mirror of
https://github.com/rdkit/rdkit.git
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0986d22c58
* Make kekulization deterministic * Add tautomer order-independence regression (python) * Adjust tautomer tests for deterministic kekulization * Update graphmol wedged-bond kekulization checks * SmilesParse: update aromatic bond index expectations * SmilesParse: refresh cxsmilesTest expected files * Depictor: update testDepictor expected MolBlocks * Depictor: update depictorCatch expectations * Depictor Wrap: update expected MolBlock for pyDepictor * MarvinParse: update testMrvToMol expected outputs * FileParsers: refresh testAtropisomers expected outputs * FileParsers: update tests for deterministic kekulization * MolDraw2D: refresh brittle bond assertions * RascalMCES: update expected cluster size * MinimalLib: make cffi wedging check order-independent * documentation fix * MinimalLib: update Kekulé bond table in aligned-coords test * Hoist duplicated lambdas to TEST_CASE scope * Remove unused originalWedges variable * Remove redundant bounds check; clarify wedge-end preference * Pre-sort allAtms by wedge-end + rank * Use mol.atomNeighbors() for neighbor iteration * Check inAllAtms before linear-scanning done * Drop redundant optsV/wedgedOptsV sorts * Remove unused Canon.h include * Add canonical parameter to Kekulize; skip ranking during sanitization * Test canonical re-kekulization preserves stereo across atom orderings * MinimalLib: update Kekulé bond orders in invertedWedges * Change Kekulize canonical default to false, expose in Python wrappers * keep rank order, push_back * Revert "RascalMCES: update expected cluster size" This reverts commita81bb39495. * docstring change * expose new flag to python wrapper * document changes in ReleaseNotes.md * revert minimallib test changes again * canonical = true defaults * Revert "revert minimallib test changes again" This reverts commit039e1d84da. * Reapply "RascalMCES: update expected cluster size" This reverts commit7b83a7a3e8. --------- Co-authored-by: greg landrum <greg.landrum@gmail.com>
622 lines
24 KiB
C++
622 lines
24 KiB
C++
//
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// Copyright (C) 2002-2021 Collaboartive Drug Discovery and other RDKit
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// 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/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/SequenceParsers.h>
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#include <GraphMol/FileParsers/SequenceWriters.h>
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#include <GraphMol/FileParsers/MolFileStereochem.h>
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#include <GraphMol/Depictor/RDDepictor.h>
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#include <GraphMol/ChemReactions/Reaction.h>
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#include <GraphMol/ChemReactions/ReactionParser.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/Atropisomers.h>
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#include <GraphMol/Chirality.h>
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#include <GraphMol/test_fixtures.h>
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#include <string>
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#include <fstream>
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#include <sstream>
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#include <vector>
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#include <boost/lexical_cast.hpp>
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#include <filesystem>
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using namespace RDKit;
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class MolAtropTest {
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public:
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public:
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std::string testToRun;
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bool generateExpectedFiles;
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MolAtropTest() {
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testToRun = "";
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generateExpectedFiles = false;
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}
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public:
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class MolTest {
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public:
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unsigned int atomCount;
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unsigned int bondCount;
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std::string fileName;
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bool expectedResult;
