pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-04 21:54:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
e5d76df3bc222d4cd4e35f09a4cf442b6f4fe584
rdkit/Code/GraphMol/ChemTransforms/testChemTransforms.cpp
Greg Landrum e5d76df3bc add a test
2007-08-03 03:55:13 +00:00

540 lines
13 KiB
C++
Raw Blame History

// $Id$
//
// 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);
//std::cerr <<"MOL: " << smi << std::endl;
// 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]");
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");
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=="[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);
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;
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);
}
Reference in New Issue View Git Blame Copy Permalink