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rdkit/Code/GraphMol/molopstest.cpp
Greg Landrum 2805355f34 First pass at the rewrite: 
this gets rid of all the "preceding atom" code and passes all tests on linux

builds on other OS's and more extensive regression testing is required
2010-05-31 14:08:11 +00:00

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// $Id$
//
// Copyright (C) 2002-2010 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
#include <RDGeneral/utils.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/MolWriters.h>
#include <iostream>
using namespace RDKit;
using namespace std;
RWMol _t;
typedef class ROMol Mol;
void test1(){
string smi;
Mol *m;
INT_VECT iv;
unsigned int count;
std::vector<ROMOL_SPTR> frags;
smi = "CCCC(=O)O";
m = SmilesToMol(smi);
CHECK_INVARIANT(m,"smiles parse failed");
count = MolOps::getMolFrags(*m,iv);
CHECK_INVARIANT(count==1,"bad frag count");
frags = MolOps::getMolFrags(*m);
CHECK_INVARIANT(frags.size()==1,"bad frag count");
TEST_ASSERT(frags[0]->getNumAtoms()==6);
delete m;
smi = "CCCC(=O)[O-].[Na+]";
m = SmilesToMol(smi);
CHECK_INVARIANT(m,"smiles parse failed");
count = MolOps::getMolFrags(*m,iv);
CHECK_INVARIANT(count==2,"bad frag count");
frags = MolOps::getMolFrags(*m);
CHECK_INVARIANT(frags.size()==2,"bad frag count");
TEST_ASSERT(frags[0]->getNumAtoms()==6);
TEST_ASSERT(frags[1]->getNumAtoms()==1);
frags = MolOps::getMolFrags(*m,true,&iv);
CHECK_INVARIANT(frags.size()==2,"bad frag count");
TEST_ASSERT(frags[0]->getNumAtoms()==6);
TEST_ASSERT(frags[1]->getNumAtoms()==1);
TEST_ASSERT(iv.size()==7);
TEST_ASSERT(iv[0]==0)
TEST_ASSERT(iv[6]==1)
delete m;
smi = "CCCC(=O)[O-].[Na+].[NH4+].[Cl-]";
m = SmilesToMol(smi);
CHECK_INVARIANT(m,"smiles parse failed");
count = MolOps::getMolFrags(*m,iv);
CHECK_INVARIANT(count==4,"bad frag count");
frags = MolOps::getMolFrags(*m);
CHECK_INVARIANT(frags.size()==4,"bad frag count");
TEST_ASSERT(frags[0]->getNumAtoms()==6);
TEST_ASSERT(frags[1]->getNumAtoms()==1);
TEST_ASSERT(frags[2]->getNumAtoms()==1);
TEST_ASSERT(frags[3]->getNumAtoms()==1);
delete m;
};
void test2(){
string smi;
Mol *m;
INT_VECT iv;
int count;
smi = "CCCC(=O)O";
m = SmilesToMol(smi);
CHECK_INVARIANT(m,"smiles parse failed");
count = MolOps::getMolFrags(*m,iv);
CHECK_INVARIANT(count==1,"bad frag count");
CHECK_INVARIANT(iv[0]==0,"bad frag membership");
CHECK_INVARIANT(iv[1]==0,"bad frag membership");
CHECK_INVARIANT(iv[4]==0,"bad frag membership");
CHECK_INVARIANT(iv[5]==0,"bad frag membership");
delete m;
smi = "CCCC(=O)[O-].[Na+]";
m = SmilesToMol(smi);
CHECK_INVARIANT(m,"smiles parse failed");
count = MolOps::getMolFrags(*m,iv);
CHECK_INVARIANT(count==2,"bad frag count");
CHECK_INVARIANT(iv[0]==0,"bad frag membership");
CHECK_INVARIANT(iv[1]==0,"bad frag membership");
CHECK_INVARIANT(iv[4]==0,"bad frag membership");
CHECK_INVARIANT(iv[5]==0,"bad frag membership");
CHECK_INVARIANT(iv[6]==1,"bad frag membership");
delete m;
};
void test3(){
string smi;
Mol *m;
VECT_INT_VECT sssr;
INT_VECT rings;
int count;
smi = "C1CC1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getRingInfo()->numRings()==1);
count = MolOps::findSSSR(*m,sssr);
TEST_ASSERT(count==1);
TEST_ASSERT(sssr[0].size()==3);
TEST_ASSERT(m->getRingInfo()->numRings()==1);
for(unsigned int i=0;i<m->getNumAtoms();i++){
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(i,3));
TEST_ASSERT(!m->getRingInfo()->isAtomInRingOfSize(i,4));
TEST_ASSERT(m->getRingInfo()->numAtomRings(i)==1);
}
for(unsigned int i=0;i<m->getNumBonds();i++){
TEST_ASSERT(m->getRingInfo()->isBondInRingOfSize(i,3));
TEST_ASSERT(!m->getRingInfo()->isBondInRingOfSize(i,4));
TEST_ASSERT(m->getRingInfo()->numBondRings(i)==1);
}
BOOST_LOG(rdInfoLog) << smi << "\n";
delete m;
smi = "C1CCC1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getRingInfo()->numRings()==1);
count = MolOps::findSSSR(*m,sssr);
TEST_ASSERT(count==1);
TEST_ASSERT(sssr[0].size()==4);
TEST_ASSERT(m->getRingInfo()->numRings()==1);
for(unsigned int i=0;i<m->getNumAtoms();i++){
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(i,4));
TEST_ASSERT(!m->getRingInfo()->isAtomInRingOfSize(i,3));
TEST_ASSERT(m->getRingInfo()->numAtomRings(i)==1);
}
TEST_ASSERT(m->getRingInfo()->isBondInRingOfSize(0,4));
TEST_ASSERT(m->getRingInfo()->numBondRings(0)==1);
BOOST_LOG(rdInfoLog) << smi << "\n";
delete m;
smi = "C1CCCCCC1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getRingInfo()->numRings()==1);
count = MolOps::findSSSR(*m,sssr);
TEST_ASSERT(count==1);
TEST_ASSERT(sssr[0].size()==7);
TEST_ASSERT(m->getRingInfo()->numRings()==1);
for(unsigned int i=0;i<m->getNumAtoms();i++){
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(i,7));
TEST_ASSERT(m->getRingInfo()->numAtomRings(i)==1);
}
TEST_ASSERT(m->getRingInfo()->isBondInRingOfSize(0,7));
TEST_ASSERT(m->getRingInfo()->numBondRings(0)==1);
BOOST_LOG(rdInfoLog) << smi << "\n";
delete m;
smi = "C1C(CCC)CC(C(C)CCC(CC))CCC1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
count = MolOps::findSSSR(*m,sssr);
TEST_ASSERT(count==1);
TEST_ASSERT(sssr[0].size()==7);
TEST_ASSERT(m->getRingInfo()->numAtomRings(0)==1);
TEST_ASSERT(m->getRingInfo()->numBondRings(m->getBondBetweenAtoms(0,1)->getIdx()));
TEST_ASSERT(!m->getRingInfo()->numBondRings(m->getBondBetweenAtoms(1,2)->getIdx()));
BOOST_LOG(rdInfoLog) << smi << "\n";
delete m;
smi = "CC1CCC1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
count = MolOps::findSSSR(*m,sssr);
TEST_ASSERT(count==1);
TEST_ASSERT(sssr[0].size()==4);
TEST_ASSERT(!m->getBondBetweenAtoms(0,1)->hasProp("ringMembership"));
TEST_ASSERT(!m->getRingInfo()->numBondRings(m->getBondBetweenAtoms(0,1)->getIdx()));
TEST_ASSERT(m->getRingInfo()->numBondRings(m->getBondBetweenAtoms(1,2)->getIdx()));
BOOST_LOG(rdInfoLog) << smi << "\n";
delete m;
smi = "CC1C(C2)CCC2C1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
count = MolOps::findSSSR(*m, sssr);
TEST_ASSERT(count==2)
TEST_ASSERT(sssr[0].size()==5);
TEST_ASSERT(sssr[1].size()==5);
TEST_ASSERT(!m->getRingInfo()->isAtomInRingOfSize(0,5));
TEST_ASSERT(m->getRingInfo()->numAtomRings(0)==0);
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(1,5));
TEST_ASSERT(m->getRingInfo()->numAtomRings(1)==1);
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(2,5));
TEST_ASSERT(m->getRingInfo()->numAtomRings(2)==2);
BOOST_LOG(rdInfoLog) << smi << "\n";
delete m;
smi = "C(C1C2C3C41)(C2C35)C45"; // cubane
//smi = "C1(C2C3C4C5C6C72)C3C4C5C6C71"; // from Figureras paper
//smi = "C17C5C4C3C2C1C6C2C3C4C5C67";
// we cannot use the sanitzation code, because that finds *symmetric*
// rings, which will break this case:
m = SmilesToMol(smi,0,0);
int bfs = MolOps::findSSSR(*m);
TEST_ASSERT(bfs==5);
BOOST_LOG(rdInfoLog) << "BFSR: " << bfs << "\n";
VECT_INT_VECT bfrs;
bfrs.resize(0);
bfs = MolOps::symmetrizeSSSR(*m, bfrs);
TEST_ASSERT(bfs==6);
BOOST_LOG(rdInfoLog) << "BFSR: " << bfs << "\n";
//VECT_INT_VECT_I ri;
//for (ri == bfrs.begin(); ri != bfrs.end(); ri++) {
for (unsigned int ri = 0; ri < bfrs.size(); ri++) {
INT_VECT_I mi;
INT_VECT bring = bfrs[ri];
BOOST_LOG(rdInfoLog) << "( ";
//for (mi = (*ri).begin(); mi != (*ri).end(); mi++) {
for (mi = bring.begin(); mi != bring.end(); mi++) {
BOOST_LOG(rdInfoLog) << " " << (*mi);
}
BOOST_LOG(rdInfoLog) << ")\n";
}
BOOST_LOG(rdInfoLog) << smi << "\n";
delete m;
smi = "C1CC2C1CCC2";
m = SmilesToMol(smi);
TEST_ASSERT(m);
count = MolOps::findSSSR(*m,sssr);
TEST_ASSERT(count==2);
TEST_ASSERT(sssr[0].size()==4);
TEST_ASSERT(sssr[1].size()==5);
BOOST_LOG(rdInfoLog) << smi << "\n";
delete m;
smi = "C12=C3C=CC=C1C=CC2=CC=C3";
BOOST_LOG(rdInfoLog) << "\n" << smi << "\n";
m = SmilesToMol(smi,0,0);
TEST_ASSERT(m);
count = MolOps::findSSSR(*m,sssr);
TEST_ASSERT(count==3);
TEST_ASSERT(sssr[0].size()==6);
TEST_ASSERT(sssr[1].size()==5);
TEST_ASSERT(sssr[2].size()==6);
BOOST_LOG(rdInfoLog) << smi << "\n";
delete m;
smi = "C1(O)C(O)C(O)C1O";
m = SmilesToMol(smi,0,0);
TEST_ASSERT(m);
count = MolOps::findSSSR(*m,sssr);
TEST_ASSERT(count==1);
TEST_ASSERT(sssr[0].size()==4);
for(unsigned i=0;i<m->getNumAtoms();i++){
if(!(i%2)){
TEST_ASSERT(m->getRingInfo()->numAtomRings(i)==1);
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(i,4));
} else {
TEST_ASSERT(m->getRingInfo()->numAtomRings(i)==0);
}
}
BOOST_LOG(rdInfoLog) << smi << "\n";
delete m;
// this molecule is from issue 134
// it should come up with three rings
smi = "SC(C3C1CC(C3)CC(C2S)(O)C1)2S";
m = SmilesToMol(smi,0,0);
TEST_ASSERT(m);
count = MolOps::findSSSR(*m,sssr);
TEST_ASSERT(count==3);
TEST_ASSERT(sssr[0].size()==5);
TEST_ASSERT(sssr[1].size()==6);
TEST_ASSERT(sssr[2].size()==6);
// this yet another painful case
smi = "CC1=CC=C(C=C1)S(=O)(=O)O[CH]2[CH]3CO[CH](O3)[CH]4OC(C)(C)O[CH]24";
m = SmilesToMol(smi,0,0);
TEST_ASSERT(m);
count = MolOps::findSSSR(*m,sssr);
TEST_ASSERT(count==4);
TEST_ASSERT(sssr[0].size()==6);
TEST_ASSERT(sssr[1].size()==5);
TEST_ASSERT(sssr[2].size()==5);
TEST_ASSERT(sssr[3].size()==6);