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MolTest(std::string fileNameInit, bool expectedResultInit,
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int atomCountInit, int bondCountInit)
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: atomCount(atomCountInit),
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bondCount(bondCountInit),
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fileName(fileNameInit),
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expectedResult(expectedResultInit) {};
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};
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class KekuleTest {
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public:
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unsigned int atomCount;
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unsigned int bondCount;
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std::string smiles;
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std::string expectedOutput;
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bool expectedResult;
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KekuleTest(std::string smilesInit, std::string nameInit,
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bool expectedResultInit, int atomCountInit, int bondCountInit)
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: atomCount(atomCountInit),
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bondCount(bondCountInit),
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smiles(smilesInit),
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expectedOutput(nameInit),
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expectedResult(expectedResultInit) {};
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};
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void generateNewExpectedFilesIfSoSpecified(std::string filename,
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std::string dataToWrite) {
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if (generateExpectedFiles) {
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std::ofstream out;
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out.open(filename);
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out << dataToWrite;
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}
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}
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std::string GetExpectedValue(std::string expectedFileName) {
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std::stringstream expectedMolStr;
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std::ifstream in;
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in.open(expectedFileName);
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expectedMolStr << in.rdbuf();
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return expectedMolStr.str();
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}
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void testMolFiles(const MolTest *molFileTest) {
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BOOST_LOG(rdInfoLog) << "testing mol files with atropisomers" << 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/atropisomers/" +
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molFileTest->fileName;
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// first pass - no sanitiaton, but reapplyMolBlockWedging is ON
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try {
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std::unique_ptr<RWMol> mol(MolFileToMol(fName, false, false, false));
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RDKit::Chirality::removeNonExplicit3DChirality(*mol);
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TEST_ASSERT(mol != nullptr);
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TEST_ASSERT(mol->getNumAtoms() == molFileTest->atomCount)
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TEST_ASSERT(mol->getNumBonds() == molFileTest->bondCount)
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{
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MolOps::Kekulize(*mol);
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RDKit::Chirality::reapplyMolBlockWedging(*mol);
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std::string outMolStr = MolToMolBlock(*mol, true, 0, true, true);
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generateNewExpectedFilesIfSoSpecified(fName + ".NEW.sdf", outMolStr);
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TEST_ASSERT(GetExpectedValue(fName + ".expected.sdf") == outMolStr);
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}
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// 2nd pass without reapplying the mol block wedging -
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// the itropisomers will be marked automatically
