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91008ff11d
* Address compile warnings & trivial improvements * revert unwanted initializers; use RDUNUSED_PARAM for unused params * revert fix in testRDFcustom; marked with 'TO DO' comment
92 lines
3.2 KiB
C++
92 lines
3.2 KiB
C++
//
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// Copyright (C) 2018 Susan H. Leung
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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 <GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h>
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#include <GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h>
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#include "Normalize.h"
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#include <RDGeneral/Invariant.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/ROMol.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/FileParsers/FileParsers.h>
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#include <RDGeneral/FileParseException.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/MolStandardize/MolStandardize.h>
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#include <iostream>
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#include <fstream>
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using namespace RDKit;
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using namespace MolStandardize;
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void test1() {
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BOOST_LOG(rdInfoLog) << "-----------------------\n test1" << std::endl;
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std::string smi1, smi2, smi3, smi4, smi5, smi6, smi7;
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Normalizer normalizer;
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// Test sulfoxide normalization.
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smi1 = "CS(C)=O";
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std::shared_ptr<ROMol> m1(SmilesToMol(smi1));
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ROMOL_SPTR normalized(normalizer.normalize(*m1));
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TEST_ASSERT(MolToSmiles(*normalized) == "C[S+](C)[O-]");
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// Test sulfone
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smi2 = "C[S+2]([O-])([O-])O";
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std::shared_ptr<ROMol> m2(SmilesToMol(smi2));
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ROMOL_SPTR normalized2(normalizer.normalize(*m2));
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TEST_ASSERT(MolToSmiles(*normalized2) == "CS(=O)(=O)O");
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// Test 1,3-separated charges are recombined.
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smi3 = "CC([O-])=[N+](C)C";
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std::shared_ptr<ROMol> m3(SmilesToMol(smi3));
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ROMOL_SPTR normalized3(normalizer.normalize(*m3));
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TEST_ASSERT(MolToSmiles(*normalized3) == "CC(=O)N(C)C");
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// Test 1,3-separated charges are recombined.
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smi4 = "C[n+]1ccccc1[O-]";
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std::shared_ptr<ROMol> m4(SmilesToMol(smi4));
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ROMOL_SPTR normalized4(normalizer.normalize(*m4));
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TEST_ASSERT(MolToSmiles(*normalized4) == "Cn1ccccc1=O");
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// Test a case where 1,3-separated charges should not be recombined.
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smi5 = "CC12CCCCC1(Cl)[N+]([O-])=[N+]2[O-]";
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std::shared_ptr<ROMol> m5(SmilesToMol(smi5));
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ROMOL_SPTR normalized5(normalizer.normalize(*m5));
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TEST_ASSERT(MolToSmiles(*normalized5) ==
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"CC12CCCCC1(Cl)[N+]([O-])=[N+]2[O-]");
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// Test 1,5-separated charges are recombined.
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smi6 = R"(C[N+](C)=C\C=C\[O-])";
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std::shared_ptr<ROMol> m6(SmilesToMol(smi6));
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ROMOL_SPTR normalized6(normalizer.normalize(*m6));
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TEST_ASSERT(MolToSmiles(*normalized6) == "CN(C)C=CC=O");
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// Test a case where 1,5-separated charges should not be recombined.
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smi7 = "C[N+]1=C2C=[N+]([O-])C=CN2CCC1";
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std::shared_ptr<ROMol> m7(SmilesToMol(smi7));
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ROMOL_SPTR normalized7(normalizer.normalize(*m7));
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TEST_ASSERT(MolToSmiles(*normalized7) == "C[N+]1=C2C=[N+]([O-])C=CN2CCC1");
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// Failed on 1k normalize test sanitizeMol step
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std::string smi8 = "O=c1cc([O-])[n+](C2OC(CO)C(O)C2O)c2sccn12";
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std::shared_ptr<ROMol> m8(SmilesToMol(smi8));
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ROMOL_SPTR normalized8(normalizer.normalize(*m8));
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TEST_ASSERT(MolToSmiles(*normalized8) ==
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"O=c1cc([O-])[n+](C2OC(CO)C(O)C2O)c2sccn12");
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BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
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}
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int main() {
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test1();
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return 0;
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}
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