smi = "C1CC2C1C2";
m = SmilesToMol(smi,0,0);
TEST_ASSERT(m);
count = MolOps::findSSSR(*m,sssr);
TEST_ASSERT(count==2);
TEST_ASSERT(sssr[0].size()==4);
TEST_ASSERT(sssr[1].size()==3);
TEST_ASSERT(m->getRingInfo()->numAtomRings(0)==1);
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(0,4));
TEST_ASSERT(m->getRingInfo()->numAtomRings(1)==1);
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(1,4));
TEST_ASSERT(m->getRingInfo()->numAtomRings(2)==2);
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(2,3));
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(2,4));
TEST_ASSERT(m->getRingInfo()->numAtomRings(3)==2);
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(3,4));
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(3,3));
TEST_ASSERT(m->getRingInfo()->numAtomRings(4)==1);
TEST_ASSERT(!m->getRingInfo()->isAtomInRingOfSize(4,4));
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(4,3));
delete m;
// This is a test of Issue 217
smi = "C=C1C2CC1C2";
m = SmilesToMol(smi,0,0);
TEST_ASSERT(m);
count = MolOps::findSSSR(*m,sssr);
TEST_ASSERT(count==2);
TEST_ASSERT(sssr[0].size()==4);
TEST_ASSERT(sssr[1].size()==4);
count = MolOps::symmetrizeSSSR(*m,sssr);
TEST_ASSERT(count==3);
TEST_ASSERT(sssr[0].size()==4);
TEST_ASSERT(sssr[1].size()==4);
TEST_ASSERT(sssr[2].size()==4);
TEST_ASSERT(m->getRingInfo()->numAtomRings(0)==0);
TEST_ASSERT(m->getRingInfo()->numAtomRings(1)==2);
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(1,4));
TEST_ASSERT(m->getRingInfo()->numAtomRings(2)==3);
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(2,4));
TEST_ASSERT(m->getRingInfo()->numAtomRings(3)==2);
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(3,4));
TEST_ASSERT(m->getRingInfo()->numAtomRings(4)==3);
TEST_ASSERT(m->getRingInfo()->isAtomInRingOfSize(4,4));
delete m;
}
void test4(){
string smi;
Mol *m;
INT_VECT iv;
VECT_INT_VECT sssr;
smi = "CC";
m = SmilesToMol(smi);
TEST_ASSERT(m);
double *adjMat = MolOps::getAdjacencyMatrix(*m);
TEST_ASSERT(adjMat);
TEST_ASSERT(adjMat[0]==0);
TEST_ASSERT(adjMat[1]==1);
TEST_ASSERT(adjMat[2]==1);
TEST_ASSERT(adjMat[3]==0);
adjMat = MolOps::getAdjacencyMatrix(*m);
TEST_ASSERT(adjMat);
TEST_ASSERT(adjMat[0]==0);
TEST_ASSERT(adjMat[1]==1);
TEST_ASSERT(adjMat[2]==1);
TEST_ASSERT(adjMat[3]==0);
}
void test5(){
string smi;
Mol *m;
VECT_INT_VECT sssr;
int count;
smi = "C1C4C5C3C(=O)C2C5C1C2C34";
m = SmilesToMol(smi,0,0);
count = MolOps::findSSSR(*m,sssr);
BOOST_LOG(rdInfoLog) << "Count: " << count << "\n";
CHECK_INVARIANT(count==5,"");
smi = "C1C(C2)CCC2C1";
m = SmilesToMol(smi);
count = MolOps::findSSSR(*m,sssr);
CHECK_INVARIANT(count==2,"");
}
/*
void test6(){
string smi;
Mol *m;
VECT_INT_VECT sssr;
int c1,c2;
smi = "C1(Cl)C(Cl)C1Cl";
m = SmilesToMol(smi);
INT_SET ringAtoms,ringBonds;
//boost::tie(c1,c2) = MolOps::findRingAtomsAndBonds(*m,ringAtoms,ringBonds);
CHECK_INVARIANT(c1==3,"bad nRingAtoms");
CHECK_INVARIANT(ringAtoms.count(0)==1,"bad RingAtoms");
CHECK_INVARIANT(ringAtoms.count(1)==0,"bad RingAtoms");
CHECK_INVARIANT(ringAtoms.count(2)==1,"bad RingAtoms");
CHECK_INVARIANT(ringAtoms.count(3)==0,"bad RingAtoms");
CHECK_INVARIANT(ringAtoms.count(4)==1,"bad RingAtoms");
CHECK_INVARIANT(ringAtoms.count(5)==0,"bad RingAtoms");
CHECK_INVARIANT(c2==3,"bad nRingBonds");
CHECK_INVARIANT(ringBonds.count(0)==0,"");
CHECK_INVARIANT(ringBonds.count(1)==1,"");
CHECK_INVARIANT(ringBonds.count(2)==0,"");
CHECK_INVARIANT(ringBonds.count(3)==1,"");
CHECK_INVARIANT(ringBonds.count(4)==0,"");
CHECK_INVARIANT(ringBonds.count(5)==1,"");
}
*/
void test7(){
#if 0
string smi;
Mol *m;
INT_VECT tree;
#if 1
smi = "C(CO)OCC";
m = SmilesToMol(smi);
MolOps::findSpanningTree(*m,tree);
CHECK_INVARIANT(tree.size()==5,"bad mst");
delete m;
smi = "C1CC1";
m = SmilesToMol(smi);
MolOps::findSpanningTree(*m,tree);
CHECK_INVARIANT(tree.size()==2,"bad mst");
delete m;
smi = "C1C=C1";
m = SmilesToMol(smi);
MolOps::findSpanningTree(*m,tree);
CHECK_INVARIANT(tree.size()==2,"bad mst");
CHECK_INVARIANT(std::find(tree.begin(),tree.end(),1)==tree.end(),"bogus idx in mst");
delete m;
#endif
smi = "C1C=CC=CC=1";
m = SmilesToMol(smi);
MolOps::findSpanningTree(*m,tree);
CHECK_INVARIANT(tree.size()==5,"bad mst");
delete m;
smi = "C1C(=CC1)";
m = SmilesToMol(smi);
MolOps::findSpanningTree(*m,tree);
CHECK_INVARIANT(tree.size()==3,"bad mst");
delete m;
smi = "C1C(C=C1)";
m = SmilesToMol(smi);
MolOps::findSpanningTree(*m,tree);
CHECK_INVARIANT(tree.size()==3,"bad mst");
delete m;
smi = "C1C(C2)CCC2C1";
m = SmilesToMol(smi);
MolOps::findSpanningTree(*m,tree);
CHECK_INVARIANT(tree.size()==6,"bad mst");
delete m;
smi = "C1C2CC3CCCCC3CC2CCC1";
m = SmilesToMol(smi);
MolOps::findSpanningTree(*m,tree);
CHECK_INVARIANT(tree.size()==13,"bad mst");
delete m;
#endif
}
void test8()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Hydrogen Ops" << std::endl;
ROMol *m,*m2,*m3;
INT_VECT tree;
std::string smi = "CCC";
m = SmilesToMol(smi);
CHECK_INVARIANT(m,"");
CHECK_INVARIANT(m->getNumAtoms()==3,"");
//BOOST_LOG(rdInfoLog) << "1" << std::endl;
m2 = MolOps::addHs(*m);
CHECK_INVARIANT(m2->getNumAtoms()==11,"");
smi = "CC(=O)[OH]";
delete m;
m = SmilesToMol(smi);
CHECK_INVARIANT(m,"");
CHECK_INVARIANT(m->getNumAtoms()==4,"");
//BOOST_LOG(rdInfoLog) << "2" << std::endl;
delete m2;
m2 = MolOps::addHs(*m,true);
CHECK_INVARIANT(m2->getNumAtoms()==5,"");
//BOOST_LOG(rdInfoLog) << "3" << std::endl;
m3 = MolOps::addHs(*m2,false);
CHECK_INVARIANT(m3->getNumAtoms()==8,"");
//BOOST_LOG(rdInfoLog) << "4" << std::endl;
delete m2;
m2 = MolOps::addHs(*m,false);
CHECK_INVARIANT(m2->getNumAtoms()==8,"");
delete m3;
// remove all
//BOOST_LOG(rdInfoLog) << "5" << std::endl;
m3 = MolOps::removeHs(*m2,false);
CHECK_INVARIANT(m3->getNumAtoms()==4,"");
delete m3;
// remove only implicit
//BOOST_LOG(rdInfoLog) << "6" << std::endl;
m3 = MolOps::removeHs(*m2,true);
CHECK_INVARIANT(m3->getNumAtoms()==5,"");
delete m2;
//BOOST_LOG(rdInfoLog) << "7" << std::endl;
// remove all after removing only implicit
m2 = MolOps::removeHs(*m3,false);
CHECK_INVARIANT(m2->getNumAtoms()==4,"");
// this test is also done in the same order in the python tests:
delete m;
m = SmilesToMol(smi);
CHECK_INVARIANT(m,"");
CHECK_INVARIANT(m->getNumAtoms()==4,"");
delete m2;
m2 = MolOps::addHs(*m,true);
CHECK_INVARIANT(m2->getNumAtoms()==5,"");
//BOOST_LOG(rdInfoLog) << "8" << std::endl;
m3 = MolOps::removeHs(*m2,true);
CHECK_INVARIANT(m3->getNumAtoms()==5,"");
delete m3;
//BOOST_LOG(rdInfoLog) << "9" << std::endl;
m3 = MolOps::removeHs(*m2,false);
CHECK_INVARIANT(m3->getNumAtoms()==4,"");
delete m2;
//BOOST_LOG(rdInfoLog) << "10" << std::endl;
m2 = MolOps::addHs(*m,false);
CHECK_INVARIANT(m2->getNumAtoms()==8,"");
delete m3;
//BOOST_LOG(rdInfoLog) << "11" << std::endl;
m3 = MolOps::removeHs(*m2,true);
CHECK_INVARIANT(m3->getNumAtoms()==5,"");
delete m3;
//BOOST_LOG(rdInfoLog) << "12" << std::endl;
m3 = MolOps::removeHs(*m2,false);
CHECK_INVARIANT(m3->getNumAtoms()==4,"");
// related to RDTrack Issues 109 and 110:
smi = "C1C=C([C@H](N)C(=O)N[C@@]2([H])[C@]3([H])SC(C)(C)[C@@H](C(=O)O)N3C(=O)2)C=CC=1";
delete m;
m = SmilesToMol(smi);
CHECK_INVARIANT(m,"");
CHECK_INVARIANT(m->getNumAtoms()==24,"");
delete m3;
//BOOST_LOG(rdInfoLog) << "13" << std::endl;
m3 = MolOps::removeHs(*m,false);
CHECK_INVARIANT(m3->getNumAtoms()==24,"");
// RDTrack Issue 130:
delete m;
smi = "[H][N+]([H])([H])[H]";
m = SmilesToMol(smi,false,false);
CHECK_INVARIANT(m,"");
CHECK_INVARIANT(m->getNumAtoms()==5,"");
delete m2;
//BOOST_LOG(rdInfoLog) << "14" << std::endl;
m2 = MolOps::removeHs(*m,0,false);
CHECK_INVARIANT(m2->getNumAtoms()==1,"");
delete m;
smi = "[H][N+]([H])([H])[H]";
m = SmilesToMol(smi);
CHECK_INVARIANT(m,"");
CHECK_INVARIANT(m->getNumAtoms()==1,"");
delete m;
smi = "[H][H]";
m = SmilesToMol(smi,false,false);
CHECK_INVARIANT(m,"");
CHECK_INVARIANT(m->getNumAtoms()==2,"");
delete m2;
//BOOST_LOG(rdInfoLog) << "15" << std::endl;
m2 = MolOps::removeHs(*m,0,false);
CHECK_INVARIANT(m2->getNumAtoms()==2,"");
std::string sma;
delete m;
smi = "CC";
m = SmartsToMol(smi);
MolOps::sanitizeMol(*((RWMol *)m));
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==2);
sma = SmartsWrite::GetAtomSmarts(static_cast<const QueryAtom *>(m->getAtomWithIdx(0)));
TEST_ASSERT(sma=="C");
delete m2;
//BOOST_LOG(rdInfoLog) << "16" << std::endl;
m2 = MolOps::addHs(*m);
TEST_ASSERT(m2->getNumAtoms()==8);
sma = SmartsWrite::GetAtomSmarts(static_cast<const QueryAtom *>(m2->getAtomWithIdx(0)));
TEST_ASSERT(sma=="C");
delete m;
//BOOST_LOG(rdInfoLog) << "17" << std::endl;
m = MolOps::mergeQueryHs(*m2);
TEST_ASSERT(m->getNumAtoms()==2);
sma = SmartsWrite::GetAtomSmarts(static_cast<const QueryAtom *>(m->getAtomWithIdx(0)));
TEST_ASSERT(sma=="[C&!H0]");
// RDTrack Issue 1228:
delete m;
smi = "c1c[nH]cc1";
m = SmilesToMol(smi);
CHECK_INVARIANT(m,"");
CHECK_INVARIANT(m->getNumAtoms()==5,"");
delete m2;
//BOOST_LOG(rdInfoLog) << "18" << std::endl;