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// SANITIZATION IS ON
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mol = std::unique_ptr<RWMol>(MolFileToMol(fName, true, false, false));
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RDKit::Chirality::removeNonExplicit3DChirality(*mol);
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{
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MolOps::Kekulize(*mol);
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std::string outMolStr = MolToMolBlock(*mol, true, 0, true, true);
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generateNewExpectedFilesIfSoSpecified(fName + ".NEW2.sdf", outMolStr);
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TEST_ASSERT(GetExpectedValue(fName + ".expected2.sdf") == outMolStr);
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}
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// CXSMILES
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mol = std::unique_ptr<RWMol>(MolFileToMol(fName, false, false, false));
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RDKit::Chirality::removeNonExplicit3DChirality(*mol);
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{
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std::string expectedFileName = fName + ".expected.cxsmi";
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SmilesWriteParams ps;
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ps.canonical = false;
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ps.doKekule = true;
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unsigned int flags = SmilesWrite::CXSmilesFields::CX_COORDS |
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SmilesWrite::CXSmilesFields::CX_MOLFILE_VALUES |
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SmilesWrite::CXSmilesFields::CX_ATOM_PROPS |
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SmilesWrite::CXSmilesFields::CX_BOND_CFG |
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SmilesWrite::CXSmilesFields::CX_ENHANCEDSTEREO
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//| SmilesWrite::CXSmilesFields::CX_ALL
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;
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std::string smilesOut =
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MolToCXSmiles(*mol, ps, flags, RestoreBondDirOptionTrue);
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generateNewExpectedFilesIfSoSpecified(fName + ".NEW.cxsmi", smilesOut);
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TEST_ASSERT(GetExpectedValue(fName + ".expected.cxsmi") == smilesOut);
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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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TEST_ASSERT(molFileTest->expectedResult == true);
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return;
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}
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void testAromAtropMolFile(const MolTest *molFileTest) {
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BOOST_LOG(rdInfoLog) << "testing aromtizing mol files with atropisomers"
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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/atropisomers/" +
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molFileTest->fileName;
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UseLegacyStereoPerceptionFixture useLegacy(false);
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std::unique_ptr<RWMol> mol =
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std::unique_ptr<RWMol>(MolFileToMol(fName, false, false, false));
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TEST_ASSERT(mol->getNumAtoms() == molFileTest->atomCount)
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TEST_ASSERT(mol->getNumBonds() == molFileTest->bondCount)
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testAromAtropMol(mol.get(), molFileTest->expectedResult, fName);
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}
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void testAromAtropMol(RWMol *mol, bool expectedResult, std::string fName) {
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try {
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RDKit::Chirality::removeNonExplicit3DChirality(*mol);
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auto sanitizeOps =
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MolOps::SANITIZE_SETAROMATICITY + MolOps::SANITIZE_CLEANUPCHIRALITY +
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MolOps::SANITIZE_SETHYBRIDIZATION + MolOps::SANITIZE_SETCONJUGATION;
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unsigned int operationThatFailed = 0;
