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a6b26253ff
* do not use new on loggers * del pointers in testDistGeom * Update Dict hasNonPOD status on bulk update * delete new Dicts in memtest1.cpp * fixes in MolSuppliers and testFMCS * PeriodicTable singleton as unique_ptr * fix EEM_arrays leak * fix leaks in testPBF * fix ParamCollection leak in test UFF * fix leaks in MMFF * clear prop dict before read in in pickler * fix leaks in testFreeSASA * fix leaks in test3D * modernize Dict.h & SmilesParse.cpp * fix leaks in testQuery * fix leaks in testCrystalFF * fix leaks in cxsmilesTest * fix leaks in Catalog & mol cat test * fix leaks in ShapeUtils & tests * fix leaks in testSubgraphs1 * fix leaks testFingerprintGenerators * fix leaks in Catalog/FilterCatalog * fix leaks in graphmolqueryTest * these changes reduce bison parse leaks * fixed leaks in testChirality.cpp * fix leaks + 2 tests in testMolWriter * fix 4m leaks in substructLibraryTest * small improvements to molTautomerTest; still leaks * fix leaks in testRGroupDecomp * fix leaks in test; parser still leaks * fix leaks in itertest * fix 4m leaks in testDepictor * fixes in smatest; still leaking due to parser * fixes in testSLNParse; still leaking due to parser * flex/bison: always add atoms with ownership; smarts error cleanup * fix leaks in testReaction * fix leaks in testSubstructMatch * fix leaks in resMolSupplierTest * fix leaks in testChemTransforms + bug in ChemTransforms * fix leaks in testPickler * fix leaks in testMolTransform * fix leaks in testFragCatalog * fix leak in testSLNParse. Still leaks due to Smiles * fixed most leaks in testMolSupplier * pre bison fix * fix some atom & bond parse problems; others still fail * bison smiles & smarts, atoms & bonds more or less fixed * fix leaks in molopstest.cpp * fix leaks in testFingerprints, MACCS.cpp & AtomPairs.cpp * fix leaks in moldraw2Dtest1 * fix leaks in testDescriptors * fix leaks in testInchi * fix leaks in testUFFForceFieldHelpers * fix leaks in hanoiTest & new_canon.h * fix leaks in testMMFFForceField * fix leaks in graphmolTest1 * fix leaks in testMMFFForceFieldHelpers * fix leaks in testDistGeomHelpers * fix leaks in testMolAlign * initialize occupancy & temp facto with default values * fix leak in TautomerTransform * updated suppressions * fix testStructChecker * fix logging & py tests * fix TautomerTransform class/struct issue * remove misplaced delete in testSLNParse * deinit in testAvalonLib1 * fix Avalon-triggered(?) bug in StructChecker/Pattern.cpp * fix random testMolWriter/Supplier fails - diversify output file names to avoid clashing. - unify Writers close/destruct behavior. - flushing/closing in tests. * use reset in FFs Params.cpp * comments on testMMFFForceField * unrequired 'if's added to mol suppliers * correct cast in FilterCatalog.h * use unique_ptr in MACCS Patterns * remove unrequred if in new_canon * update & move suppressions
124 lines
3.5 KiB
C++
124 lines
3.5 KiB
C++
// $Id$
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//
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// Copyright (C) 2006 Greg Landrum
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//
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#include <RDGeneral/test.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/RDKitQueries.h>
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#include <RDGeneral/RDLog.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include "MolCatalog.h"
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#include "MolCatalogEntry.h"
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#include "MolCatalogParams.h"
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#include <stdlib.h>
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#include <iostream>
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#include <fstream>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <RDGeneral/types.h>
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#include <RDGeneral/FileParseException.h>
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#include <DataStructs/BitVects.h>
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using namespace RDKit;
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void test1() {
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BOOST_LOG(rdInfoLog) << ">>------------- Test 1" << std::endl;
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// MolCatalogParams are currently unused, so testing is easy:
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auto *mparams = new MolCatalogParams();
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std::string pkl = mparams->Serialize();
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TEST_ASSERT(pkl.empty());
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auto *mcat = new MolCatalog(mparams);
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delete mparams;
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TEST_ASSERT(mcat->getNumEntries() == 0);
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TEST_ASSERT(mcat->getFPLength() == 0);
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MolCatalogEntry *entry;
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std::string smi;
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RWMol *mol;
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mol = SmilesToMol("c1ccc(O)cc1C(=O)O");
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entry = new MolCatalogEntry(mol);
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TEST_ASSERT(entry->getMol() == mol);
