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//
// Copyright (C) 2018 Susan H. Leung
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h>
#include <GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h>
#include "Normalize.h"
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <RDGeneral/FileParseException.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/MolStandardize/MolStandardize.h>
#include <iostream>
#include <fstream>
using namespace RDKit;
using namespace MolStandardize;
void test1() {
BOOST_LOG(rdInfoLog) << "-----------------------\n test1" << std::endl;
std::string smi1, smi2, smi3, smi4, smi5, smi6, smi7;
Normalizer normalizer;
// Test sulfoxide normalization.
smi1 = "CS(C)=O";
std::shared_ptr<ROMol> m1(SmilesToMol(smi1));
ROMOL_SPTR normalized(normalizer.normalize(*m1));
TEST_ASSERT(MolToSmiles(*normalized) == "C[S+](C)[O-]");
// Test sulfone
smi2 = "C[S+2]([O-])([O-])O";
std::shared_ptr<ROMol> m2(SmilesToMol(smi2));
ROMOL_SPTR normalized2(normalizer.normalize(*m2));
TEST_ASSERT(MolToSmiles(*normalized2) == "CS(=O)(=O)O");
// Test 1,3-separated charges are recombined.
smi3 = "CC([O-])=[N+](C)C";
std::shared_ptr<ROMol> m3(SmilesToMol(smi3));
ROMOL_SPTR normalized3(normalizer.normalize(*m3));
TEST_ASSERT(MolToSmiles(*normalized3) == "CC(=O)N(C)C");
// Test 1,3-separated charges are recombined.
smi4 = "C[n+]1ccccc1[O-]";
std::shared_ptr<ROMol> m4(SmilesToMol(smi4));
ROMOL_SPTR normalized4(normalizer.normalize(*m4));
TEST_ASSERT(MolToSmiles(*normalized4) == "Cn1ccccc1=O");
// Test a case where 1,3-separated charges should not be recombined.
smi5 = "CC12CCCCC1(Cl)[N+]([O-])=[N+]2[O-]";
std::shared_ptr<ROMol> m5(SmilesToMol(smi5));
ROMOL_SPTR normalized5(normalizer.normalize(*m5));
TEST_ASSERT(MolToSmiles(*normalized5) ==
"CC12CCCCC1(Cl)[N+]([O-])=[N+]2[O-]");
// Test 1,5-separated charges are recombined.
smi6 = R"(C[N+](C)=C\C=C\[O-])";
std::shared_ptr<ROMol> m6(SmilesToMol(smi6));
ROMOL_SPTR normalized6(normalizer.normalize(*m6));
TEST_ASSERT(MolToSmiles(*normalized6) == "CN(C)C=CC=O");
// Test a case where 1,5-separated charges should not be recombined.
smi7 = "C[N+]1=C2C=[N+]([O-])C=CN2CCC1";
std::shared_ptr<ROMol> m7(SmilesToMol(smi7));
ROMOL_SPTR normalized7(normalizer.normalize(*m7));
TEST_ASSERT(MolToSmiles(*normalized7) == "C[N+]1=C2C=[N+]([O-])C=CN2CCC1");
// Failed on 1k normalize test sanitizeMol step
std::string smi8 = "O=c1cc([O-])[n+](C2OC(CO)C(O)C2O)c2sccn12";
std::shared_ptr<ROMol> m8(SmilesToMol(smi8));
ROMOL_SPTR normalized8(normalizer.normalize(*m8));
TEST_ASSERT(MolToSmiles(*normalized8) ==
"O=c1cc([O-])[n+](C2OC(CO)C(O)C2O)c2sccn12");
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
int main() {
test1();
return 0;
}
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