m2 = MolOps::addHs(*m,false,false);
CHECK_INVARIANT(m2->getNumAtoms()==10,"");
delete m;
//BOOST_LOG(rdInfoLog) << "19" << std::endl;
m = MolOps::removeHs(*m2);
CHECK_INVARIANT(m,"");
CHECK_INVARIANT(m->getNumAtoms()==5,"");
// labelling:
delete m;
smi = "c1cn([H])cc1";
m = SmilesToMol(smi);
CHECK_INVARIANT(m,"");
CHECK_INVARIANT(m->getNumAtoms()==5,"");
delete m2;
//BOOST_LOG(rdInfoLog) << "19" << std::endl;
m2 = MolOps::removeHs(*m);
CHECK_INVARIANT(m,"");
CHECK_INVARIANT(m->getNumAtoms()==5,"");
delete m;
smi = "c1cn([2H])cc1";
m = SmilesToMol(smi);
CHECK_INVARIANT(m,"");
CHECK_INVARIANT(m->getNumAtoms()==6,"");
delete m2;
//BOOST_LOG(rdInfoLog) << "19" << std::endl;
m2 = MolOps::removeHs(*m);
CHECK_INVARIANT(m,"");
CHECK_INVARIANT(m->getNumAtoms()==6,"");
delete m;
delete m2;
smi = "CC[H]";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==3);
m2 = MolOps::mergeQueryHs(*m);
TEST_ASSERT(m2->getNumAtoms()==2);
TEST_ASSERT(!m->getAtomWithIdx(1)->hasQuery());
TEST_ASSERT(m2->getAtomWithIdx(1)->hasQuery());
delete m;
delete m2;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test9()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Distance Matrix Operations" << std::endl;
ROMol *m;
std::string smi = "CC=C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==3);
double *dMat;
dMat = MolOps::getDistanceMat(*m,false,false);
TEST_ASSERT(dMat);
TEST_ASSERT(dMat[0]==0.0);
TEST_ASSERT(dMat[1]==1.0);
TEST_ASSERT(dMat[2]==2.0);
TEST_ASSERT(dMat[3]==1.0);
TEST_ASSERT(dMat[4]==0.0);
TEST_ASSERT(dMat[5]==1.0);
TEST_ASSERT(dMat[6]==2.0);
TEST_ASSERT(dMat[7]==1.0);
TEST_ASSERT(dMat[8]==0.0);
dMat = MolOps::getDistanceMat(*m,false,false);
TEST_ASSERT(dMat);
TEST_ASSERT(dMat[0]==0.0);
TEST_ASSERT(dMat[1]==1.0);
TEST_ASSERT(dMat[2]==2.0);
TEST_ASSERT(dMat[3]==1.0);
TEST_ASSERT(dMat[4]==0.0);
TEST_ASSERT(dMat[5]==1.0);
TEST_ASSERT(dMat[6]==2.0);
TEST_ASSERT(dMat[7]==1.0);
TEST_ASSERT(dMat[8]==0.0);
// test Issue328:
dMat = MolOps::getDistanceMat(*m,true,false);
TEST_ASSERT(dMat);
TEST_ASSERT(dMat[0]==0.0);
TEST_ASSERT(dMat[1]==1.0);
TEST_ASSERT(dMat[2]==1.5);
TEST_ASSERT(dMat[3]==1.0);
TEST_ASSERT(dMat[4]==0.0);
TEST_ASSERT(dMat[5]==0.5);
TEST_ASSERT(dMat[6]==1.5);
TEST_ASSERT(dMat[7]==0.5);
TEST_ASSERT(dMat[8]==0.0);
dMat = MolOps::getDistanceMat(*m,false,false);
TEST_ASSERT(dMat);
TEST_ASSERT(dMat[0]==0.0);
TEST_ASSERT(dMat[1]==1.0);
TEST_ASSERT(dMat[2]==2.0);
TEST_ASSERT(dMat[3]==1.0);
TEST_ASSERT(dMat[4]==0.0);
TEST_ASSERT(dMat[5]==1.0);
TEST_ASSERT(dMat[6]==2.0);
TEST_ASSERT(dMat[7]==1.0);
TEST_ASSERT(dMat[8]==0.0);
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test10()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Atom Ranking" << std::endl;
ROMol *m;
std::string smi = "FC(Cl)(Br)C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
INT_VECT ranks;
ranks.resize(m->getNumAtoms());
Chirality::assignAtomCIPRanks(*m,ranks);
int cip1,cip2;
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPRank"));
m->getAtomWithIdx(0)->getProp("_CIPRank",cip1);
TEST_ASSERT(cip1==ranks[0]);
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPRank"));
m->getAtomWithIdx(2)->getProp("_CIPRank",cip2);
TEST_ASSERT(cip2==ranks[2]);
TEST_ASSERT(cip1<cip2);
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp("_CIPRank"));
m->getAtomWithIdx(4)->getProp("_CIPRank",cip2);
TEST_ASSERT(cip1>cip2);
m->getAtomWithIdx(2)->getProp("_CIPRank",cip1);
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("_CIPRank"));
m->getAtomWithIdx(3)->getProp("_CIPRank",cip2);
TEST_ASSERT(cip1<cip2);
delete m;
smi = "FC(Cl)(Br)C(F)(F)F";
m = SmilesToMol(smi);
TEST_ASSERT(m);
ranks.resize(m->getNumAtoms());
Chirality::assignAtomCIPRanks(*m,ranks);
for(unsigned int i=0;i<m->getNumAtoms();i++){
int cip;
TEST_ASSERT(m->getAtomWithIdx(i)->hasProp("_CIPRank"));
m->getAtomWithIdx(i)->getProp("_CIPRank",cip);
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test11()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing CIP chirality" << std::endl;
ROMol *m;
std::string cip;
std::string smi = "F[C@]([C@])(Cl)Br";
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
// make sure the cleanup worked:
TEST_ASSERT(m->getAtomWithIdx(2)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(!(m->getAtomWithIdx(0)->hasProp("_CIPCode")));
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
TEST_ASSERT(!(m->getAtomWithIdx(2)->hasProp("_CIPCode")));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete m;
smi = "F[C@H](C)C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(!(m->getAtomWithIdx(0)->hasProp("_CIPCode")));
TEST_ASSERT(!(m->getAtomWithIdx(1)->hasProp("_CIPCode")));
TEST_ASSERT(!(m->getAtomWithIdx(2)->hasProp("_CIPCode")));
// test Issue 194:
TEST_ASSERT(m->getAtomWithIdx(1)->getNumExplicitHs()==0);
delete m;
smi = "F[C@]1CC(Cl)C1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(!(m->getAtomWithIdx(1)->hasProp("_CIPCode")));
delete m;
smi = "F[C@H]1C(Cl)CC1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
delete m;
smi = "F[C@@](C)(Cl)Br";
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(!(m->getAtomWithIdx(0)->hasProp("_CIPCode")));
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
TEST_ASSERT(!(m->getAtomWithIdx(2)->hasProp("_CIPCode")));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
delete m;
smi = "F[C@](Br)(C)Cl";
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete m;
smi = "F[C@](Cl)(Br)C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete m;
smi = "FC(F)(F)[C@](Br)(F)C(Cl)(Cl)Cl";
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp("_CIPCode"));
m->getAtomWithIdx(4)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete m;
smi = "C[C@](C=C)(F)Br";
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
delete m;
smi = "CC[C@](C=C)(F)Br";
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPCode"));
m->getAtomWithIdx(2)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
delete m;
smi = "[CH2-][C@](C)(F)Br";
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
delete m;
smi = "F[C@]([H])(Cl)Br";
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete m;
smi = "[C@H](Cl)(F)Br";
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete m;
smi = "[C@]([H])(Cl)(F)Br";
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete m;
smi = "F[C@H](Cl)Br";
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete m;
smi = "CC[C@H](C=C)C";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPCode"));
m->getAtomWithIdx(2)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete m;
smi = "OC[C@H](C=C)C";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPCode"));
m->getAtomWithIdx(2)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
delete m;
smi = "CC[C@H](C=C)O";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPCode"));
m->getAtomWithIdx(2)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete m;
smi = "OC[C@H](C=C)O";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPCode"));
m->getAtomWithIdx(2)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
delete m;
smi = "C[C@H]1C[C@H](C=C1)N";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("_CIPCode"));
m->getAtomWithIdx(3)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
// a couple random molecules from the BBB data set
delete m;
smi = "OC[C@H]1C[C@@H](N2C=NC3=C2N=C(N)N=C3NC4CC4)C=C1";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPCode"));
m->getAtomWithIdx(2)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp("_CIPCode"));
m->getAtomWithIdx(4)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
delete m;
smi = "N[C@H]1O[C@@H](SC1)CO";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("_CIPCode"));
m->getAtomWithIdx(3)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
delete m;
smi = "C1(N([C@H]2O[C@H](CO)SC2)C=CC(N)=N1)=O";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPCode"));
m->getAtomWithIdx(2)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp("_CIPCode"));
m->getAtomWithIdx(4)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
// this is Issue 152:
smi = "C1[C@H](N)C[C@H](C)C=1";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp("_CIPCode"));
m->getAtomWithIdx(4)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
// -----------------------------------------------
// these are related to Issue 397:
smi = "C(=O)[C@@H](C)N";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPCode"));
m->getAtomWithIdx(2)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
smi = "C(=O)[C@@H](CO)N";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPCode"));
m->getAtomWithIdx(2)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
smi = "C(O)[C@@H](C)N";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPCode"));
m->getAtomWithIdx(2)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
// -----------------------------------------------
// NOTE: This test gives correct results according to the current
// CIP ranking procedure, but the results are actually incorrect.
