pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-05 22:04:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
2a754639594a94de64080795b6cb72b942911101
rdkit/Code/GraphMol/ChemTransforms/testChemTransforms.cpp
Nadine Schneider 5d963846b8 merge
2015-04-10 09:44:18 +02:00

1617 lines
45 KiB
C++
Raw Blame History

// $Id$
//
// Copyright (C) 2006-2015 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 <RDGeneral/utils.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>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <RDGeneral/Exceptions.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 testReplaceSubstructs2()
{
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "More testing of replaceSubstruct" << std::endl;
{
std::string smi = "CCC(=O)O";
ROMol *mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
std::string sma = "[$(O-C(=O))]";
ROMol *matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
std::string repl = "NC";
ROMol *frag = SmilesToMol(repl);
TEST_ASSERT(frag);
std::vector<ROMOL_SPTR> vect=replaceSubstructs(*mol1,*matcher1,*frag);
TEST_ASSERT(vect.size()==1);
TEST_ASSERT(mol1->getNumAtoms()==5);
TEST_ASSERT(vect[0]->getNumAtoms()==6);
std::string csmi1 = MolToSmiles(*vect[0],true);
repl = "CN";
delete frag;
frag = SmilesToMol(repl);
TEST_ASSERT(frag);
vect=replaceSubstructs(*mol1,*matcher1,*frag,true,1);
TEST_ASSERT(vect.size()==1);
TEST_ASSERT(mol1->getNumAtoms()==5);
TEST_ASSERT(vect[0]->getNumAtoms()==6);
std::string csmi2 = MolToSmiles(*vect[0],true);
TEST_ASSERT(csmi2==csmi1);
delete mol1;
delete matcher1;
}
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]1CCCO1");
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");
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testReplaceCorePositions()
{
ROMol *mol1=0,*mol2=0,*matcher1=0;
std::string smi,sma;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing that atom positions are correctly copied by replaceCore" << std::endl;
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ChemTransforms/testData/core_location.mol";
mol1 = MolFileToMol(pathName);
TEST_ASSERT(mol1);
TEST_ASSERT(mol1->getNumAtoms()==8);
sma = "c1ccccc1";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
mol2 = replaceCore(*mol1,*matcher1);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==4);
RDGeom::Point3D op,np;
op = mol1->getConformer().getAtomPos(6);
np = mol2->getConformer().getAtomPos(0);
TEST_ASSERT(feq(op.x,np.x));
TEST_ASSERT(feq(op.y,np.y));
TEST_ASSERT(feq(op.z,np.z));
op = mol1->getConformer().getAtomPos(7);
np = mol2->getConformer().getAtomPos(1);
TEST_ASSERT(feq(op.x,np.x));
TEST_ASSERT(feq(op.y,np.y));
TEST_ASSERT(feq(op.z,np.z));
op = mol1->getConformer().getAtomPos(0);
np = mol2->getConformer().getAtomPos(2);
TEST_ASSERT(feq(op.x,np.x));
TEST_ASSERT(feq(op.y,np.y));
TEST_ASSERT(feq(op.z,np.z));
op = mol1->getConformer().getAtomPos(4);
np = mol2->getConformer().getAtomPos(3);
TEST_ASSERT(feq(op.x,np.x));
TEST_ASSERT(feq(op.y,np.y));
TEST_ASSERT(feq(op.z,np.z));
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testMurckoDecomp()
{
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing murcko decomposition" << std::endl;
const char *testMolecules[][2]=
{
{"C1CC1CCC1CC(C)C1", "C1CC1CCC1CCC1"},
{"CC1CCC1", "C1CCC1"},
{"NCNCC2CC2C1CC1O", "C1CC1C1CC1"},