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RDKit::MolOps::sanitizeMol(*mol, operationThatFailed, sanitizeOps);
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for (const auto &atom : mol->atoms()) {
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if (atom->getChiralTag() != Atom::CHI_UNSPECIFIED) {
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BOOST_LOG(rdInfoLog) << "atom with stereo" << std::endl;
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}
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}
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for (const auto &bond : mol->bonds()) {
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if (bond->getBondDir() != Bond::BondDir::NONE) {
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BOOST_LOG(rdInfoLog) << "bond with wedging" << std::endl;
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}
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}
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{
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SmilesWriteParams ps;
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ps.canonical = true;
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ps.doKekule = false;
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ps.allBondsExplicit = false;
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ps.allHsExplicit = false;
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ps.doIsomericSmiles = true;
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ps.doKekule = false;
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ps.doRandom = false;
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ps.rootedAtAtom = -1;
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unsigned int flags = SmilesWrite::CXSmilesFields::CX_COORDS |
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SmilesWrite::CXSmilesFields::CX_MOLFILE_VALUES |
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SmilesWrite::CXSmilesFields::CX_ATOM_PROPS |
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SmilesWrite::CXSmilesFields::CX_BOND_CFG |
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SmilesWrite::CXSmilesFields::CX_ENHANCEDSTEREO;
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std::string smilesOut =
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MolToCXSmiles(*mol, ps, flags, RestoreBondDirOptionClear);
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std::string expectedFileName = fName + ".expectedArom.cxsmi";
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generateNewExpectedFilesIfSoSpecified(fName + ".NEWArom.cxsmi",
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smilesOut);
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TEST_ASSERT(GetExpectedValue(fName + ".expectedArom.cxsmi") ==
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smilesOut);
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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 (expectedResult != false) {
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throw;
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}
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return;
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}
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TEST_ASSERT(expectedResult == true);
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}
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void testKekuleWedgeError(RWMol *mol, std::string expectedSmi,
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bool expectedResult, unsigned int expectedAtomCount,
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unsigned int expectedBondCount) {
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BOOST_LOG(rdInfoLog) << "testing aromatic atropisomers" << std::endl;
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TEST_ASSERT(mol != nullptr);
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TEST_ASSERT(mol->getNumAtoms() == expectedAtomCount)
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TEST_ASSERT(mol->getNumBonds() == expectedBondCount)
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try {
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SmilesWriteParams ps;
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ps.canonical = true;
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ps.doKekule = true;
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ps.allBondsExplicit = false;
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ps.allHsExplicit = false;
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ps.doIsomericSmiles = true;
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ps.doRandom = false;
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ps.rootedAtAtom = -1;
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unsigned int flags = SmilesWrite::CXSmilesFields::CX_MOLFILE_VALUES |
