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rdkit/Code/GraphMol/ChemTransforms/testChemTransforms.cpp
Greg Landrum f3fbef45c5 update copyright statements
2010-09-26 17:04:37 +00:00

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// $Id$
//
// Copyright (C) 2006 Greg Landrum
//
// @@ 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 <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()
{
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()
{
ROMol *mol1=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()
{
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,true);
TEST_ASSERT(smi=="[1*]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,true);
// there's no way to guarantee the order here:
TEST_ASSERT(smi=="[1*]C([2*])=O"||smi=="[2*]C([1*])=O");
delete mol1;
delete mol2;
delete matcher1;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testReplaceCore()
{
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 = "C1CC1";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(!mol2);
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,true);
// there's no way to guarantee the order here:
TEST_ASSERT(smi=="[1*]Cl.[2*]F"||smi=="[2*]Cl.[1*]F");
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,true);
TEST_ASSERT(smi=="[1*]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,true);
// there's no way to guarantee the order here:
TEST_ASSERT(smi=="[1*]CCC[2*]"||smi=="[1*]CCC[2*]");
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,true);
// there's no way to guarantee the order here:
TEST_ASSERT(smi=="[1*]C.[2*]C"||smi=="[2*]C.[1*]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,true);
TEST_ASSERT(mol2->getNumAtoms()==4);
smi = MolToSmiles(*mol2,true);
// there's no way to guarantee the order here:
TEST_ASSERT(smi=="[2*]C([1*])O"||smi=="[1*]C([2*])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=="[1*]C/C=C/C.[2*]/C=C/O"||smi=="[1*]/C=C/O.[2*]C/C=C/C");
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=="[1*][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=="[1*][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);
TEST_ASSERT(smi=="[1*][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=="[1*][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=="[1*][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=="[1*][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=="[1*][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=="[1*][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);
TEST_ASSERT(smi=="[1*][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=="[1*][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=="[1*][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,true);
TEST_ASSERT(mol2->getNumAtoms()==4);
smi = MolToSmiles(*mol2,true);
// there's no way to guarantee the order here:
TEST_ASSERT(smi=="[1*]F.[2*]Cl"||smi=="[1*]Cl.[2*]F");
delete mol1;
delete mol2;
delete matcher1;
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testReplaceCoreLabels()
{
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing replaceCore with labels" << std::endl;
{
std::string sma = "n1cocc1";
ROMol *matcher = SmartsToMol(sma);
TEST_ASSERT(matcher);
std::string smi = "n1c(CC)oc(C)c1";
ROMol *mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
ROMol *mol2 = replaceCore(*mol1,*matcher,true,true);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==5);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(smi=="[1*]CC.[3*]C");
delete mol1;
delete mol2;
delete matcher;
}
{
std::string sma = "n1cocc1";
ROMol *matcher = SmartsToMol(sma);
TEST_ASSERT(matcher);
std::string smi = "n1c(C)oc(CC)c1";
ROMol *mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
ROMol *mol2 = replaceCore(*mol1,*matcher,true,true);
TEST_ASSERT(mol2);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(smi=="[1*]C.[3*]CC");
delete mol1;
delete mol2;
delete matcher;
}
{
std::string sma = "n1cocc1";
ROMol *matcher = SmartsToMol(sma);
TEST_ASSERT(matcher);
std::string smi = "CCC1=C(OC)N=C(C)O1";
ROMol *mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
ROMol *mol2 = replaceCore(*mol1,*matcher,true,true);
TEST_ASSERT(mol2);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(smi=="[1*]C.[3*]CC.[4*]OC");
delete mol1;
delete mol2;
delete matcher;
}
{
std::string sma = "n1cocc1";
ROMol *matcher = SmartsToMol(sma);
TEST_ASSERT(matcher);
std::string smi = "C1=C(OC)N=CO1";
ROMol *mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
ROMol *mol2 = replaceCore(*mol1,*matcher,true,true);
TEST_ASSERT(mol2);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(smi=="[4*]OC");
delete mol1;
delete mol2;
delete matcher;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testReplaceCoreCrash()
{
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;
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ChemTransforms/testData/oldcrash.mol";
mol1 = MolFileToMol(pathName);
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,true);
// there's no way to guarantee the order here:
TEST_ASSERT(smi=="[1*]CC.[2*]CC"||smi=="[2*]CC.[1*]CC");
}
int main() {
RDLog::InitLogs();
BOOST_LOG(rdInfoLog) << "********************************************************\n";
BOOST_LOG(rdInfoLog) << "Testing Chemical Transforms \n";
#if 1
testDeleteSubstruct();
testReplaceSubstructs();
testReplaceSidechains();
#endif
testReplaceCore();
testReplaceCoreLabels();
testReplaceCoreCrash();
BOOST_LOG(rdInfoLog) << "*******************************************************\n";
return(0);
}
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