{"OC2C(C)C21C(N)C1C", "C2CC12CC1"}, // Spiro
{"C1CC1C(=O)OC", "C1CC1"}, // Carbonyl outside scaffold
{"C1CC1C=C", "C1CC1"}, // Double bond outside scaffold
{"C1CC1C=CC1CC1C=CNNCO", "C1CC1C=CC1CC1"}, // Double bond in scaffold
{"CC1CC1C(N)C1C(N)C1", "C1CC1CC1CC1"},
{"C1CC1S(=O)C1CC1C=CNNCO", "C1CC1S(=O)C1CC1"}, // S=O group in scaffold
{"O=SCNC1CC1S(=O)C1CC1C=CNNCO", "C1CC1S(=O)C1CC1"}, // S=O group outside scaffold
{"C1CC1S(=O)(=O)C1CC1C=CNNCO", "C1CC1S(=O)(=O)C1CC1"}, // SO2 group in scaffold
{"O=S(CNCNC)(=O)CNC1CC1S(=O)(=O)C1CC1C=CNNCO", "C1CC1S(=O)(=O)C1CC1"}, // SO2 group outside scaffold
{"C1CC1C=NO","C1CC1"}, //Hydroxamide
{"C1CC1C(C(C)C)=NC1CC1","C1CC1C=NC1CC1"}, //Hydroxamide
{"C1CC1C#N","C1CC1"}, //Cyano group
{"C1CC1C#CNC","C1CC1"}, //Acetylene group
{"O=C1N(C)C(=O)N1C#CNC","O=C1NC(=O)N1"}, //Acetylene group
{"[O-][N+](=O)c1cc(ccc1Cl)NS(=O)(=O)Cc2ccccc2","c1ccccc1NS(=O)(=O)Cc2ccccc2"},
{"Cn1cccc1", "c1ccc[nH]1"},
{"C1CC1[CH](C)C1CC1", "C1CC1CC1CC1"},
{"CC(C)c1c(Cl)cc(F)c(Nc2ccc(C)cc2CC(=O)O)c1F","c1ccc(Nc2ccccc2)cc1"},
{"C1CC1C[C@](Cl)(F)C1CCC1","C1CC1CCC1CCC1"},
{"C1CC1.C1CC1", "C1CC1.C1CC1"}, // this was a crash at one point
{"CCC", ""},
{"EOS","EOS"}
};
unsigned int i=0;
while(1){
std::string smi=testMolecules[i][0];
std::string tgt=testMolecules[i][1];
++i;
if(smi=="EOS") break;
ROMol *mol=SmilesToMol(smi);
ROMol *nMol=MurckoDecompose(*mol);
TEST_ASSERT(nMol);
delete mol;
if(tgt!=""){
TEST_ASSERT(nMol->getNumAtoms());
MolOps::sanitizeMol(static_cast<RWMol &>(*nMol));
smi = MolToSmiles(*nMol,true);
mol = SmilesToMol(tgt);
TEST_ASSERT(mol);
tgt=MolToSmiles(*mol,true);
delete mol;
TEST_ASSERT(smi==tgt);
} else {
TEST_ASSERT(nMol->getNumAtoms()==0);
}
delete nMol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testReplaceCoreRequireDummies()
{
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing replaceCore requiring dummy atoms" << std::endl;
{
std::string sma = "n1c(*)oc(*)c1";
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,false,true,false);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms()==5);
smi = MolToSmiles(*mol2,true);
TEST_ASSERT(smi=="[1*]CC.[4*]C");
delete mol1;
delete mol2;
smi = "n1c(CC)oc(C)c1C";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
mol2 = replaceCore(*mol1,*matcher,false,true,true);
TEST_ASSERT(!mol2);
delete mol1;
smi = "n1c(CC)occ1C";
mol1 = SmilesToMol(smi);
TEST_ASSERT(mol1);
mol2 = replaceCore(*mol1,*matcher,false,true,true);
TEST_ASSERT(!mol2);
delete mol1;
delete matcher;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue3453144()
{
ROMol *mol1=0,*matcher1=0,*replacement=0;
std::string smi,sma;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing that atom positions are correctly copied by replaceSubstructs" << std::endl;
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ChemTransforms/testData/ethanol.mol";
mol1 = MolFileToMol(pathName);
TEST_ASSERT(mol1);
TEST_ASSERT(mol1->getNumAtoms()==3);
sma = "O";
matcher1 = SmartsToMol(sma);
TEST_ASSERT(matcher1);
smi="N";
replacement = SmilesToMol(smi);
TEST_ASSERT(replacement);
std::vector<ROMOL_SPTR> rs;
rs = replaceSubstructs(*mol1,*matcher1,*replacement);
TEST_ASSERT(rs.size()==1);
TEST_ASSERT(rs[0]->getNumAtoms()==3);
TEST_ASSERT(rs[0]->getAtomWithIdx(2)->getAtomicNum()==7);
TEST_ASSERT(rs[0]->getNumConformers()==mol1->getNumConformers());