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SmilesWrite::CXSmilesFields::CX_ATOM_PROPS |
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SmilesWrite::CXSmilesFields::CX_BOND_CFG |
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SmilesWrite::CXSmilesFields::CX_ENHANCEDSTEREO;
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std::string smilesOut =
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MolToCXSmiles(*mol, ps, flags, RestoreBondDirOptionClear);
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TEST_ASSERT(expectedSmi == smilesOut);
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} catch (const std::exception &e) {
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if (expectedResult != false) {
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throw;
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}
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return;
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}
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TEST_ASSERT(expectedResult == true);
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return;
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}
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void testKekuleWedgeErrorSmiles(const KekuleTest *kekuleTest) {
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BOOST_LOG(rdInfoLog) << "testing aromatic atropisomers" << std::endl;
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UseLegacyStereoPerceptionFixture useLegacy(false);
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RDKit::SmilesParserParams params;
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params.allowCXSMILES = true; // recognize and parse CXSMILES
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params.debugParse = false; // disable debugging in the SMILES parser
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params.parseName = true; // parse (and set) the molecule name as well
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params.removeHs = false; // do not remove Hs
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params.replacements = nullptr; // no SMILES "macros"
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params.sanitize = true; // do not sanitize the molecule
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params.skipCleanup =
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false; // do not skip the final cleanup stage (for internal RDKit use)
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params.strictCXSMILES =
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false; // do not throw an exception if the CXSMILES parsing fails
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std::unique_ptr<RWMol> mol =
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std::unique_ptr<RWMol>(SmilesToMol(kekuleTest->smiles, params));
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testKekuleWedgeError(mol.get(), kekuleTest->expectedOutput,
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kekuleTest->expectedResult, kekuleTest->atomCount,
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kekuleTest->bondCount);
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}
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void testKekuleWedgeErrorMol(const MolTest *kekuleTest) {
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BOOST_LOG(rdInfoLog) << "testing aromatic atropisomers" << std::endl;
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UseLegacyStereoPerceptionFixture useLegacy(false);
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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/atropisomers/" +
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kekuleTest->fileName;
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std::unique_ptr<RWMol> mol(MolFileToMol(fName, true, false, false));
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testKekuleWedgeError(mol.get(), GetExpectedValue(fName + ".expected.cxsmi"),
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kekuleTest->expectedResult, kekuleTest->atomCount,
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kekuleTest->bondCount);
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}
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void RunTests() {
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// the molecule tests
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if (testToRun == "" || testToRun == "sdfTests") {
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std::list<MolTest> sdfTests{
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MolTest("atropWedgeTest.sdf", true, 16, 16),
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MolTest("AtropTest.sdf", true, 38, 41),
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MolTest("AtropManyChiralsEnhanced.sdf", true, 20, 20),