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entry->setDescription("top");
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TEST_ASSERT(entry->getDescription() == "top");
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entry->setOrder(0);
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TEST_ASSERT(entry->getOrder() == 0);
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mcat->addEntry(entry);
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TEST_ASSERT(mcat->getNumEntries() == 1);
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TEST_ASSERT(mcat->getFPLength() == 1);
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TEST_ASSERT(mcat->getEntryWithBitId(0) == entry);
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mol = SmilesToMol("O");
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entry = new MolCatalogEntry(mol);
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entry->setDescription("child1");
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entry->setOrder(1);
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mcat->addEntry(entry);
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mol = SmilesToMol("C(=O)O");
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entry = new MolCatalogEntry(mol);
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entry->setDescription("child2");
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entry->setOrder(1);
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mcat->addEntry(entry);
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TEST_ASSERT(mcat->getNumEntries() == 3);
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TEST_ASSERT(mcat->getFPLength() == 3);
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TEST_ASSERT(mcat->getEntryWithBitId(0)->getMol()->getNumAtoms() == 10);
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TEST_ASSERT(mcat->getEntryWithBitId(1)->getMol()->getNumAtoms() == 1);
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TEST_ASSERT(mcat->getEntryWithBitId(2)->getMol()->getNumAtoms() == 3);
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TEST_ASSERT(mcat->getDownEntryList(0).size() == 0);
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TEST_ASSERT(mcat->getDownEntryList(1).size() == 0);
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TEST_ASSERT(mcat->getDownEntryList(2).size() == 0);
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TEST_ASSERT(mcat->getEntriesOfOrder(0).size() == 1);
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TEST_ASSERT(mcat->getEntriesOfOrder(1).size() == 2);
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TEST_ASSERT(mcat->getEntriesOfOrder(2).size() == 0);
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mcat->addEdge(0, 1);
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mcat->addEdge(0, 2);
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TEST_ASSERT(mcat->getDownEntryList(0).size() == 2);
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TEST_ASSERT(mcat->getDownEntryList(1).size() == 0);
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TEST_ASSERT(mcat->getDownEntryList(2).size() == 0);
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TEST_ASSERT(mcat->getEntriesOfOrder(0).size() == 1);
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TEST_ASSERT(mcat->getEntriesOfOrder(1).size() == 2);
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TEST_ASSERT(mcat->getEntriesOfOrder(2).size() == 0);
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pkl = mcat->Serialize();
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delete mcat;
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mcat = new MolCatalog(pkl);
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TEST_ASSERT(mcat->getNumEntries() == 3);
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TEST_ASSERT(mcat->getFPLength() == 3);
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TEST_ASSERT(mcat->getDownEntryList(0).size() == 2);
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TEST_ASSERT(mcat->getDownEntryList(1).size() == 0);
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TEST_ASSERT(mcat->getDownEntryList(2).size() == 0);
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TEST_ASSERT(mcat->getEntriesOfOrder(0).size() == 1);
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TEST_ASSERT(mcat->getEntriesOfOrder(1).size() == 2);
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TEST_ASSERT(mcat->getEntriesOfOrder(2).size() == 0);
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TEST_ASSERT(mcat->getEntryWithBitId(0)->getMol()->getNumAtoms() == 10);
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TEST_ASSERT(mcat->getEntryWithBitId(1)->getMol()->getNumAtoms() == 1);
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TEST_ASSERT(mcat->getEntryWithBitId(2)->getMol()->getNumAtoms() == 3);
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delete mcat;
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BOOST_LOG(rdInfoLog) << "<<-------------- Done" << std::endl;
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}
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int main() {
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RDLog::InitLogs();
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test1();
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return 0;
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}
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