RDGeom::Point3D op,np;
op = mol1->getConformer().getAtomPos(0);
np = rs[0]->getConformer().getAtomPos(0);
TEST_ASSERT(feq(op.x,np.x));
TEST_ASSERT(feq(op.y,np.y));
TEST_ASSERT(feq(op.z,np.z));
op = mol1->getConformer().getAtomPos(1);
np = rs[0]->getConformer().getAtomPos(1);
TEST_ASSERT(feq(op.x,np.x));
TEST_ASSERT(feq(op.y,np.y));
TEST_ASSERT(feq(op.z,np.z));
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue3537675()
{
std::string smi,sma;
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing handling of substituted non-carbon aromatic atoms" << std::endl;
{
std::string smi = "c1cccp1C";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
ROMol *nMol=MurckoDecompose(*mol);
TEST_ASSERT(nMol->getAtomWithIdx(4)->getNumExplicitHs());
delete mol;
delete nMol;
}
{
std::string smi = "c1cccn1C";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
ROMol *nMol=MurckoDecompose(*mol);
TEST_ASSERT(nMol->getAtomWithIdx(4)->getNumExplicitHs());
delete mol;
delete nMol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testCombineMols()
{
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing combination of molecules" << std::endl;
{
std::string smi1="C1CCC1";
std::string smi2="C1CC1";
ROMol *mol1=SmilesToMol(smi1);
ROMol *mol2=SmilesToMol(smi2);
ROMol *mol3=combineMols(*mol1,*mol2);
TEST_ASSERT(mol3->getNumAtoms()==(mol1->getNumAtoms()+mol2->getNumAtoms()));
MolOps::findSSSR(*mol3);
TEST_ASSERT(mol3->getRingInfo()->numRings()==2);
}
{
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ChemTransforms/testData/ethanol.mol";
ROMol *mol1 = MolFileToMol(pathName);
TEST_ASSERT(mol1);
ROMol *mol2 = MolFileToMol(pathName);
TEST_ASSERT(mol2);
TEST_ASSERT(mol1->getNumAtoms()==3);
TEST_ASSERT(mol2->getNumAtoms()==3);
ROMol *mol3=combineMols(*mol1,*mol2);
TEST_ASSERT(mol3->getNumAtoms()==(mol1->getNumAtoms()+mol2->getNumAtoms()));
TEST_ASSERT(mol3->getNumConformers()==1);
TEST_ASSERT(feq(mol3->getConformer().getAtomPos(0).x,
mol3->getConformer().getAtomPos(3).x));
TEST_ASSERT(feq(mol3->getConformer().getAtomPos(0).y,
mol3->getConformer().getAtomPos(3).y));
TEST_ASSERT(feq(mol3->getConformer().getAtomPos(0).z,
mol3->getConformer().getAtomPos(3).z));
delete mol3;
mol3=combineMols(*mol1,*mol2,RDGeom::Point3D(1,0,0));
TEST_ASSERT(mol3->getNumAtoms()==(mol1->getNumAtoms()+mol2->getNumAtoms()));
TEST_ASSERT(mol3->getNumConformers()==1);
TEST_ASSERT(!feq(mol3->getConformer().getAtomPos(0).x,
mol3->getConformer().getAtomPos(3).x));
TEST_ASSERT(feq(mol3->getConformer().getAtomPos(0).y,
mol3->getConformer().getAtomPos(3).y));
TEST_ASSERT(feq(mol3->getConformer().getAtomPos(0).z,
mol3->getConformer().getAtomPos(3).z));
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testAddRecursiveQueries()
{
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing adding recursive queries to a molecule" << std::endl;
{
std::string smi1="CC";
ROMol *mol1=SmilesToMol(smi1);
std::string smi2="CO";
ROMOL_SPTR q1(SmilesToMol(smi2));
std::map<std::string,ROMOL_SPTR> mp;
mp["foo"]=q1;
TEST_ASSERT(!mol1->getAtomWithIdx(0)->hasQuery());
addRecursiveQueries(*mol1,mp,"replaceme");
TEST_ASSERT(!mol1->getAtomWithIdx(0)->hasQuery());
mol1->getAtomWithIdx(0)->setProp("replaceme","foo");
addRecursiveQueries(*mol1,mp,"replaceme");