// This arises because of the inclusion of hybridization in the
// chiral atom invariants
// (see the note in Chirality.cpp:buildCIPInvariants())
smi = "[H][C@@](O)(C=C)C(C)CC";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
smi = "[H][C@@](O)(C=C)C(C)CO";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
smi = "[H][C@@]12C[C@@](NC1)(OC2)[H]";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPCode"));
m->getAtomWithIdx(2)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
smi = "[H][C@@]12C[C@@](C=C1)(CC2)[H]";
#ifdef VERBOSE_CANON
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
#endif
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPCode"));
m->getAtomWithIdx(2)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
smi = "[H][C@@]12O[C@@](CC1)(C3C2C(NC3=O)=O)[H]";
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPCode"));
m->getAtomWithIdx(2)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
smi = "[H][C@@]12O[C@@](C=C1)(C3C2C(NC3=O)=O)[H]";
BOOST_LOG(rdDebugLog) << " ----------------- ------------- ----------------" << std::endl;
BOOST_LOG(rdDebugLog) << "\t>" << smi << std::endl;
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPCode"));
m->getAtomWithIdx(2)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
// -----------------------------------------------
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test12()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing double bond stereochemistry" << std::endl;
ROMol *m;
RWMol *m2;
std::string smi = "F\\C=C/Cl";
std::string refSmi;
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(0)->getStereo() == Bond::STEREONONE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo() == Bond::STEREOZ);
TEST_ASSERT(m->getBondWithIdx(2)->getStereo() == Bond::STEREONONE);
delete m;
smi = "F/C=CCl";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
delete m;
smi = "F/C=C/Cl";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo()==Bond::STEREOE);
delete m;
smi = "F/C=C(/Br)Cl";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo()==Bond::STEREOE);
delete m;
smi = "F/C=C(/Cl)Br";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo()==Bond::STEREOZ);
delete m;
smi = "F/C(Br)=C/Cl";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(2)->getStereo()==Bond::STEREOZ);
delete m;
smi = "F/C=C(/Cl)Cl";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo() == Bond::STEREONONE);
// build a molecule from scratch to test problems
// around Issue 180. The molecule corresponds to SMILES
// F/C=C(/Br)C
delete m;
m2 = new RWMol();
m2->addAtom(new Atom(9),true,true);
m2->addAtom(new Atom(6),true,true);
m2->addAtom(new Atom(6),true,true);
m2->addAtom(new Atom(35),true,true);
m2->addAtom(new Atom(6),true,true);
m2->addBond(0,1,Bond::SINGLE);
m2->addBond(1,2,Bond::DOUBLE);
m2->addBond(2,3,Bond::SINGLE);
m2->addBond(2,4,Bond::SINGLE);
m2->getBondWithIdx(0)->setBondDir(Bond::ENDUPRIGHT);
m2->getBondWithIdx(2)->setBondDir(Bond::ENDUPRIGHT);
m2->getBondWithIdx(3)->setBondDir(Bond::ENDDOWNRIGHT);
MolOps::sanitizeMol(*m2);
MolOps::assignStereochemistry(*m2);
TEST_ASSERT(m2->getBondWithIdx(1)->getStereo()==Bond::STEREOE);
m2->getBondWithIdx(0)->setBondDir(Bond::ENDDOWNRIGHT);
MolOps::assignStereochemistry(*m2,true,true);
TEST_ASSERT(m2->getBondWithIdx(1)->getStereo()==Bond::STEREOZ);
delete m2;
m2 = new RWMol();
m2->addAtom(new Atom(9),true,true);
m2->addAtom(new Atom(6),true,true);
m2->addAtom(new Atom(6),true,true);
m2->addAtom(new Atom(35),true,true);
m2->addAtom(new Atom(6),true,true);
m2->addBond(1,0,Bond::SINGLE);
m2->addBond(1,2,Bond::DOUBLE);
m2->addBond(2,3,Bond::SINGLE);
m2->addBond(2,4,Bond::SINGLE);
m2->getBondWithIdx(0)->setBondDir(Bond::ENDUPRIGHT);
m2->getBondWithIdx(2)->setBondDir(Bond::ENDUPRIGHT);
m2->getBondWithIdx(3)->setBondDir(Bond::ENDDOWNRIGHT);
MolOps::sanitizeMol(*m2);
MolOps::assignStereochemistry(*m2);
TEST_ASSERT(m2->getBondWithIdx(1)->getStereo()==Bond::STEREOZ);
m2->getBondWithIdx(0)->setBondDir(Bond::ENDDOWNRIGHT);
MolOps::assignStereochemistry(*m2,true,true);
TEST_ASSERT(m2->getBondWithIdx(1)->getStereo()==Bond::STEREOE);
// ----------------------
// test Issue 174:
delete m2;
smi = "O\\N=C\\C=N/O";
m2 = SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(m2->getBondWithIdx(1)->getStereo()==Bond::STEREOE);
TEST_ASSERT(m2->getBondWithIdx(3)->getStereo()==Bond::STEREOZ);
refSmi = MolToSmiles(*m2,1);
m = SmilesToMol(refSmi);
TEST_ASSERT(m);
smi = MolToSmiles(*m,1);
TEST_ASSERT(refSmi==smi);
delete m;
delete m2;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testIssue183()
{
// ----------------------
// test "unsetting" of redundant bond directions:
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Issue 183\n" << std::endl;
RWMol *m,*m2;
std::string smi;
std::string refSmi;
smi = "Cl\\C(C)=C(\\C(F)=C(/F)C)/C(C)=C(\\F)C";
m2 = SmilesToMol(smi);
TEST_ASSERT(m2);
TEST_ASSERT(m2->getBondWithIdx(2)->getStereo()==Bond::STEREOE);
TEST_ASSERT(m2->getBondWithIdx(4)->getStereo()==Bond::STEREOE);
TEST_ASSERT(m2->getBondWithIdx(10)->getStereo()==Bond::STEREOZ);
refSmi = MolToSmiles(*m2,1);
//BOOST_LOG(rdInfoLog) << "ref: " << refSmi << std::endl;
m = SmilesToMol(refSmi);
TEST_ASSERT(m);
smi = MolToSmiles(*m,1);
//BOOST_LOG(rdInfoLog) << "smi: " << smi << std::endl;
TEST_ASSERT(refSmi==smi);
int nEs=0,nZs=0,nDbl=0;
for(RWMol::BondIterator bondIt=m->beginBonds();
bondIt!=m->endBonds();
bondIt++){
if((*bondIt)->getBondType()==Bond::DOUBLE){
nDbl++;
if((*bondIt)->getStereo()==Bond::STEREOE) nEs++;
else if((*bondIt)->getStereo()==Bond::STEREOZ) nZs++;
}
}
//BOOST_LOG(rdInfoLog) << ">> " << nDbl << " " << nEs << " " << nZs << std::endl;
TEST_ASSERT(nDbl==3);
TEST_ASSERT(nEs==2);
TEST_ASSERT(nZs==1);
delete m;
delete m2;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testIssue188()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Issue 188: bad CIP rankings" << std::endl;
ROMol *m;
std::string smi;
int cip1,cip2,cip3;
smi = "OC[C@H](C=C)C";
m = SmilesToMol(smi);
INT_VECT ranks;
ranks.resize(m->getNumAtoms());
Chirality::assignAtomCIPRanks(*m,ranks);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPRank"));
m->getAtomWithIdx(1)->getProp("_CIPRank",cip1);
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("_CIPRank"));
m->getAtomWithIdx(3)->getProp("_CIPRank",cip2);
TEST_ASSERT(cip1>cip2);
TEST_ASSERT(m->getAtomWithIdx(5)->hasProp("_CIPRank"));
m->getAtomWithIdx(5)->getProp("_CIPRank",cip3);
TEST_ASSERT(cip1>cip3);
TEST_ASSERT(cip2>cip3);
delete m;
smi = "CC(=N\\N)/C=N/N";
m = SmilesToMol(smi);
TEST_ASSERT(m);
ranks.resize(m->getNumAtoms());
Chirality::assignAtomCIPRanks(*m,ranks);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPRank"));
m->getAtomWithIdx(0)->getProp("_CIPRank",cip1);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPRank"));
m->getAtomWithIdx(1)->getProp("_CIPRank",cip2);
TEST_ASSERT(cip2>cip1);
TEST_ASSERT(m->getAtomWithIdx(4)->hasProp("_CIPRank"));
m->getAtomWithIdx(4)->getProp("_CIPRank",cip3);
TEST_ASSERT(cip3>cip1);
TEST_ASSERT(cip2>cip3);
delete m;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testIssue189()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Issue 189: BondDirs not getting properly cleared." << std::endl;
ROMol *m;
std::string smi,refSmi;
int count;
smi = "C(=S)/N=c(/n1C)scc1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(2)->getBondType()==Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(2)->getStereo()==Bond::STEREOZ);
count = 0;
for(unsigned int i=0;i<m->getNumBonds();i++){
if(m->getBondWithIdx(i)->getBondDir()!=Bond::NONE){
count++;
}
}
TEST_ASSERT(count==2);
refSmi = MolToSmiles(*m,1);
count = 0;
for(unsigned int i=0;i<m->getNumBonds();i++){
if(m->getBondWithIdx(i)->getBondDir()!=Bond::NONE){
count++;
}
}
TEST_ASSERT(count==2);
delete m;
m = SmilesToMol(refSmi);
TEST_ASSERT(m);
count = 0;
for(unsigned int i=0;i<m->getNumBonds();i++){
if(m->getBondWithIdx(i)->getBondDir()!=Bond::NONE){
count++;
}
}
TEST_ASSERT(count==2);
smi = MolToSmiles(*m,1);
count = 0;
for(unsigned int i=0;i<m->getNumBonds();i++){
if(m->getBondWithIdx(i)->getBondDir()!=Bond::NONE){
count++;
}
}
TEST_ASSERT(count==2);
TEST_ASSERT(smi==refSmi);
delete m;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testIssue190()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Issue 190: BondDirs incorrectly cleared." << std::endl;
ROMol *m;
std::string smi,refSmi;
int count;
smi ="O\\N=C\\NC(\\C)=N/OC";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
TEST_ASSERT(m->getBondWithIdx(5)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(5)->getStereo() == Bond::STEREOZ);
refSmi = MolToSmiles(*m,1);
count = 0;
for(unsigned int i=0;i<m->getNumBonds();i++){
if(m->getBondWithIdx(i)->getBondDir()!=Bond::NONE){
count++;
}
}
TEST_ASSERT(count==4);
delete m;
m = SmilesToMol(refSmi);
TEST_ASSERT(m);
count = 0;
for(unsigned int i=0;i<m->getNumBonds();i++){
if(m->getBondWithIdx(i)->getBondDir()!=Bond::NONE){
count++;
}
}
TEST_ASSERT(count==4);
smi = MolToSmiles(*m,1);
count = 0;
for(unsigned int i=0;i<m->getNumBonds();i++){
if(m->getBondWithIdx(i)->getBondDir()!=Bond::NONE){
count++;
}
}
TEST_ASSERT(count==4);
TEST_ASSERT(smi==refSmi);
delete m;
smi ="O\\N=C\\CC(\\C)=N/OC";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
TEST_ASSERT(m->getBondWithIdx(5)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(5)->getStereo() == Bond::STEREOZ);
refSmi = MolToSmiles(*m,1);
count = 0;
for(unsigned int i=0;i<m->getNumBonds();i++){
if(m->getBondWithIdx(i)->getBondDir()!=Bond::NONE){
count++;
}
}
TEST_ASSERT(count==4);
delete m;
m = SmilesToMol(refSmi);
TEST_ASSERT(m);
count = 0;
for(unsigned int i=0;i<m->getNumBonds();i++){
if(m->getBondWithIdx(i)->getBondDir()!=Bond::NONE){
count++;
}
}
TEST_ASSERT(count==4);
smi = MolToSmiles(*m,1);
count = 0;
for(unsigned int i=0;i<m->getNumBonds();i++){
