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rdkit/Code/GraphMol/ChemTransforms/testChemTransforms.cpp
Greg Landrum 1d40302dcb This builds and tests correctly with msvc8. Linux and msvc7 tests are still required. 
The primary changes consist of cleaning up edge cases that lead to memory errors (under VC8 with debugging turned out)
2008-02-16 05:25:53 +00:00

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// $Id$
//
// Copyright (C) 2006 Greg Landrum
//
// @@ All Rights Reserved @@
//
#include <RDGeneral/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include <string>
#include <iostream>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/ChemTransforms/ChemTransforms.h>
#include <GraphMol/FileParsers/FileParsers.h>
using namespace RDKit;
void testDeleteSubstruct()
{
int i = 0;
ROMol *mol1=0,*mol2=0,*matcher1=0,*matcher2=0,*matcher3=0;
std::string smi,sma;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing deleteSubstruct" << std::endl;
// a lot of the seemingly repetitive stuff is here for Issue96
smi = "CCC(=O).C=O";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
TEST_ASSERT(mol1->getNumAtoms()==6)
sma = "C=O";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
mol2 = deleteSubstructs(*mol1,*matcher1,0);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==2)
mol2 = deleteSubstructs(*mol2,*matcher1,0);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==2)
delete matcher1;
sma = "[Cl;H1&X1,-]";
matcher1 = SmartsToMol(sma);
sma = "[Na+]";
matcher2 = SmartsToMol(sma);
sma = "[O;H2,H1&-,X0&-2]";
matcher3 = SmartsToMol(sma);
delete mol1;
mol1 = SmilesToMol("CCO.Cl");
TEST_ASSERT(mol1);
TEST_ASSERT(mol1->getNumAtoms()==4);
delete mol2;
mol2 = deleteSubstructs(*mol1,*matcher1,true);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==3);
mol2 = deleteSubstructs(*mol2,*matcher2,true);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==3);
mol2 = deleteSubstructs(*mol2,*matcher3,true);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==3);
delete mol1;
mol1 = SmilesToMol("CC(=O)[O-].[Na+]");
TEST_ASSERT(mol1);
TEST_ASSERT(mol1->getNumAtoms()==5);
delete matcher1;
matcher1 = SmartsToMol("[Cl;H1&X1,-]");
delete matcher2;
matcher2 = SmartsToMol("[Na+]");
mol2 = deleteSubstructs(*mol1,*matcher1,true);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==5);
mol2 = deleteSubstructs(*mol2,*matcher2,true);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==4);
mol2 = deleteSubstructs(*mol2,*matcher1,true);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==4);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testReplaceSubstructs()
{
int i = 0;
ROMol *mol1=0,*mol2=0,*matcher1=0,*frag=0;
std::string smi,sma;
std::vector<ROMOL_SPTR> vect;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing replaceSubstruct" << std::endl;
smi = "CCCC";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
sma = "C(=O)O";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
smi = "N";
frag = SmilesToMol(smi);
TEST_ASSERT(frag);
vect = replaceSubstructs(*mol1,*matcher1,*frag);
TEST_ASSERT(vect.size()==1);
TEST_ASSERT(mol1->getNumAtoms()==4);
TEST_ASSERT(vect[0]->getNumAtoms()==4);
delete mol1;
smi = "CCCC(=O)O";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
vect = replaceSubstructs(*mol1,*matcher1,*frag);
TEST_ASSERT(vect.size()==1);
TEST_ASSERT(mol1->getNumAtoms()==6);
TEST_ASSERT(vect[0]->getNumAtoms()==4);
vect = replaceSubstructs(*mol1,*matcher1,*frag,true);
TEST_ASSERT(vect.size()==1);
TEST_ASSERT(mol1->getNumAtoms()==6);
TEST_ASSERT(vect[0]->getNumAtoms()==4);
delete mol1;
smi = "OC(=O)CCCC(=O)O";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
vect = replaceSubstructs(*mol1,*matcher1,*frag);
TEST_ASSERT(vect.size()==2);
TEST_ASSERT(mol1->getNumAtoms()==9);
TEST_ASSERT(vect[0]->getNumAtoms()==7);
TEST_ASSERT(vect[1]->getNumAtoms()==7);
// use replaceAll when a single replacement is available:
vect = replaceSubstructs(*mol1,*matcher1,*frag,true);
TEST_ASSERT(vect.size()==1);
TEST_ASSERT(mol1->getNumAtoms()==9);
TEST_ASSERT(vect[0]->getNumAtoms()==5);
delete matcher1;
sma = "C=O";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
delete mol1;
smi = "CC(=O)C";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
vect = replaceSubstructs(*mol1,*matcher1,*frag);
TEST_ASSERT(vect.size()==1);
TEST_ASSERT(mol1->getNumAtoms()==4);
TEST_ASSERT(vect[0]->getNumAtoms()==3);
delete mol1;
smi = "C1C(=O)C1";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
vect = replaceSubstructs(*mol1,*matcher1,*frag);
TEST_ASSERT(vect.size()==1);
TEST_ASSERT(mol1->getNumAtoms()==4);
TEST_ASSERT(vect[0]->getNumAtoms()==3);
TEST_ASSERT(vect[0]->getNumBonds()==3);
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testReplaceSidechains()
{
int i = 0;
ROMol *mol1=0,*mol2=0,*matcher1=0;
std::string smi,sma;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing replaceSidechains" << std::endl;
smi = "ClC1CC(F)C1";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
sma = "C1CCC1";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
mol2 = replaceSidechains(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==6);
delete mol1;
smi = "ClC1C(F)C1";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
mol2 = replaceSidechains(*mol1,*matcher1);
TEST_ASSERT(!mol2);
delete matcher1;
sma = "C=O";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
delete mol1;
smi = "CC=O";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete mol2;
mol2 = replaceSidechains(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==3);
smi = MolToSmiles(*mol2);
TEST_ASSERT(smi=="[Xa]C=O");
delete mol1;
smi = "CC(C)=O";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete mol2;
mol2 = replaceSidechains(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==4);
smi = MolToSmiles(*mol2);
// there's no way to guarantee the order here:
TEST_ASSERT(smi=="[Xa]C([Xb])=O"||smi=="[Xb]C([Xa])=O");
delete mol1;
delete mol2;
delete matcher1;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testReplaceCore()
{
int i = 0;
ROMol *mol1=0,*mol2=0,*matcher1=0;
std::string smi,sma;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing replaceCore" << std::endl;
smi = "ClC1CC(F)C1";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
sma = "C1CCC1";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==4);
smi = MolToSmiles(*mol2);
// there's no way to guarantee the order here:
TEST_ASSERT(smi=="[Xa]F.Cl[Xb]"||smi=="[Xb]F.Cl[Xa]");
delete mol1;
smi = "CCC=O";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete matcher1;
sma = "C=O";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==3);
smi = MolToSmiles(*mol2);
TEST_ASSERT(smi=="[Xa]CC");
delete mol1;
smi = "C1C(=O)CC1";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete matcher1;
sma = "C=O";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==5);
smi = MolToSmiles(*mol2);
// there's no way to guarantee the order here:
TEST_ASSERT(smi=="[Xa]CCC[Xb]"||smi=="[Xb]CCC[Xa]");
delete mol1;
smi = "CNC";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete matcher1;
sma = "N";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==4);
smi = MolToSmiles(*mol2);
// there's no way to guarantee the order here:
TEST_ASSERT(smi=="[Xa]C.[Xb]C"||smi=="[Xb]C.[Xa]C");
delete mol1;
smi = "OC1CCC1";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete matcher1;
sma = "[CH2][CH2][CH2]";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
smi = MolToSmiles(*mol2);
TEST_ASSERT(mol2->getNumAtoms()==4);
smi = MolToSmiles(*mol2);
// there's no way to guarantee the order here:
TEST_ASSERT(smi=="[Xb]C([Xa])O"||smi=="[Xa]C([Xb])O");
delete mol1;
smi = "C/C=C/CN/C=C/O";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete matcher1;
sma = "N";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==9);
smi = MolToSmiles(*mol2,true);
// there's no way to guarantee the order here:
TEST_ASSERT(smi=="[Xa]C/C=C/C.O/C=C/[Xb]"||smi=="[Xb]C/C=C/C.O/C=C/[Xa]"||
smi=="[Xa]/C=C/O.C/C=C/C[Xb]"||smi=="[Xb]/C=C/O.C/C=C/C[Xa]");
delete mol1;
smi = "C[C@](F)(Cl)N";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete matcher1;
sma = "N";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==5);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(smi=="[Xa][C@@](C)(F)Cl");
delete mol1;
smi = "C[C@](F)(N)Cl";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==5);
smi = MolToSmiles(*mol2,true);
BOOST_LOG(rdInfoLog)<<"smiles: "<<smi <<std::endl;
TEST_ASSERT(smi=="[Xa][C@](C)(F)Cl");
delete mol1;
smi = "N[C@](C)(F)Cl";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==5);
smi = MolToSmiles(*mol2,true);
BOOST_LOG(rdInfoLog)<<"smiles: "<<smi <<std::endl;
TEST_ASSERT(smi=="[Xa][C@](C)(F)Cl");
delete mol1;
smi = "C[C@@](F)(Cl)N";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete matcher1;
sma = "N";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==5);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(smi=="[Xa][C@](C)(F)Cl");
delete mol1;
smi = "C[C@@](F)(N)Cl";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==5);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(smi=="[Xa][C@@](C)(F)Cl");
smi = "C[C@@](N)(Cl)F";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==5);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(smi=="[Xa][C@@](C)(F)Cl");
delete mol1;
smi = "C[C@H](F)N";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete matcher1;
sma = "N";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==4);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(smi=="[Xa][C@H](C)F");
delete mol1;
smi = "C[C@H](N)F";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==4);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(smi=="[Xa][C@@H](C)F");
delete mol1;
smi = "N[C@H](C)F";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==4);
smi = MolToSmiles(*mol2,true);
BOOST_LOG(rdInfoLog)<<"smiles: "<<smi <<std::endl;
TEST_ASSERT(smi=="[Xa][C@H](C)F");
delete mol1;
smi = "F[C@H](C)N";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==4);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(smi=="[Xa][C@@H](C)F");
delete mol1;
smi = "N[C@H]1CCCO1";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete mol2;
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==6);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(smi=="[Xa][C@@H]1OCCC1");
delete mol1;
smi = "ClC1CC(F)C1";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
delete matcher1;
sma = "[*]C1CC([*])C1";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
mol2 = replaceCore(*mol1,*matcher1,false);
TEST_ASSERT(mol2);
smi = MolToSmiles(*mol2);
BOOST_LOG(rdInfoLog)<<"smiles: "<<smi <<std::endl;
TEST_ASSERT(mol2->getNumAtoms()==4);
smi = MolToSmiles(*mol2);
// there's no way to guarantee the order here:
TEST_ASSERT(smi=="[Xa]F.Cl[Xb]"||smi=="[Xb]F.Cl[Xa]");
delete mol1;
delete mol2;
delete matcher1;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testReplaceCoreCrash()
{
int i = 0;
ROMol *mol1=0,*mol2=0,*matcher1=0;
std::string smi,sma;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing a former crash in replaceCore" << std::endl;
mol1 = MolFileToMol("testData/oldcrash.mol");
TEST_ASSERT(mol1);
sma = "N";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==6);
smi = MolToSmiles(*mol2);
// there's no way to guarantee the order here:
TEST_ASSERT(smi=="[Xa]CC.[Xb]CC"||smi=="[Xb]CC.[Xa]CC");
}
int main() {
RDLog::InitLogs();
BOOST_LOG(rdInfoLog) << "********************************************************\n";
BOOST_LOG(rdInfoLog) << "Testing Chemical Transforms \n";
#if 1
testDeleteSubstruct();
testReplaceSubstructs();
testReplaceSidechains();
#endif
testReplaceCore();
testReplaceCoreCrash();
BOOST_LOG(rdInfoLog) << "*******************************************************\n";
return(0);
}
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