TEST_ASSERT(mol1->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(mol1->getAtomWithIdx(0)->getQuery()->getDescription()=="AtomAnd");
TEST_ASSERT(!mol1->getAtomWithIdx(1)->hasQuery());
mol1->getAtomWithIdx(0)->setProp("replaceme","bar");
bool ok=false;
try{
addRecursiveQueries(*mol1,mp,"replaceme");
} catch (KeyErrorException &e) {
ok=true;
}
TEST_ASSERT(ok);
delete mol1;
}
{
std::string smi1="CC";
ROMol *mol1=SmilesToMol(smi1);
std::string smi2="CO";
ROMOL_SPTR q1(SmilesToMol(smi2));
std::map<std::string,ROMOL_SPTR> mp;
mp["foo"]=q1;
std::vector<std::pair<unsigned int, std::string> > labels;
mol1->getAtomWithIdx(0)->setProp("replaceme","foo");
addRecursiveQueries(*mol1,mp,"replaceme", &labels);
TEST_ASSERT(mol1->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(labels.size()==1);
delete mol1;
}
{
std::string smi1="CC";
ROMol *mol1=SmilesToMol(smi1);
std::string smi2="CO";
ROMOL_SPTR q1(SmilesToMol(smi2));
std::map<std::string,ROMOL_SPTR> mp;
mp["foo"]=q1;
smi2="OC";
ROMOL_SPTR q2(SmilesToMol(smi2));
mp["bar"]=q2;
std::vector<std::pair<unsigned int, std::string> > labels;
mol1->getAtomWithIdx(0)->setProp("replaceme","foo");
mol1->getAtomWithIdx(1)->setProp("replaceme","bar");
addRecursiveQueries(*mol1, mp, "replaceme", &labels);
TEST_ASSERT(mol1->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(mol1->getAtomWithIdx(1)->hasQuery());
TEST_ASSERT(mol1->getAtomWithIdx(0)->getQuery()->getDescription()=="AtomAnd");
TEST_ASSERT(mol1->getAtomWithIdx(1)->getQuery()->getDescription()=="AtomAnd");
TEST_ASSERT(labels.size()==2);
delete mol1;
}
{
std::string smi1="CC";
ROMol *mol1=SmilesToMol(smi1);
std::string smi2="CO";
ROMOL_SPTR q1(SmilesToMol(smi2));
std::map<std::string,ROMOL_SPTR> mp;
mp["foo"]=q1;
smi2="CN";
ROMOL_SPTR q2(SmilesToMol(smi2));
mp["bar"]=q2;
mol1->getAtomWithIdx(0)->setProp("replaceme","foo,bar");
addRecursiveQueries(*mol1, mp, "replaceme");
TEST_ASSERT(mol1->getAtomWithIdx(0)->hasQuery());
TEST_ASSERT(!mol1->getAtomWithIdx(1)->hasQuery());
TEST_ASSERT(mol1->getAtomWithIdx(0)->getQuery()->getDescription()=="AtomAnd");
MatchVectType mv;
std::string msmi="CCC";
ROMol *mmol=SmilesToMol(msmi);
TEST_ASSERT(mmol);
TEST_ASSERT(!SubstructMatch(*mmol,*mol1,mv));
delete mmol;
msmi="CCO";
mmol=SmilesToMol(msmi);
TEST_ASSERT(mmol);
TEST_ASSERT(SubstructMatch(*mmol,*mol1,mv));
delete mmol;
msmi="CCN";
mmol=SmilesToMol(msmi);
TEST_ASSERT(mmol);
TEST_ASSERT(SubstructMatch(*mmol,*mol1,mv));
delete mmol;
delete mol1;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testParseQueryDefFile()
{
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing parsing query definition file" << std::endl;
{
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ChemTransforms/testData/query_file1.txt";
std::map<std::string,ROMOL_SPTR> qdefs;
parseQueryDefFile(pathName,qdefs,false);
TEST_ASSERT(!qdefs.empty());
TEST_ASSERT(qdefs.size()==7);
TEST_ASSERT(qdefs.find("AcidChloride")!=qdefs.end());
TEST_ASSERT(qdefs.find("AcideChloride")==qdefs.end());
TEST_ASSERT(qdefs.find("AcidChloride.Aliphatic")!=qdefs.end());
TEST_ASSERT(qdefs.find("CarboxylicAcid.AlphaAmino")!=qdefs.end());
std::string msmi="CCC(=O)Cl";
ROMol *mmol=SmilesToMol(msmi);
TEST_ASSERT(mmol);
MatchVectType mv;
TEST_ASSERT(SubstructMatch(*mmol,*(qdefs["AcidChloride"]),mv));
delete mmol;
}
{