if(m->getBondWithIdx(i)->getBondDir()!=Bond::NONE){
count++;
}
}
TEST_ASSERT(count==4);
TEST_ASSERT(smi==refSmi);
delete m;
smi ="O\\N=C\\C(=O)C(\\C)=N/OC";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondWithIdx(1)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(1)->getStereo() == Bond::STEREOE);
TEST_ASSERT(m->getBondWithIdx(6)->getBondType() == Bond::DOUBLE);
TEST_ASSERT(m->getBondWithIdx(6)->getStereo() == Bond::STEREOZ);
refSmi = MolToSmiles(*m,1);
count = 0;
for(unsigned int i=0;i<m->getNumBonds();i++){
if(m->getBondWithIdx(i)->getBondDir()!=Bond::NONE){
count++;
}
}
TEST_ASSERT(count==4);
delete m;
m = SmilesToMol(refSmi);
TEST_ASSERT(m);
count = 0;
for(unsigned int i=0;i<m->getNumBonds();i++){
if(m->getBondWithIdx(i)->getBondDir()!=Bond::NONE){
count++;
}
}
TEST_ASSERT(count==4);
smi = MolToSmiles(*m,1);
count = 0;
for(unsigned int i=0;i<m->getNumBonds();i++){
if(m->getBondWithIdx(i)->getBondDir()!=Bond::NONE){
count++;
}
}
TEST_ASSERT(count==4);
TEST_ASSERT(smi==refSmi);
delete m;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testShortestPath() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing shortest path code. This should finish very quickly." << std::endl;
{
std::string smi ="CC(OC1C(CCCC3)C3C(CCCC2)C2C1OC(C)=O)=O";
ROMol *m = SmilesToMol(smi);
INT_LIST path = MolOps::getShortestPath(*m, 1, 20);
CHECK_INVARIANT(path.size() == 7, "");
INT_LIST_CI pi = path.begin();
CHECK_INVARIANT((*pi) == 1, ""); pi++;
CHECK_INVARIANT((*pi) == 2, ""); pi++;
CHECK_INVARIANT((*pi) == 3, ""); pi++;
CHECK_INVARIANT((*pi) == 16, ""); pi++;
CHECK_INVARIANT((*pi) == 17, ""); pi++;
CHECK_INVARIANT((*pi) == 18, ""); pi++;
CHECK_INVARIANT((*pi) == 20, ""); pi++;
delete m;
}
{
// issue 2219400
std::string smi ="CC.C";
ROMol *m = SmilesToMol(smi);
INT_LIST path = MolOps::getShortestPath(*m, 0, 1);
std::cerr<<"path: "<<path.size()<<std::endl;
CHECK_INVARIANT(path.size() == 2, "");
INT_LIST_CI pi = path.begin();
CHECK_INVARIANT((*pi) == 0, ""); pi++;
CHECK_INVARIANT((*pi) == 1, "");
path = MolOps::getShortestPath(*m, 1, 2);
CHECK_INVARIANT(path.size() == 0, "");
path = MolOps::getShortestPath(*m, 0, 2);
CHECK_INVARIANT(path.size() == 0, "");
delete m;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testIssue210()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Issue 210" << std::endl;
ROMol *m,*m2;
std::string smi = "C1CC1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==3);
TEST_ASSERT(m->getRingInfo()->isInitialized());
m2 = MolOps::addHs(*m);
TEST_ASSERT(m2->getNumAtoms()==9);
TEST_ASSERT(m2->getRingInfo()->isInitialized());
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
delete m;
delete m2;
}
void testIssue211()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Issue 211" << std::endl;
ROMol *m;
std::string smi = "P(c1ccccc1)(c1ccccc1)c1ccccc1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==19);
const Atom *at=m->getAtomWithIdx(0);
TEST_ASSERT(at->getHybridization()==Atom::SP3);
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testIssue212()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Issue 212" << std::endl;
ROMol *m,*m2;
std::string smi,mb;
smi = "C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==1);
Conformer *conf = new Conformer(1);
m->addConformer(conf);
conf->setAtomPos(0,RDGeom::Point3D(0,0,0));
m2 = MolOps::addHs(*m,false,true);
TEST_ASSERT(m2->getNumAtoms()==5);
try{
mb = MolToMolBlock(*m2);
} catch (...) {
TEST_ASSERT(0); //,"MolToMolBlock() failed");
}
delete m;
delete m2;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testAddHsCoords()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing AddHs with coordinates" << std::endl;
ROMol *m,*m2;
RDGeom::Point3D v;
double bondLength = PeriodicTable::getTable()->getRb0(1) +
PeriodicTable::getTable()->getRb0(6);
double tetDist=2.*sin((109.471/2.)*M_PI/180)*bondLength;
double sp2Dist=2.*sin(60.*M_PI/180)*bondLength;
std::string smi;
smi = "C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==1);
Conformer *conf = new Conformer(1);
m->addConformer(conf);
conf->setAtomPos(0,RDGeom::Point3D(0,0,0));
m2 = MolOps::addHs(*m,false,true);
const Conformer *conf2 = &(m2->getConformer());
TEST_ASSERT(m2->getNumAtoms()==5);
TEST_ASSERT(feq((conf2->getAtomPos(0) - conf2->getAtomPos(1)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(0) - conf2->getAtomPos(2)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(0) - conf2->getAtomPos(3)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(0) - conf2->getAtomPos(4)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(1) - conf2->getAtomPos(2)).length(),
tetDist));
TEST_ASSERT(feq((conf2->getAtomPos(1) - conf2->getAtomPos(3)).length(),
tetDist));
TEST_ASSERT(feq((conf2->getAtomPos(1) - conf2->getAtomPos(4)).length(),
tetDist));
TEST_ASSERT(feq((conf2->getAtomPos(2) - conf2->getAtomPos(3)).length(),
tetDist));
TEST_ASSERT(feq((conf2->getAtomPos(2) - conf2->getAtomPos(4)).length(),
tetDist));
TEST_ASSERT(feq((conf2->getAtomPos(3) - conf2->getAtomPos(4)).length(),
tetDist));
delete m;
delete m2;
smi = "CC";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==2);
conf = new Conformer(2);
m->addConformer(conf);
conf->setAtomPos(0,RDGeom::Point3D(0,0,0));
conf->setAtomPos(1,RDGeom::Point3D(1.54,0,0));
m2 = MolOps::addHs(*m,false,true);
conf2 = &(m2->getConformer());
TEST_ASSERT(m2->getNumAtoms()==8);
TEST_ASSERT(feq((conf2->getAtomPos(0) - conf2->getAtomPos(2)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(0) - conf2->getAtomPos(3)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(0) - conf2->getAtomPos(4)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(2) - conf2->getAtomPos(3)).length(),
tetDist));
TEST_ASSERT(feq((conf2->getAtomPos(2) - conf2->getAtomPos(4)).length(),
tetDist));
TEST_ASSERT(feq((conf2->getAtomPos(3) - conf2->getAtomPos(4)).length(),
tetDist));
TEST_ASSERT(feq((conf2->getAtomPos(1) - conf2->getAtomPos(5)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(1) - conf2->getAtomPos(6)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(1) - conf2->getAtomPos(7)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(5) - conf2->getAtomPos(6)).length(),
tetDist));
TEST_ASSERT(feq((conf2->getAtomPos(5) - conf2->getAtomPos(7)).length(),
tetDist));
TEST_ASSERT(feq((conf2->getAtomPos(6) - conf2->getAtomPos(7)).length(),
tetDist));
delete m;
delete m2;
smi = "C=C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==2);
conf = new Conformer(2);
m->addConformer(conf);
conf->setAtomPos(0,RDGeom::Point3D(0,0,0));
conf->setAtomPos(1,RDGeom::Point3D(1.3,0,0));
m2 = MolOps::addHs(*m,false,true);
conf2 = &(m2->getConformer());
TEST_ASSERT(m2->getNumAtoms()==6);
TEST_ASSERT(feq((conf2->getAtomPos(0) - conf2->getAtomPos(2)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(0) - conf2->getAtomPos(3)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(1) - conf2->getAtomPos(4)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(1) - conf2->getAtomPos(5)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(2) - conf2->getAtomPos(3)).length(),
sp2Dist));
TEST_ASSERT(feq((conf2->getAtomPos(4) - conf2->getAtomPos(5)).length(),
sp2Dist));
delete m;
delete m2;
smi = "C#C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==2);
conf = new Conformer(2);
m->addConformer(conf);
conf->setAtomPos(0,RDGeom::Point3D(0,0,0));
conf->setAtomPos(1,RDGeom::Point3D(1.2,0,0));
m2 = MolOps::addHs(*m,false,true);
conf2 = &(m2->getConformer());
TEST_ASSERT(m2->getNumAtoms()==4);
TEST_ASSERT(feq((conf2->getAtomPos(0) - conf2->getAtomPos(2)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(1) - conf2->getAtomPos(3)).length(),
bondLength));
TEST_ASSERT(feq((conf2->getAtomPos(0) - conf2->getAtomPos(3)).length(),
bondLength+1.2));
TEST_ASSERT(feq((conf2->getAtomPos(1) - conf2->getAtomPos(2)).length(),
bondLength+1.2));
delete m;
delete m2;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testSanitOps()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Sanitization special cases" << std::endl;
ROMol *m;
std::string smi,pathName;
smi = "CN(=O)=O";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
TEST_ASSERT(m->getAtomWithIdx(1)->getFormalCharge()==1);
delete m;
smi = "C[N+](=O)[O-]";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
TEST_ASSERT(m->getAtomWithIdx(1)->getFormalCharge()==1);
delete m;
smi = "Cl(=O)(=O)(=O)[O-]";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
TEST_ASSERT(m->getAtomWithIdx(0)->getFormalCharge()==3);
delete m;
pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/";
m = MolFileToMol(pathName+"perchlorate1.mol");
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==51);
TEST_ASSERT(m->getAtomWithIdx(7)->getFormalCharge()==3);
delete m;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testAddConformers() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Add Confomers" << std::endl;
std::string smi = "CC";
ROMol *m = SmilesToMol(smi);
unsigned int i;
for (i = 0; i < 5; i++) {
Conformer *conf = new Conformer(2);
conf->setAtomPos(0, RDGeom::Point3D(0.0, 0.0, 0.0));
conf->setAtomPos(1, RDGeom::Point3D(1.5, 0.0, 0.0));
m->addConformer(conf, true);
}
CHECK_INVARIANT(m->getNumConformers() == 5, "");
ROMol *m2 = MolOps::addHs(*m,false,true);
CHECK_INVARIANT(m2->getNumConformers() == 5, "");
//const ROMol::CONF_SPTR_LIST &confs = m2->getConformers();
ROMol::ConstConformerIterator ci;
i = 0;
for (ci = m2->beginConformers(); ci != m2->endConformers(); ci++) {
CHECK_INVARIANT((*ci)->getNumAtoms() == 8, "");
CHECK_INVARIANT((*ci)->getId() == i, "");
const ROMol *mn = &((*ci)->getOwningMol());
CHECK_INVARIANT(mn->getNumAtoms() == 8, "");
i++;
}
//std::cout << m2->getNumAtoms() << " " << m2->getNumConformers() << "\n";
delete m;
delete m2;
BOOST_LOG(rdInfoLog) << "Finished \n ";
}
void testIssue252() {
