 27,
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26, 0),
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ScsiMolTest::ScsiTest("SgroupFoundTwice.mol", false,
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SCSRBaseHbondOptions::UseSapAll, 0, 0, 0, 0, 0,
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0),
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};
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ScsiMolTest scsiMolTest;
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for (auto scsiTest : scsiTests) {
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BOOST_LOG(rdInfoLog) << "Test: " << scsiTest.fileName << std::endl;
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scsiMolTest.testScsiFiles(&scsiTest);
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}
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}
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}
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TEST_CASE("nestedParens", "nestedParens") {
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SECTION("basics") {
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BOOST_LOG(rdInfoLog) << "testing names with parens" << std::endl;
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std::string filename = "Ugly.mol";
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INFO(filename);
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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/macromols/" + filename;
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RDKit::v2::FileParsers::MolFileParserParams pp;
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pp.sanitize = true;
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pp.removeHs = false;
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pp.strictParsing = true;
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RDKit::v2::FileParsers::MolFromSCSRParams molFromSCSRParams;
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molFromSCSRParams.includeLeavingGroups = true;
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molFromSCSRParams.scsrBaseHbondOptions = SCSRBaseHbondOptions::Auto;
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std::unique_ptr<RDKit::RWMol> mol;
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REQUIRE_NOTHROW(mol = MolFromSCSRFile(fName, pp, molFromSCSRParams));
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CHECK(mol != nullptr);
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CHECK(mol->getNumAtoms() == 140);
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CHECK(mol->getNumBonds() == 151);
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CHECK(getSubstanceGroups(*mol).size() == 11);
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// check that the macro atoms parsed have the correct names. In the
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// output mol these names will not appear in the SGROUP that defined the
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// macroatom. we willcheck just a couple of them
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std::string sgroupName;
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getSubstanceGroups(*mol)[1].getProp("LABEL", sgroupName);
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std::string expected = "((cPr)O(2S-Me)Et)NGly";
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CHECK(sgroupName.substr(0, expected.length()) == expected);
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getSubstanceGroups(*mol)[5].getProp("LABEL", sgroupName);
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expected = "Phe(b-Me2)";
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CHECK(sgroupName.substr(0, expected.length()) == expected);
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getSubstanceGroups(*mol)[7].getProp("LABEL", sgroupName);
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expected = "(PhO(2S-Me)Et)NGly";
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CHECK(sgroupName.substr(0, expected.length()) == expected);
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}
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}
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TEST_CASE("threeLetterCodeTest", "threeLetterCodeTest") {
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SECTION("basics") {
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std::list<ScsiMolTest::ScsiTest> scsiTests{
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ScsiMolTest::ScsiTest("PepTla.mol", true,
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SCSRBaseHbondOptions::UseSapAll, 26, 25, 7, 26,
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25, 7),
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};
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ScsiMolTest scsiMolTest;
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for (auto scsiTest : scsiTests) {
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BOOST_LOG(rdInfoLog) << "Test: " << scsiTest.fileName << std::endl;
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scsiMolTest.threeLetterCodeTest(&scsiTest);
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}
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}
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}
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