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ChemTransforms/testData/query_file2.txt";
std::map<std::string,ROMOL_SPTR> qdefs;
parseQueryDefFile(pathName,qdefs);
TEST_ASSERT(qdefs.empty());
}
/*{
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ChemTransforms/testData/query_file1.txt";
std::map<std::string, ROMOL_SPTR> qdefs;
parseQueryDefFile(pathName, qdefs);
TEST_ASSERT(!qdefs.empty());
TEST_ASSERT(qdefs.size()==7);
TEST_ASSERT(qdefs.find("acidchloride")!=qdefs.end());
TEST_ASSERT(qdefs.find("AcidChloride")==qdefs.end());
}*/
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testIssue275()
{
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing sf.net issue 275: Murcko decomposition with chiral atoms"<< std::endl;
{
std::string smi = "CCCCC[C@H]1CC[C@H](C(=O)O)CC1";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
ROMol *nMol=MurckoDecompose(*mol);
smi = MolToSmiles(*nMol,true);
TEST_ASSERT(smi=="C1CCCCC1");
delete mol;
delete nMol;
}
{
std::string smi = "CCCCC[C@H]1CC[C@H](C(=O)O)CC1";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
ROMol *nMol=MurckoDecompose(*mol);
smi = MolToSmiles(*nMol,false);
TEST_ASSERT(smi=="C1CCCCC1");
delete mol;
delete nMol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testFragmentOnBonds()
{
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing fragmentOnBonds"<< std::endl;
{
std::string smi = "OCCCN";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==5);
unsigned int indices[]={0,3};
std::vector<unsigned int> bindices(indices,indices+(sizeof(indices)/sizeof(indices[0])));
ROMol *nmol=MolFragmenter::fragmentOnBonds(*mol,bindices,false);
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms()==5);
delete mol;
delete nmol;
}
{
std::string smi = "OCCCN";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==5);
unsigned int indices[]={0,1};
std::vector<unsigned int> bindices(indices,indices+(sizeof(indices)/sizeof(indices[0])));
std::vector<unsigned int> cutsPerAtom(mol->getNumAtoms());
ROMol *nmol=MolFragmenter::fragmentOnBonds(*mol,bindices,false,0,0,&cutsPerAtom);
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms()==5);
TEST_ASSERT(cutsPerAtom[0]==1);
TEST_ASSERT(cutsPerAtom[1]==2);
TEST_ASSERT(cutsPerAtom[2]==1);
TEST_ASSERT(cutsPerAtom[3]==0);
delete mol;
delete nmol;
}
{
std::string smi = "OCCCN";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==5);
TEST_ASSERT(mol->getBondBetweenAtoms(0,1));
TEST_ASSERT(mol->getBondBetweenAtoms(3,4));
unsigned int indices[]={0,3};
std::vector<unsigned int> bindices(indices,indices+(sizeof(indices)/sizeof(indices[0])));
ROMol *nmol=MolFragmenter::fragmentOnBonds(*mol,bindices);
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms()==9);
TEST_ASSERT(!nmol->getBondBetweenAtoms(0,1));
TEST_ASSERT(!nmol->getBondBetweenAtoms(3,4));
TEST_ASSERT(nmol->getAtomWithIdx(5)->getAtomicNum()==0);
TEST_ASSERT(nmol->getAtomWithIdx(5)->getIsotope()==0);
TEST_ASSERT(nmol->getBondBetweenAtoms(1,5));
TEST_ASSERT(nmol->getAtomWithIdx(6)->getAtomicNum()==0);
TEST_ASSERT(nmol->getAtomWithIdx(6)->getIsotope()==1);
TEST_ASSERT(nmol->getBondBetweenAtoms(0,6));
TEST_ASSERT(nmol->getAtomWithIdx(7)->getAtomicNum()==0);
TEST_ASSERT(nmol->getAtomWithIdx(7)->getIsotope()==3);
TEST_ASSERT(nmol->getBondBetweenAtoms(4,7));
TEST_ASSERT(nmol->getAtomWithIdx(8)->getAtomicNum()==0);