// lets check if we can sanitize C60
std::string smi = "C12=C3C4=C5C6=C1C7=C8C9=C1C%10=C%11C(=C29)C3=C2C3=C4C4=C5C5=C9C6=C7C6=C7C8=C1C1=C8C%10=C%10C%11=C2C2=C3C3=C4C4=C5C5=C%11C%12=C(C6=C95)C7=C1C1=C%12C5=C%11C4=C3C3=C5C(=C81)C%10=C23";
ROMol *mol = SmilesToMol(smi);
for(ROMol::BondIterator it=mol->beginBonds();
it!=mol->endBonds();it++){
TEST_ASSERT((*it)->getIsAromatic());
}
std::string asmi = MolToSmiles(*mol);
// check if we can do it in the aromatic form
ROMol *nmol = SmilesToMol(asmi);
for(ROMol::BondIterator it=nmol->beginBonds();
it!=nmol->endBonds();it++){
TEST_ASSERT((*it)->getIsAromatic());
}
std::string nsmi = MolToSmiles(*nmol);
delete mol;
delete nmol;
// This is a check for Issue253
CHECK_INVARIANT(asmi == nsmi, "");
}
void testIssue276() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Issue 276" << std::endl;
std::string smi = "CP1(C)=CC=CN=C1C";
ROMol *mol = SmilesToMol(smi);
TEST_ASSERT(mol);
// as of this writing, I'm not 100% sure what the right answer is here,
// but the hybridization definitely should *not* be SP2:
TEST_ASSERT(mol->getAtomWithIdx(1)->getHybridization()>Atom::SP2);
delete mol;
BOOST_LOG(rdInfoLog) << "Finished \n ";
}
void testHsAndAromaticity() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Additional Aromaticity Cases" << std::endl;
std::string smi;
ROMol *mol;
smi = "[CH]1-[CH]-[CH]-[CH]-[CH]-[CH]-1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
//std::cerr << mol->getAtomWithIdx(0)->getHybridization() << std::endl;
TEST_ASSERT(mol->getAtomWithIdx(0)->getHybridization()==Atom::SP3);
TEST_ASSERT(mol->getAtomWithIdx(0)->getImplicitValence()==0);
TEST_ASSERT(mol->getAtomWithIdx(0)->getNumImplicitHs()==0);
TEST_ASSERT(mol->getAtomWithIdx(0)->getNumRadicalElectrons()==1);
TEST_ASSERT(!mol->getAtomWithIdx(0)->getIsAromatic());
TEST_ASSERT(!mol->getBondBetweenAtoms(0,1)->getIsAromatic());
smi = "C1=CC(=C)C(=C)C=C1";
mol = SmilesToMol(smi);
TEST_ASSERT(mol);
TEST_ASSERT(mol->getAtomWithIdx(0)->getHybridization()==Atom::SP2);
TEST_ASSERT(mol->getAtomWithIdx(2)->getHybridization()==Atom::SP2);
TEST_ASSERT(mol->getAtomWithIdx(0)->getIsAromatic());
TEST_ASSERT(mol->getBondBetweenAtoms(0,1)->getIsAromatic());
delete mol;
BOOST_LOG(rdInfoLog) << "Finished \n ";
}
void testSFIssue1694023()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing sf.net issue 1694023 (bad chiral smiles after removing Hs) " << std::endl;
ROMol *m;
std::string smi;
smi = "[C@@]([H])(F)(Cl)Br";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
smi = "[C@@](F)([H])(Cl)Br";
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
smi = "[C@@](F)(Cl)([H])Br";
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
smi = "[C@@](F)(Cl)(Br)[H]";
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
smi = "[H][C@@](F)(Cl)Br";
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
TEST_ASSERT(m->getAtomWithIdx(0)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
smi = "F[C@@]([H])(Cl)Br";
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
smi = "F[C@@](Cl)([H])Br";
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
smi = "F[C@@](Cl)(Br)[H]";
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==4);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CW);
smi = "C1CO[C@@H]1Cl";
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
TEST_ASSERT(m->getAtomWithIdx(3)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
smi = "C1CO[C@]1([H])Cl";
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
TEST_ASSERT(m->getAtomWithIdx(3)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
smi = "C1CO[C@@]1(Cl)[H]";
delete m;
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getNumAtoms()==5);
TEST_ASSERT(m->getAtomWithIdx(3)->getChiralTag()==Atom::CHI_TETRAHEDRAL_CCW);
delete m;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testSFIssue1719053()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing sf.net issue 1719053 (Ring stereochemistry incorrectly removed) " << std::endl;
ROMol *m;
std::string smi;
smi = "C[C@@H]1CCCCC1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
delete m;
smi = "C[C@@H]1CC[C@@H](C)CC1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
TEST_ASSERT(m->getAtomWithIdx(4)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
delete m;
smi = "C[C@@H]1C(C)CCCC1C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
delete m;
smi = "C[C@@H]1[C@H](C)CCC[C@H]1C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
// this is a truly symmetric case, so the stereochem should be removed:
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(m->getAtomWithIdx(2)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
TEST_ASSERT(m->getAtomWithIdx(7)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
delete m;
smi = "C[C@@H]1C=C[C@@H](C)C=C1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
TEST_ASSERT(m->getAtomWithIdx(4)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
delete m;
smi = "C[N@@]1C=C[C@@H](C)C=C1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()==Atom::CHI_UNSPECIFIED);
TEST_ASSERT(m->getAtomWithIdx(4)->getChiralTag()==Atom::CHI_UNSPECIFIED);
delete m;
smi = "C[N@@]1CC[C@@H](C)CC1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
TEST_ASSERT(m->getAtomWithIdx(4)->getChiralTag()!=Atom::CHI_UNSPECIFIED);
delete m;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testSFIssue1811276()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing sf.net issue 1811276 (kekulization failing) " << std::endl;
ROMol *m;
std::string smi;
smi = "[O-]N1C=C[N+](=O)C=C1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
smi = MolToSmiles(*m);
TEST_ASSERT(smi=="O=[n+]1ccn([O-])cc1");
delete m;
smi="o1ccc(=O)cc1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
smi = MolToSmiles(*m);
TEST_ASSERT(smi=="O=c1ccocc1");
smi="O=[n+]1ccocc1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
smi = MolToSmiles(*m);
TEST_ASSERT(smi=="O=[n+]1ccocc1");
smi="O=[n+]1ccn([O-])cc1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
smi = MolToSmiles(*m);
TEST_ASSERT(smi=="O=[n+]1ccn([O-])cc1");
smi="O=n1ccccc1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
smi = MolToSmiles(*m);
TEST_ASSERT(smi=="[O-][n+]1ccccc1");
delete m;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testSFIssue1836576()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing sf.net issue 1836576 (sanitization crash) " << std::endl;
RWMol *m;
std::string smi;
bool ok;
// the original form of the test runs foul of the rules for explicit
// valence on B:
smi = "[BH]123[BH]45[BH]167[BH]289[BH]312[BH]838[BH]966[Co]74479%10%11%12[CH]633[BH]811[CH]345[BH]21[BH]1234[BH]75[BH]911[BH]226[BH]%1011[BH]227[BH]633[BH]44[BH]322[CH]%1145[CH]%12271";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
ok=false;
try {
MolOps::sanitizeMol(*m);
} catch (MolSanitizeException &vee){
ok=true;
}
TEST_ASSERT(ok);
// this version throws the original error:
smi = "C123C45C11C44C55C22C33C14C523";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
ok=false;
try {
MolOps::sanitizeMol(*m);
} catch (ValueErrorException &vee){
ok=true;
}
TEST_ASSERT(ok);
delete m;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testChiralityAndRemoveHs()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing impact of removeHs on chirality" << std::endl;
ROMol *m,*m2;
std::string smi,code;
smi = "F[C@]([H])(Cl)Br";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
m2=MolOps::removeHs(*m);
TEST_ASSERT(m2);
MolOps::assignStereochemistry(*m2,true,true);
TEST_ASSERT(m2->getAtomWithIdx(1)->hasProp("_CIPCode"));
m2->getAtomWithIdx(1)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
delete m;
delete m2;
smi = "F[C@H](Cl)Br";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
m2=MolOps::removeHs(*m);
TEST_ASSERT(m2);
MolOps::assignStereochemistry(*m2,true,true);
TEST_ASSERT(m2->getAtomWithIdx(1)->hasProp("_CIPCode"));
m2->getAtomWithIdx(1)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
delete m;
delete m2;
smi = "[C@]([H])(Cl)(F)Br";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
m2=MolOps::removeHs(*m);
TEST_ASSERT(m2);
MolOps::assignStereochemistry(*m2,true,true);
TEST_ASSERT(m2->getAtomWithIdx(0)->hasProp("_CIPCode"));
m2->getAtomWithIdx(0)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
delete m;
delete m2;
smi = "[C@H](Cl)(F)Br";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
m2=MolOps::removeHs(*m);
TEST_ASSERT(m2);
MolOps::assignStereochemistry(*m2,true,true);
TEST_ASSERT(m2->getAtomWithIdx(0)->hasProp("_CIPCode"));
m2->getAtomWithIdx(0)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
delete m;
delete m2;
smi = "[H]1.F[C@]1(Cl)Br";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getAtomWithIdx(2)->hasProp("_CIPCode"));
m->getAtomWithIdx(2)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
m2=MolOps::removeHs(*m);
TEST_ASSERT(m2);
MolOps::assignStereochemistry(*m2,true,true);
TEST_ASSERT(m2->getAtomWithIdx(1)->hasProp("_CIPCode"));
m2->getAtomWithIdx(1)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
delete m;
delete m2;
smi = "F[C@]1(Cl)Br.[H]1";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
m2=MolOps::removeHs(*m);
TEST_ASSERT(m2);
MolOps::assignStereochemistry(*m2,true,true);
TEST_ASSERT(m2->getAtomWithIdx(1)->hasProp("_CIPCode"));
m2->getAtomWithIdx(1)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
delete m;
delete m2;
smi = "[H]1.[C@]1(Cl)(F)Br";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getAtomWithIdx(1)->hasProp("_CIPCode"));
m->getAtomWithIdx(1)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
m2=MolOps::removeHs(*m);
TEST_ASSERT(m2);
MolOps::assignStereochemistry(*m2,true,true);
TEST_ASSERT(m2->getAtomWithIdx(0)->hasProp("_CIPCode"));
m2->getAtomWithIdx(0)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
delete m;
delete m2;