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MolTest("AtropManyChiralsEnhanced2.sdf", true, 20, 20),
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MolTest("AtropManyChirals.sdf", true, 20, 20),
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MolTest("BMS-986142.sdf", true, 42, 47),
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MolTest("BMS-986142_3d_chiral.sdf", true, 72, 77),
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MolTest("BMS-986142_3d.sdf", true, 72, 77),
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MolTest("BMS-986142_atrop1.sdf", true, 42, 47),
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MolTest("BMS-986142_atrop2.sdf", true, 42, 47),
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MolTest("BMS-986142_atrop3.sdf", true, 42, 47),
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MolTest("BMS-986142_atrop4.sdf", true, 42, 47),
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MolTest("BMS-986142_atrop5.sdf", true, 42, 47),
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MolTest("BMS-986142_atrop6.sdf", true, 42, 47),
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MolTest("BMS-986142_atrop7.sdf", true, 42, 47),
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MolTest("BMS-986142_atrop8.sdf", true, 42, 47),
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MolTest("BMS-986142_atropBad2.sdf", true, 42, 47),
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MolTest("JDQ443.sdf", true, 38, 44),
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MolTest("JDQ443_3d.sdf", true, 66, 72),
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MolTest("JDQ443_atrop1.sdf", true, 38, 44),
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MolTest("JDQ443_atrop2.sdf", true, 38, 44),
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MolTest("JDQ443_atrop3.sdf", true, 38, 44),
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MolTest("JDQ443_atropBad1.sdf", true, 38, 44),
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MolTest("RP-6306.sdf", true, 24, 26),
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MolTest("RP-6306_atrop1.sdf", true, 24, 26),
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MolTest("RP-6306_atrop2.sdf", true, 24, 26),
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MolTest("RP-6306_atrop3.sdf", true, 24, 26),
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MolTest("RP-6306_atrop4.sdf", true, 24, 26),
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MolTest("RP-6306_atrop5.sdf", true, 24, 26),
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MolTest("RP-6306_atropBad1.sdf", true, 24, 26),
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MolTest("RP-6306_atropBad2.sdf", true, 24, 26),
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// note the rp-6306_3d.sdf is backwards from the 2D versions
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// the 2D version were based on images from drug hunter
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// the 3D version came from PUBCHEM
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MolTest("RP-6306_3d.sdf", true, 44, 46),
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MolTest("Sotorasib.sdf", true, 41, 45),
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MolTest("Sotorasib_atrop1.sdf", true, 41, 45),
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MolTest("Sotorasib_atrop2.sdf", true, 41, 45),
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MolTest("Sotorasib_atrop3.sdf", true, 41, 45),
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MolTest("Sotorasib_atrop4.sdf", true, 41, 45),
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MolTest("Sotorasib_atrop5.sdf", true, 41, 45),
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MolTest("Sotorasib_atropBad1.sdf", true, 41, 45),
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MolTest("Sotorasib_atropBad2.sdf", true, 41, 45),
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// note the sotorasib_3d.sdf is backwards from the 2D versions
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// the 2D version were based on images from drug hunter
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// the 3D version came from PUBCHEM
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MolTest("Sotorasib_3d.sdf", true, 71, 75),
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MolTest("ZM374979.sdf", true, 45, 49),
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MolTest("ZM374979_atrop1.sdf", true, 45, 49),
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MolTest("ZM374979_atrop2.sdf", true, 45, 49),
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MolTest("ZM374979_atrop3.sdf", true, 45, 49),
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MolTest("ZM374979_atropBad1.sdf", true, 45, 49),