TEST_ASSERT(nmol->getAtomWithIdx(8)->getIsotope()==4);
TEST_ASSERT(nmol->getBondBetweenAtoms(3,8));
delete mol;
delete nmol;
}
{
std::string smi = "OCCCN";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==5);
TEST_ASSERT(mol->getBondBetweenAtoms(0,1));
TEST_ASSERT(mol->getBondBetweenAtoms(3,4));
unsigned int indices[]={0,3};
std::vector<unsigned int> bindices(indices,indices+(sizeof(indices)/sizeof(indices[0])));
std::vector< std::pair<unsigned int,unsigned int> > dummyLabels(2);
dummyLabels[0] =std::make_pair(10,11);
dummyLabels[1] =std::make_pair(100,110);
ROMol *nmol=MolFragmenter::fragmentOnBonds(*mol,bindices,true,&dummyLabels);
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms()==9);
TEST_ASSERT(!nmol->getBondBetweenAtoms(0,1));
TEST_ASSERT(!nmol->getBondBetweenAtoms(3,4));
TEST_ASSERT(nmol->getAtomWithIdx(5)->getAtomicNum()==0);
TEST_ASSERT(nmol->getAtomWithIdx(5)->getIsotope()==10);
TEST_ASSERT(nmol->getBondBetweenAtoms(1,5));
TEST_ASSERT(nmol->getAtomWithIdx(6)->getAtomicNum()==0);
TEST_ASSERT(nmol->getAtomWithIdx(6)->getIsotope()==11);
TEST_ASSERT(nmol->getBondBetweenAtoms(0,6));
TEST_ASSERT(nmol->getAtomWithIdx(7)->getAtomicNum()==0);
TEST_ASSERT(nmol->getAtomWithIdx(7)->getIsotope()==100);
TEST_ASSERT(nmol->getBondBetweenAtoms(4,7));
TEST_ASSERT(nmol->getAtomWithIdx(8)->getAtomicNum()==0);
TEST_ASSERT(nmol->getAtomWithIdx(8)->getIsotope()==110);
TEST_ASSERT(nmol->getBondBetweenAtoms(3,8));
delete mol;
delete nmol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testFragmentOnBRICSBonds()
{
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing fragmentOnBRICSBonds"<< std::endl;
{
std::string smi = "c1ccccc1OC";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==8);
TEST_ASSERT(mol->getBondBetweenAtoms(5,6));
TEST_ASSERT(mol->getBondBetweenAtoms(6,7));
std::vector<MolFragmenter::FragmenterBondType> fbts;
MolFragmenter::constructBRICSBondTypes(fbts);
ROMol *nmol=MolFragmenter::fragmentOnBonds(*mol,fbts);
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms()==10);
TEST_ASSERT(!nmol->getBondBetweenAtoms(5,6));
TEST_ASSERT(nmol->getBondBetweenAtoms(6,7));
smi = MolToSmiles(*nmol,true);
TEST_ASSERT(smi=="[16*]c1ccccc1.[3*]OC");
TEST_ASSERT(nmol->getAtomWithIdx(8)->getAtomicNum()==0);
TEST_ASSERT(nmol->getAtomWithIdx(8)->getIsotope()==3);
TEST_ASSERT(nmol->getBondBetweenAtoms(6,8));
TEST_ASSERT(nmol->getAtomWithIdx(9)->getAtomicNum()==0);
TEST_ASSERT(nmol->getAtomWithIdx(9)->getIsotope()==16);
TEST_ASSERT(nmol->getBondBetweenAtoms(5,9));
delete mol;
delete nmol;
}
{
std::string smi = "c1ccccc1";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==6);
std::vector<MolFragmenter::FragmenterBondType> fbts;
MolFragmenter::constructBRICSBondTypes(fbts);
ROMol *nmol=MolFragmenter::fragmentOnBonds(*mol,fbts);
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms()==6);
smi = MolToSmiles(*nmol,true);
TEST_ASSERT(smi=="c1ccccc1");
delete mol;
delete nmol;
}
{
std::string smi = "OC(C)=CC";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==5);
std::vector<MolFragmenter::FragmenterBondType> fbts;
MolFragmenter::constructBRICSBondTypes(fbts);
ROMol *nmol=MolFragmenter::fragmentOnBonds(*mol,fbts);
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms()==7);
smi = MolToSmiles(*nmol,true);
TEST_ASSERT(smi=="[7*]=C(C)O.[7*]=CC");