smi = "[C@]1(Cl)(F)Br.[H]1";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
m2=MolOps::removeHs(*m);
TEST_ASSERT(m2);
MolOps::assignStereochemistry(*m2,true,true);
TEST_ASSERT(m2->getAtomWithIdx(0)->hasProp("_CIPCode"));
m2->getAtomWithIdx(0)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
delete m;
delete m2;
smi = "Cl1.F2.Br3.[C@H]123";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("_CIPCode"));
m->getAtomWithIdx(3)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
delete m;
smi = "[C@H]123.Cl1.F2.Br3";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getAtomWithIdx(0)->hasProp("_CIPCode"));
m->getAtomWithIdx(0)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
delete m;
smi = "F2.Cl1.Br3.[C@H]123";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("_CIPCode"));
m->getAtomWithIdx(3)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
delete m;
smi = "Cl2.F1.Br3.[C@H]213";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
MolOps::assignStereochemistry(*m,true,true);
TEST_ASSERT(m->getAtomWithIdx(3)->hasProp("_CIPCode"));
m->getAtomWithIdx(3)->getProp("_CIPCode",code);
TEST_ASSERT(code=="R");
delete m;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testSFIssue1894348()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing SFIssue1894348 (impact of removeHs on bond stereo atoms" << std::endl;
RWMol *m,*m2;
std::string smi;
smi = "Cl/C([H])=C/Cl";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
MolOps::assignStereochemistry(*m);
TEST_ASSERT(m->getBondWithIdx(2)->getStereoAtoms().size()==2);
TEST_ASSERT(m->getBondWithIdx(2)->getStereoAtoms()[0]==0);
TEST_ASSERT(m->getBondWithIdx(2)->getStereoAtoms()[1]==4);
m2=static_cast<RWMol *>(MolOps::removeHs(*m));
TEST_ASSERT(m->getBondWithIdx(2)->getStereoAtoms().size()==2);
TEST_ASSERT(m->getBondWithIdx(2)->getStereoAtoms()[0]==0);
TEST_ASSERT(m->getBondWithIdx(2)->getStereoAtoms()[1]==4);
TEST_ASSERT(m2->getBondWithIdx(1)->getStereoAtoms().size()==2);
TEST_ASSERT(m2->getBondWithIdx(1)->getStereoAtoms()[0]==0);
TEST_ASSERT(m2->getBondWithIdx(1)->getStereoAtoms()[1]==3);
delete m;
delete m2;
smi = "Cl/C([H])=C/Cl";
m = SmilesToMol(smi,false,false);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
TEST_ASSERT(m->getBondWithIdx(2)->getStereoAtoms().size()==0);
m2=static_cast<RWMol *>(MolOps::removeHs(*m));
// if we don't assign stereocodes in the original we shouldn't have them here:
TEST_ASSERT(m2->getBondWithIdx(1)->getStereoAtoms().size()==0);
delete m;
delete m2;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testAromaticityEdges()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing some aromaticity edge cases " << std::endl;
RWMol *m;
std::string smi;
// ------
// this was sf.net bug 1934360
smi = "C1=C=NC=N1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(!m->getAtomWithIdx(0)->getIsAromatic());
TEST_ASSERT(!m->getBondWithIdx(0)->getIsAromatic());
delete m;
smi = "C1=CNC=N1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getIsAromatic());
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic());
delete m;
smi = "C=[C+]1=CNC=N1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(!m->getAtomWithIdx(1)->getIsAromatic());
TEST_ASSERT(!m->getBondWithIdx(1)->getIsAromatic());
delete m;
// ------
// this was sf.net bug 1940646
smi = "C1#CC=C1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(!m->getAtomWithIdx(0)->getIsAromatic());
TEST_ASSERT(!m->getBondWithIdx(0)->getIsAromatic());
delete m;
smi = "C1#CC=CC=C1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getIsAromatic());
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic());
delete m;
// ------
// this was sf.net bug 2091839
smi = "c1cccc[c]1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getIsAromatic());
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic());
delete m;
smi = "C1=CC=CC=[C]1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getIsAromatic());
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic());
delete m;
smi = "c1cccc[n+]1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getIsAromatic());
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic());
delete m;
#if 0 // currently fails
smi = "[n]1cccc1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getIsAromatic());
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==1);
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic());
delete m;
#endif
smi = "[n]1ccccc1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getIsAromatic());
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==0);
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic());
delete m;
smi = "[H]n1cccc1";
m = SmilesToMol(smi,0,0);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
TEST_ASSERT(m->getAtomWithIdx(1)->getIsAromatic());
TEST_ASSERT(m->getAtomWithIdx(1)->getNumRadicalElectrons()==0);
TEST_ASSERT(!m->getAtomWithIdx(0)->getIsAromatic());
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==0);
delete m;
smi = "[H]";
m = SmilesToMol(smi,0,0);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==1);
delete m;
// ------
// this was sf.net bug 2787221.
smi = "O=C1C(=O)C=C1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getIsAromatic());
TEST_ASSERT(m->getBondBetweenAtoms(1,2)->getIsAromatic());
delete m;
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testSFIssue1942657()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing sf.net issue 1942657 " << std::endl;
RWMol *m;
std::string smi;
smi = "C[C](C)(C)(C)C";
try{
m = SmilesToMol(smi);
} catch (MolSanitizeException &e){
m=0;
}
TEST_ASSERT(!m);
smi = "C[CH](C)(C)C";
try{
m = SmilesToMol(smi);
} catch (MolSanitizeException &e){
m=0;
}
TEST_ASSERT(!m);
smi = "C[C](=C)(C)C";
try{
m = SmilesToMol(smi);
} catch (MolSanitizeException &e){
m=0;
}
TEST_ASSERT(!m);
smi = "C[Si](=C)(=C)=C";
try{
m = SmilesToMol(smi);
} catch (MolSanitizeException &e){
m=0;
}
TEST_ASSERT(!m);
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testSFIssue1968608()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing sf.net issue 198608 " << std::endl;
RWMol *m;
std::string smi;
smi = "C1CC1CC1CC1";
m = SmilesToMol(smi);
TEST_ASSERT(m->getRingInfo()->minAtomRingSize(0)==3);
TEST_ASSERT(m->getRingInfo()->minAtomRingSize(3)==0);
TEST_ASSERT(m->getRingInfo()->minBondRingSize(0)==3);
TEST_ASSERT(m->getRingInfo()->minBondRingSize(3)==0);
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testHybridization()
{
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing hybridization assignment " << std::endl;
{
RWMol *m;
std::string smi="CCC";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP3);
TEST_ASSERT(m->getAtomWithIdx(0)->getHybridization()==Atom::SP3);
delete m;
}
{
RWMol *m;
std::string smi="CNC";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP3);
TEST_ASSERT(m->getAtomWithIdx(0)->getHybridization()==Atom::SP3);
delete m;
}
{
RWMol *m;
std::string smi="COC";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP3);
TEST_ASSERT(m->getAtomWithIdx(0)->getHybridization()==Atom::SP3);
delete m;
}
{
RWMol *m;
std::string smi="C[C-2]C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP3);
TEST_ASSERT(m->getAtomWithIdx(0)->getHybridization()==Atom::SP3);
delete m;
}
{
RWMol *m;
std::string smi="C[CH-]C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP3);
TEST_ASSERT(m->getAtomWithIdx(0)->getHybridization()==Atom::SP3);
delete m;
}
{
RWMol *m;
std::string smi="C[CH]C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP3);
TEST_ASSERT(m->getAtomWithIdx(0)->getHybridization()==Atom::SP3);
delete m;
}
{
RWMol *m;
std::string smi="C[C]C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP3);
TEST_ASSERT(m->getAtomWithIdx(0)->getHybridization()==Atom::SP3);
delete m;
}
{
RWMol *m;
std::string smi="C[C-]C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP3);
TEST_ASSERT(m->getAtomWithIdx(0)->getHybridization()==Atom::SP3);
delete m;
}
{
RWMol *m;
std::string smi="C[CH+]C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP2);
TEST_ASSERT(m->getAtomWithIdx(0)->getHybridization()==Atom::SP3);
delete m;
}
{
RWMol *m;
std::string smi="CC=C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP2);
TEST_ASSERT(m->getAtomWithIdx(0)->getHybridization()==Atom::SP3);
delete m;
}
{
RWMol *m;
std::string smi="CN=C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP2);
TEST_ASSERT(m->getAtomWithIdx(0)->getHybridization()==Atom::SP3);
delete m;
}
{
RWMol *m;
std::string smi="C[C-]=C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP2);
TEST_ASSERT(m->getAtomWithIdx(0)->getHybridization()==Atom::SP3);
delete m;
}
{
RWMol *m;
std::string smi="C[C]=C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP2);
TEST_ASSERT(m->getAtomWithIdx(0)->getHybridization()==Atom::SP3);
delete m;
}
{
RWMol *m;
std::string smi="C[N+]=C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP2);
TEST_ASSERT(m->getAtomWithIdx(0)->getHybridization()==Atom::SP3);
delete m;
}
{
RWMol *m;
std::string smi="C#C";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP);
delete m;
}
{
RWMol *m;
std::string smi="C#[C-]";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP);
delete m;
}
{
RWMol *m;
std::string smi="C#[C]";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP);
delete m;
}
{
RWMol *m;
std::string smi="C[O]";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP3);
delete m;
}
{
RWMol *m;
std::string smi="C[N-]";
m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getHybridization()==Atom::SP3);
delete m;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testSFNetIssue2196817() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing sf.net issue 2196817: handling of aromatic dummies" << std::endl;
{
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/";
RWMol *m = MolFileToMol(pathName+"dummyArom.mol");
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getAtomicNum()==0);