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MolTest("Mrtx1719.sdf", true, 33, 37),
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// note the Mrtx1719_3d.sdf is backwards from the 2D versions
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// the 2D version were based on images from drug hunter
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// the 3D version came from PUBCHEM
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MolTest("Mrtx1719_3d.sdf", true, 51, 55),
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MolTest("Mrtx1719_atrop1.sdf", true, 33, 37),
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MolTest("Mrtx1719_atrop2.sdf", true, 33, 37),
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MolTest("Mrtx1719_atrop3.sdf", true, 33, 37),
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MolTest("Mrtx1719_atropBad1.sdf", true, 33, 37),
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// macrocycles
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MolTest("macrocycle-9-meta-wedge.sdf", true, 24, 26),
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MolTest("macrocycle-9-ortho-wedge.sdf", true, 24, 26),
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MolTest("macrocycle-8-meta-wedge.sdf", true, 23, 25),
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MolTest("macrocycle-8-ortho-wedge.sdf", true, 23, 25),
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MolTest("macrocycle-7-meta-wedge.sdf", true, 22, 24),
|
|
MolTest("macrocycle-7-ortho-wedge.sdf", true, 22, 24),
|
|
MolTest("macrocycle-6-meta-wedge.sdf", true, 21, 23),
|
|
MolTest("macrocycle-6-ortho-wedge.sdf", true, 21, 23),
|
|
MolTest("macrocycle-5-meta-wedge.sdf", true, 20, 22),
|
|
MolTest("macrocycle-5-ortho-wedge.sdf", true, 20, 22),
|
|
MolTest("macrocycle-9-meta-Cl-ortho-wedge.sdf", true, 25, 27),
|
|
MolTest("macrocycle-8-meta-Cl-ortho-wedge.sdf", true, 24, 26),
|
|
MolTest("macrocycle-7-meta-Cl-ortho-wedge.sdf", true, 23, 25),
|
|
MolTest("macrocycle-6-meta-Cl-ortho-wedge.sdf", true, 22, 24),
|
|
MolTest("macrocycle-5-meta-Cl-ortho-wedge.sdf", true, 21, 23),
|
|
MolTest("macrocycle-9-meta-broken-wedge.sdf", true, 24, 25),
|
|
MolTest("macrocycle-9-ortho-broken-wedge.sdf", true, 24, 25),
|
|
MolTest("macrocycle-8-meta-broken-wedge.sdf", true, 23, 24),
|
|
MolTest("macrocycle-8-ortho-broken-wedge.sdf", true, 23, 24),
|
|
MolTest("macrocycle-7-meta-broken-wedge.sdf", true, 22, 23),
|
|
MolTest("macrocycle-7-ortho-broken-wedge.sdf", true, 22, 23),
|
|
MolTest("macrocycle-6-meta-broken-wedge.sdf", true, 21, 22),
|
|
MolTest("macrocycle-6-ortho-broken-wedge.sdf", true, 21, 22),
|
|
MolTest("macrocycle-5-meta-broken-wedge.sdf", true, 20, 21),
|
|
MolTest("macrocycle-5-ortho-broken-wedge.sdf", true, 20, 21),
|
|
MolTest("macrocycle-9-meta-hash.sdf", true, 24, 26),
|
|
MolTest("macrocycle-9-ortho-hash.sdf", true, 24, 26),
|
|
MolTest("macrocycle-8-meta-hash.sdf", true, 23, 25),
|
|
MolTest("macrocycle-8-ortho-hash.sdf", true, 23, 25),
|
|
MolTest("macrocycle-7-meta-hash.sdf", true, 22, 24),
|
|
MolTest("macrocycle-7-ortho-hash.sdf", true, 22, 24),
|
|
MolTest("macrocycle-6-meta-hash.sdf", true, 21, 23),
|
|
MolTest("macrocycle-6-ortho-hash.sdf", true, 21, 23),
|
|
MolTest("macrocycle-5-meta-hash.sdf", true, 20, 22),
|
|
MolTest("macrocycle-5-ortho-hash.sdf", true, 20, 22),
|
|
MolTest("macrocycle-9-meta-Cl-ortho-hash.sdf", true, 25, 27),
|
|
MolTest("macrocycle-8-meta-Cl-ortho-hash.sdf", true, 24, 26),
|
|
MolTest("macrocycle-7-meta-Cl-ortho-hash.sdf", true, 23, 25),
|
|
MolTest("macrocycle-6-meta-Cl-ortho-hash.sdf", true, 22, 24),
|
|
MolTest("macrocycle-5-meta-Cl-ortho-hash.sdf", true, 21, 23),
|
|
MolTest("macrocycle-9-meta-broken-hash.sdf", true, 24, 25),
|
|
MolTest("macrocycle-9-ortho-broken-hash.sdf", true, 24, 25),
|
|
MolTest("macrocycle-8-meta-broken-hash.sdf", true, 23, 24),
|
|
MolTest("macrocycle-8-ortho-broken-hash.sdf", true, 23, 24),
|
|
MolTest("macrocycle-7-meta-broken-hash.sdf", true, 22, 23),
|
|
MolTest("macrocycle-7-ortho-broken-hash.sdf", true, 22, 23),
|
|
MolTest("macrocycle-6-meta-broken-hash.sdf", true, 21, 22),
|
|
MolTest("macrocycle-6-ortho-broken-hash.sdf", true, 21, 22),
|
|
MolTest("macrocycle-5-meta-broken-hash.sdf", true, 20, 21),
|
|
MolTest("macrocycle-5-ortho-broken-hash.sdf", true, 20, 21),
|
|
};
|
|
|
|
for (auto sdfTest : sdfTests) {
|
|
BOOST_LOG(rdInfoLog) << "Test: " << sdfTest.fileName << std::endl;
|
|
|
|
testMolFiles(&sdfTest);
|
|
}
|
|
}
|
|
|
|
if (testToRun == "" || testToRun == "AromAtropMol") {
|
|
std::list<MolTest> sdfTests{
|
|
MolTest("BMS-986142_atrop1.sdf", true, 42, 47),
|
|
MolTest("BMS-986142_3d_chiral.sdf", true, 72, 77),
|
|
MolTest("BMS-986142_3d.sdf", true, 72, 77),
|
|
};
|
|
|
|
for (auto sdfTest : sdfTests) {
|
|