delete mol;
delete nmol;
}
{
std::string smi = "c1ccccc1OC";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==8);
ROMol *nmol=MolFragmenter::fragmentOnBRICSBonds(*mol);
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms()==10);
smi = MolToSmiles(*nmol,true);
TEST_ASSERT(smi=="[16*]c1ccccc1.[3*]OC");
delete mol;
delete nmol;
}
{
std::string smi = "OC(C)=CC";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==5);
ROMol *nmol=MolFragmenter::fragmentOnBRICSBonds(*mol);
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms()==7);
smi = MolToSmiles(*nmol,true);
TEST_ASSERT(smi=="[7*]=C(C)O.[7*]=CC");
delete mol;
delete nmol;
}
{
std::string smi = "CCCOCCC(=O)c1ccccc1";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==14);
ROMol *nmol=MolFragmenter::fragmentOnBRICSBonds(*mol);
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms()==20);
smi = MolToSmiles(*nmol,true);
TEST_ASSERT(smi=="[16*]c1ccccc1.[3*]O[3*].[4*]CCC.[4*]CCC([6*])=O");
MolOps::sanitizeMol(static_cast<RWMol &>(*nmol));
smi = MolToSmiles(*nmol,true);
TEST_ASSERT(smi=="[16*]c1ccccc1.[3*]O[3*].[4*]CCC.[4*]CCC([6*])=O");
delete mol;
delete nmol;
}
{
std::string smi = "Cl.CC(=O)O[C@]1(c2ccccc2)CCN(C)[C@H]2CCCC[C@@H]21";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==22);
ROMol *nmol=MolFragmenter::fragmentOnBRICSBonds(*mol);
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms()==28);
smi = MolToSmiles(*nmol,true);
//std::cerr<<smi<<std::endl;
TEST_ASSERT(smi=="Cl.[1*]C(C)=O.[15*]C1([15*])CCN(C)[C@H]2CCCC[C@@H]21.[16*]c1ccccc1.[3*]O[3*]");
MolOps::sanitizeMol(static_cast<RWMol &>(*nmol));
smi = MolToSmiles(*nmol,true);
TEST_ASSERT(smi=="Cl.[1*]C(C)=O.[15*]C1([15*])CCN(C)[C@H]2CCCC[C@@H]21.[16*]c1ccccc1.[3*]O[3*]");
delete mol;
delete nmol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void benchFragmentOnBRICSBonds()
{
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing fragmentOnBRICSBonds"<< std::endl;
{
std::string pathName=getenv("RDBASE");
pathName += "/Regress/Data/mols.1000.sdf";
SDMolSupplier suppl(pathName);
while(!suppl.atEnd()){
ROMol *m=suppl.next();
ROMol *nmol=MolFragmenter::fragmentOnBRICSBonds(*m);
delete m;
delete nmol;
}
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testFragmentOnSomeBonds()
{
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing fragmentOnSomeBonds"<< std::endl;
{
std::string smi = "OCCCCN";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms());
unsigned int indices[]={0,2,4};
std::vector<unsigned int> bindices(indices,indices+(sizeof(indices)/sizeof(indices[0])));
std::vector<ROMOL_SPTR> frags;
MolFragmenter::fragmentOnSomeBonds(*mol,bindices,frags,2);
TEST_ASSERT(frags.size()==3);
std::vector<std::vector<int> > fragMap;
TEST_ASSERT(MolOps::getMolFrags(*frags[0],fragMap)==3);
TEST_ASSERT(fragMap.size()==3);
TEST_ASSERT(fragMap[0].size()==2);
TEST_ASSERT(fragMap[1].size()==4);
TEST_ASSERT(fragMap[2].size()==4);
TEST_ASSERT(MolOps::getMolFrags(*frags[1],fragMap)==3);
TEST_ASSERT(fragMap.size()==3);
TEST_ASSERT(fragMap[0].size()==2);
TEST_ASSERT(fragMap[1].size()==6);
TEST_ASSERT(fragMap[2].size()==2);
TEST_ASSERT(MolOps::getMolFrags(*frags[2],fragMap)==3);
TEST_ASSERT(fragMap.size()==3);
TEST_ASSERT(fragMap[0].size()==4);
TEST_ASSERT(fragMap[1].size()==4);
TEST_ASSERT(fragMap[2].size()==2);