TEST_ASSERT(m->getAtomWithIdx(0)->getIsAromatic()==true);
MolOps::Kekulize(*m);
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getBondType()==Bond::SINGLE);
TEST_ASSERT(m->getBondBetweenAtoms(0,4)->getBondType()==Bond::SINGLE);
delete m;
}
{
std::string smi="*1cncc1";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getAtomicNum()==0);
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic()==true);
delete m;
}
{
std::string smi="*1C=NC=C1";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getAtomicNum()==0);
TEST_ASSERT(m->getBondWithIdx(0)->getIsAromatic()==true);
delete m;
}
{
// case where all must be ignored:
std::string smi="c1*ccc1-c1*ccc1-c1*ccc1";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
delete m;
}
{
std::string smi="c1*[nH]*c1";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
smi=MolToSmiles(*m);
TEST_ASSERT(smi=="c1c[*][nH][*]1");
delete m;
smi="c1***c1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
smi=MolToSmiles(*m);
TEST_ASSERT(smi=="[*]1:[*]cc[*]:1");
delete m;
smi="c:1:*:*:*:*1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
smi=MolToSmiles(*m);
TEST_ASSERT(smi=="[*]1:[*]:[*]c[*]:1");
delete m;
smi="*:1:*:*:*:*:1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
smi=MolToSmiles(*m);
TEST_ASSERT(smi=="[*]1:[*]:[*]:[*]:[*]:1");
delete m;
}
{
std::string smi="c1*[nH]cc1-c1*[nH]cc1-c1*ccc1";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
delete m;
smi="c1*[nH]cc1-c1*ccc1-c1*[nH]cc1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
delete m;
smi="c1*ccc1-c1*[nH]cc1-c1*[nH1]cc1";
m = SmilesToMol(smi);
TEST_ASSERT(m);
delete m;
}
{
std::string smi="c1*[nH]cc1-c1*[nH]cc1-c1*[nH]cc1";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
delete m;
}
{
std::string smi="c1ccc(C2CC(n4cc[*]c4=C2))cc1";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getIsAromatic());
TEST_ASSERT(m->getBondBetweenAtoms(0,14)->getIsAromatic());
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getBondType()==Bond::AROMATIC);
TEST_ASSERT(m->getBondBetweenAtoms(0,14)->getBondType()==Bond::AROMATIC);
MolOps::Kekulize(*m);
TEST_ASSERT(!m->getBondBetweenAtoms(0,1)->getIsAromatic());
TEST_ASSERT(!m->getBondBetweenAtoms(0,14)->getIsAromatic());
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getBondType()==Bond::DOUBLE||
m->getBondBetweenAtoms(0,14)->getBondType()==Bond::DOUBLE);
MolOps::setAromaticity(*m);
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getIsAromatic());
TEST_ASSERT(m->getBondBetweenAtoms(0,14)->getIsAromatic());
TEST_ASSERT(m->getBondBetweenAtoms(0,1)->getBondType()==Bond::AROMATIC);
TEST_ASSERT(m->getBondBetweenAtoms(0,14)->getBondType()==Bond::AROMATIC);
delete m;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testSFNetIssue2208994() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing sf.net issue 2208994 : kekulization error" << std::endl;
{
std::string smi="Cn1ccc(=O)n1C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getIsAromatic()==true);
TEST_ASSERT(m->getBondWithIdx(1)->getIsAromatic()==true);
delete m;
}
{
std::string smi="c:1:c:c:c:c:c1";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getIsAromatic()==true);
TEST_ASSERT(m->getBondWithIdx(1)->getIsAromatic()==true);
delete m;
}
{
std::string smi="c1:c:c:c:c:c:1";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(1)->getIsAromatic()==true);
TEST_ASSERT(m->getBondWithIdx(1)->getIsAromatic()==true);
delete m;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testSFNetIssue2313979() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing sf.net issue 2313979: aromaticity assignment hangs " << std::endl;
{
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/";
SDMolSupplier suppl(pathName+"Issue2313979.sdf",false);
while(!suppl.atEnd()){
ROMol *m=suppl.next();
TEST_ASSERT(m);
std::string nm;
m->getProp("_Name",nm);
BOOST_LOG(rdInfoLog) << " Doing molecule: "<<nm<< std::endl;
BOOST_LOG(rdInfoLog) << " This should finish in a few seconds. >>>" << std::endl;
MolOps::sanitizeMol(*(RWMol *)m);
delete m;
BOOST_LOG(rdInfoLog) << " <<< Done." << std::endl;
}
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testSFNetIssue2316677() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing sf.net issue 2316677 : canonicalization error" << std::endl;
{
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/";
RWMol *m = MolFileToMol(pathName+"Issue2316677.mol");
TEST_ASSERT(m);
std::string smi=MolToSmiles(*m,true);
TEST_ASSERT(smi=="Cc1ccc(S(/N=C2\\CC(=N\\C(C)(C)C)/C2=N\\C(C)(C)C)(=O)=O)cc1");
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testSanitizeNonringAromatics() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing sf.net issue 2830244: make sure that non-ring aromatic atoms generate errors:" << std::endl;
{
std::string smi="c-C";
RWMol *m = SmilesToMol(smi,0,false);
bool ok=false;
try {
MolOps::Kekulize(*m);
} catch (MolSanitizeException &vee){
ok=true;
}
TEST_ASSERT(ok);
delete m;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testSFNetIssue2951221() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing sf.net issue 2951221 : hydrogens added with bad coordinates" << std::endl;
{
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/";
RWMol *m = MolFileToMol(pathName+"Issue2951221.1.mol");
TEST_ASSERT(m);
ROMol *m2 = MolOps::addHs(*m,false,true);
TEST_ASSERT(m2);
delete m;
TEST_ASSERT(m2->getNumAtoms(false)==12);
RDGeom::Point3D coords[4];
coords[0]= m2->getConformer().getAtomPos(2);
coords[1]= m2->getConformer().getAtomPos(0);
coords[2]= m2->getConformer().getAtomPos(1);
coords[3]= m2->getConformer().getAtomPos(9);
double dot=(coords[3]-coords[0]).dotProduct((coords[1]-coords[0]).crossProduct(coords[2]-coords[0]));
TEST_ASSERT(dot>1.0);
}
{
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/";
RWMol *m = MolFileToMol(pathName+"Issue2951221.2.mol");
TEST_ASSERT(m);
ROMol *m2 = MolOps::addHs(*m,false,true);
TEST_ASSERT(m2);
delete m;
TEST_ASSERT(m2->getNumAtoms(false)==5);
MolOps::assignChiralTypesFrom3D(*m2);
MolOps::assignStereochemistry(*m2,true,true);
TEST_ASSERT(m2->getAtomWithIdx(1)->hasProp("_CIPCode"));
std::string cip;
m2->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="S");
}
{
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/";
RWMol *m = MolFileToMol(pathName+"Issue2951221.3.mol");
TEST_ASSERT(m);
ROMol *m2 = MolOps::addHs(*m,false,true);
TEST_ASSERT(m2);
delete m;
TEST_ASSERT(m2->getNumAtoms(false)==5);
MolOps::assignChiralTypesFrom3D(*m2);
MolOps::assignStereochemistry(*m2,true,true);
TEST_ASSERT(m2->getAtomWithIdx(1)->hasProp("_CIPCode"));
std::string cip;
m2->getAtomWithIdx(1)->getProp("_CIPCode",cip);
TEST_ASSERT(cip=="R");
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testSFNetIssue2952255() {
BOOST_LOG(rdInfoLog) << "-----------------------\n Testing sf.net issue 2952255 : bad assignment of radicals to early elements" << std::endl;
{
std::string smi="[C](C)(C)C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==1);
delete m;
}
{
std::string smi="[C](C)C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==2);
delete m;
}
{
std::string smi="[CH](C)C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==1);
delete m;
}
{
std::string smi="[CH+](C)C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==0);
delete m;
}
{
std::string smi="[C-](C)C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==1);
delete m;
}
{
std::string smi="[C+](C)(C)(C)C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==1);
delete m;
}
{
std::string smi="C(C)(C)(C)C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==0);
delete m;
}
{
std::string smi="[N](C)C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==1);
delete m;
}
{
std::string smi="[N+](C)(C)C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==1);
delete m;
}
{
std::string smi="[Cl]";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==1);
delete m;
}
{
std::string smi="[Cl-]";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==0);
delete m;
}
{
std::string smi="[Cl]C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==0);
delete m;
}
{
std::string smi="[Na]";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==1);
delete m;
}
{
std::string smi="[Na+]";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==0);
delete m;
}
{
std::string smi="[Na]C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==0);
delete m;
}
{
std::string smi="[Mg+]C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==0);
delete m;
}
{
std::string smi="[Mg]C";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==1);
delete m;
}
{
std::string smi="[Mg+]";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==1);
delete m;
}
{
std::string smi="[Mg+2]";
RWMol *m = SmilesToMol(smi);
TEST_ASSERT(m);
TEST_ASSERT(m->getAtomWithIdx(0)->getNumRadicalElectrons()==0);
delete m;
}
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
int main(){
RDLog::InitLogs();
//boost::logging::enable_logs("rdApp.debug");
#if 1
test1();
test2();
test3();
test4();
test5();
//test6();
test7();
test8();
test9();
test10();
test11();
test12();
testIssue183();
testIssue188();
testIssue189();
testShortestPath();
testIssue190();
testIssue211();
testIssue210();
testIssue212();
testAddHsCoords();
testAddConformers();
testSanitOps();
testIssue252();
testIssue276();
testHsAndAromaticity();
testSFIssue1694023();
testSFIssue1719053();
testSFIssue1811276();
testSFIssue1836576();
testChiralityAndRemoveHs();
test11();
testSFIssue1894348();
testSFIssue1942657();
testSFIssue1968608();
testHybridization();
testAromaticityEdges();
testSFNetIssue2196817();
testSFNetIssue2208994();
testSFNetIssue2313979();
testSFNetIssue2316677();
testSanitizeNonringAromatics();
testSFNetIssue2951221();
#endif
testSFNetIssue2952255();
return 0;
}
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