BOOST_LOG(rdInfoLog) << "Test: " << sdfTest.fileName << std::endl;
|
|
|
|
testAromAtropMolFile(&sdfTest);
|
|
}
|
|
}
|
|
|
|
if (testToRun == "" || testToRun == "KekuleWedgeError") {
|
|
std::list<KekuleTest> kekuleTests{
|
|
KekuleTest(
|
|
"CC1C(C2C(Cl)=CC=CC=2C)=C(Cl)C=CC=1 |wU:3.3,(17.57,-4.18,;17.57,-5.18,;16.71,-5.67,;15.84,-5.18,;15.84,-4.18,;16.71,-3.67,;14.98,-3.67,;14.11,-4.18,;14.11,-5.18,;14.98,-5.67,;14.98,-6.67,;16.71,-6.67,;15.84,-7.18,;17.57,-7.18,;18.44,-6.67,;18.44,-5.67,)|",
|
|
"CC1=C(C2=C(C)C=CC=C2Cl)C(Cl)=CC=C1 |wU:2.11|", true, 16, 17),
|
|
KekuleTest("CC1C(C2C(Cl)=CC=CC=2C)=C(Cl)C=CC=1 |wD:3.3|",
|
|
"CC1=C(C2=C(C)C=CC=C2Cl)C(Cl)=CC=C1 |wU:2.11|", true, 16,
|
|
17),
|
|
KekuleTest(
|
|
"CC1C=CC(O)=C(C)C=1N1C2C(=NC=CC=2OC2C=NC=CC=2)C(C(=O)N)=C1N |wD:8.7|",
|
|
"CC1=C(O)C=CC(C)=C1N1C(N)=C(C(N)=O)C2=NC=CC(OC3=CC=CN=C3)=C21 |wD:9.10|",
|
|
true, 29, 32),
|
|
};
|
|
|
|
for (auto kekuleTest : kekuleTests) {
|
|
BOOST_LOG(rdInfoLog) << "Test: " << kekuleTest.smiles << std::endl;
|
|
|
|
testKekuleWedgeErrorSmiles(&kekuleTest);
|
|
}
|
|
}
|
|
|
|
if (testToRun == "" || testToRun == "KekuleWedgeErrorMol") {
|
|
std::list<MolTest> kekuleTests{
|
|
MolTest("atropWedgeError2.mol", true, 16, 17),
|
|
MolTest("atropWedgeError.mol", true, 29, 32),
|
|
};
|
|
|
|
for (auto kekuleTest : kekuleTests) {
|
|
BOOST_LOG(rdInfoLog) << "Test: " << kekuleTest.fileName << std::endl;
|
|
|
|
testKekuleWedgeErrorMol(&kekuleTest);
|
|
}
|
|
}
|
|
}
|
|
};
|
|
|
|
void testLookForAtropisomersInSDdfFiles(std::string fileName,
|
|
unsigned int expectedHits,
|
|
unsigned int expectedMisses) {
|
|
BOOST_LOG(rdInfoLog) << "Looking for atropisomers in " << fileName
|
|
<< std::endl;
|
|
|
|
std::string rdbase = getenv("RDBASE");
|
|
std::string fName =
|
|
rdbase + "/Code/GraphMol/FileParsers/test_data/atropisomers/" + fileName;
|
|
|
|
std::ifstream in;
|
|
in.open(fName);
|
|
std::string line;
|
|
unsigned int foundCount = 0;
|
|
unsigned int notFoundCount = 0;
|
|
while (!in.eof()) {
|
|
std::string molBlock = "";
|
|
while (std::getline(in, line)) {
|
|
if (line.find("$$$$") != std::string::npos) {
|
|
break;
|
|
}
|
|
|
|
molBlock += line + "\n";
|
|
}
|
|
|
|
if (molBlock.length() < 10) {
|
|
continue; // try for another;
|
|
}
|
|
|
|
std::unique_ptr<RWMol> mol(MolBlockToMol(molBlock, false, false, false));
|
|
TEST_ASSERT(mol != nullptr);
|
|
|
|
auto hasAtropisomers = RDKit::Atropisomers::doesMolHaveAtropisomers(*mol);
|
|
|
|
if (hasAtropisomers) {
|
|
BOOST_LOG(rdInfoLog) << "Found atropisomers in " << fileName << std::endl;
|
|
foundCount++;
|
|
printf("Atropisomers- %d hits %d misses\r", foundCount, notFoundCount);
|
|
std::flush(std::cout);
|
|
std::ofstream out;
|
|
out.open(fName + "_" + std::to_string(foundCount) + ".sdf");
|
|
out << molBlock << std::endl;
|
|
} else {
|
|
notFoundCount++;
|
|
if (notFoundCount % 100 == 0) {
|
|
printf("Atropisomers- %d hits %d misses\r", foundCount,
|
|
notFoundCount);
|
|
std::flush(std::cout);
|
|
}
|
|
}
|
|
}
|
|
printf("\nFinal results:\nFound atropisomers in %s - %d hits %d misses\n",
|
|
fileName.c_str(), foundCount, notFoundCount);
|
|
|
|
TEST_ASSERT(foundCount == expectedHits);
|
|
TEST_ASSERT(notFoundCount == expectedMisses);
|
|
}
|
|
|
|
void testSulfinamideExamplesHaveNoAtropisomers() {
|
|
const std::vector<std::string> controlFiles = {
|
|
"sulfinamide-double-bond-O-R.mol",
|
|
"sulfinamide-single-bond-O-R.mol",
|
|
"sulfinamide-single-bond-O-S.mol",
|
|
};
|
|
std::string rdbase = getenv("RDBASE");
|
|
std::stringstream warningCapture;
|
|
rdWarningLog->SetTee(warningCapture);
|
|
for (const auto &file : controlFiles) {
|
|
auto fName = rdbase +
|
|
"/Code/GraphMol/FileParsers/test_data/atropisomers/" +
|
|
file;
|
|
BOOST_LOG(rdInfoLog) << "Validating absence of atropisomers in " << file
|
|
<< std::endl;
|
|
auto mol = std::unique_ptr<RWMol>(MolFileToMol(fName, true, false, false));
|
|
TEST_ASSERT(mol);
|
|
Atropisomers::detectAtropisomerChirality(*mol, &mol->getConformer());
|
|
TEST_ASSERT(!Atropisomers::doesMolHaveAtropisomers(*mol));
|
|
}
|
|
rdWarningLog->ClearTee();
|
|
TEST_ASSERT(warningCapture.str().empty());
|
|
}
|
|
|
|
int main(int argc, char *argv[]) {
|
|
(void)argc;
|
|
(void)argv;
|
|
RDLog::InitLogs();
|
|
boost::logging::enable_logs("rdApp.info");
|
|
BOOST_LOG(rdInfoLog) << " ---- Running with POSIX locale ----- " << std::endl;
|
|
|
|
MolAtropTest molAtropTest;
|
|
|
|
if (argc > 1) {
|
|
molAtropTest.testToRun = argv[1];
|
|
}
|
|
|
|
if (argc > 2 && std::string(argv[2]) == "generate") {
|
|
molAtropTest.generateExpectedFiles = true;
|
|
}
|
|
|
|
RDLog::InitLogs();
|
|
BOOST_LOG(rdInfoLog) << " ---- Running with POSIX locale ----- " << std::endl;
|
|
|
|
molAtropTest.RunTests();
|
|
testLookForAtropisomersInSDdfFiles("TestMultInSDF.sdf", 1, 4);
|
|
testSulfinamideExamplesHaveNoAtropisomers();
|
|
|
|
return 0;
|
|
}
|