delete mol;
}
{
std::string smi = "OCCCCN";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms());
unsigned int indices[]={0,2,4};
std::vector<unsigned int> bindices(indices,indices+(sizeof(indices)/sizeof(indices[0])));
std::vector<ROMOL_SPTR> frags;
std::vector<std::vector<unsigned int> > cpa;
MolFragmenter::fragmentOnSomeBonds(*mol,bindices,frags,2,false,NULL,NULL,&cpa);
TEST_ASSERT(frags.size()==3);
TEST_ASSERT(cpa.size()==3);
TEST_ASSERT(cpa[0].size()==mol->getNumAtoms());
TEST_ASSERT(cpa[1].size()==mol->getNumAtoms());
TEST_ASSERT(cpa[2].size()==mol->getNumAtoms());
delete mol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testGithubIssue429()
{
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing github issue 429: fragmentOnSomeBonds() should update implicit H count on aromatic heteroatoms when addDummies is False"<< std::endl;
{
std::string smi = "c1cccn1CC1CC1";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms());
unsigned int indices[]={4,5};
std::vector<unsigned int> bindices(indices,indices+(sizeof(indices)/sizeof(indices[0])));
std::vector<ROMOL_SPTR> frags;
MolFragmenter::fragmentOnSomeBonds(*mol,bindices,frags,1,false);
TEST_ASSERT(frags.size()==2);
std::vector<std::vector<int> > fragMap;
BOOST_FOREACH(ROMOL_SPTR romol,frags){
RWMol *rwmol=(RWMol *)(romol.get());
MolOps::sanitizeMol(*rwmol);
}
// we actually changed fragmentOnBonds(), check that too:
RWMol *nmol=(RWMol *)MolFragmenter::fragmentOnBonds(*mol,bindices,false);
MolOps::sanitizeMol(*nmol);
delete nmol;
delete mol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
void testGithubIssue430()
{
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing github issue 430: fragmentOnSomeBonds() crashes if bond list is empty"<< std::endl;
{
std::string smi = "c1cccn1CC1CC1";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms());
std::vector<unsigned int> bindices;
std::vector<ROMOL_SPTR> frags;
MolFragmenter::fragmentOnSomeBonds(*mol,bindices,frags,1,false);
TEST_ASSERT(frags.size()==0);
delete mol;
}
{
std::string smi = "c1cccn1CC1CC1";
RWMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms());
unsigned int indices[]={4,5};
std::vector<unsigned int> bindices(indices,indices+(sizeof(indices)/sizeof(indices[0])));
std::vector<ROMOL_SPTR> frags;
MolFragmenter::fragmentOnSomeBonds(*mol,bindices,frags,0,false);
TEST_ASSERT(frags.size()==0);
delete mol;
}
BOOST_LOG(rdInfoLog) << "\tdone" << std::endl;
}
int main() {
RDLog::InitLogs();
BOOST_LOG(rdInfoLog) << "********************************************************\n";
BOOST_LOG(rdInfoLog) << "Testing Chemical Transforms \n";
#if 1
testDeleteSubstruct();
testReplaceSubstructs();
testReplaceSubstructs2();
testReplaceSidechains();
testReplaceCore();
testReplaceCoreLabels();
testReplaceCoreCrash();
testReplaceCorePositions();
testMurckoDecomp();
testReplaceCoreRequireDummies();
testIssue3453144();
testIssue3537675();
testCombineMols();
testAddRecursiveQueries();
testParseQueryDefFile();
testIssue275();
testFragmentOnBonds();
testFragmentOnBRICSBonds();
#endif
testFragmentOnSomeBonds();
//benchFragmentOnBRICSBonds();
testGithubIssue429();
testGithubIssue430();
BOOST_LOG(rdInfoLog) << "*******************************************************\n";
return(0);
}
Reference in New Issue View Git Blame Copy Permalink