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rdkit/Code/GraphMol/Substruct/test1.cpp

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// $Id$
//
// Copyright (C) 2001-2006 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
//
// std bits
#include <iostream>
// RD bits
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include "SubstructMatch.h"
#include "SubstructUtils.h"
using namespace RDKit;
void test1(){
std::cout << " ----------------- Test 1" << std::endl;
MatchVectType matchV;
std::vector< MatchVectType > matches;
unsigned int n;
RWMol *m,*q1;
m = new RWMol();
m->addAtom(new Atom(8));
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addBond(0,1,Bond::SINGLE);
m->addBond(1,2,Bond::SINGLE);
q1 = new RWMol();
q1->addAtom(new QueryAtom(6));
q1->addAtom(new QueryAtom(6));
q1->addBond(0,1,Bond::SINGLE);
n = SubstructMatch(*m,*q1,matches,false);
CHECK_INVARIANT(n==2,"");
CHECK_INVARIANT(matches.size()==n,"");
CHECK_INVARIANT(matches[0].size()==2,"");
TEST_ASSERT(matches[0][0].first==0);
TEST_ASSERT(matches[0][0].second==1||matches[0][0].second==2);
TEST_ASSERT(matches[0][1].first==1);
TEST_ASSERT(matches[0][1].second!=matches[0][0].second);
TEST_ASSERT(matches[1][1].second==1||matches[0][1].second==2);
TEST_ASSERT(matches[1][0].first==0);
TEST_ASSERT(matches[1][0].second==1||matches[1][0].second==2);
TEST_ASSERT(matches[1][0].second!=matches[0][0].second);
TEST_ASSERT(matches[1][0].second==matches[0][1].second);
TEST_ASSERT(matches[1][1].first==1);
TEST_ASSERT(matches[1][1].second!=matches[1][0].second);
TEST_ASSERT(matches[1][1].second==matches[0][0].second);
n = SubstructMatch(*m,*q1,matches,true);
CHECK_INVARIANT(n==1,"");
CHECK_INVARIANT(matches.size()==n,"");
CHECK_INVARIANT(matches[0].size()==2,"");
TEST_ASSERT(matches[0][0].first==0);
TEST_ASSERT(matches[0][0].second==1||matches[0][0].second==2);
TEST_ASSERT(matches[0][1].first==1);
TEST_ASSERT(matches[0][1].second!=matches[0][0].second);
TEST_ASSERT(matches[0][1].second==1||matches[0][1].second==2);
CHECK_INVARIANT(SubstructMatch(*m,*q1,matchV),"");
CHECK_INVARIANT(matchV.size()==2,"");
// make sure we reset the match vectors.
// build a query we won't match:
q1->addAtom(new QueryAtom(6));
q1->addBond(1,2,Bond::SINGLE);
q1->addAtom(new QueryAtom(6));
q1->addBond(2,3,Bond::SINGLE);
TEST_ASSERT(!SubstructMatch(*m,*q1,matchV));
TEST_ASSERT(matchV.size()==0);
n = SubstructMatch(*m,*q1,matches,false);
TEST_ASSERT(n==0);
TEST_ASSERT(matches.size()==0);
std::cout << "Done\n" << std::endl;
}
void test2(){
std::cout << " ----------------- Test 2" << std::endl;
MatchVectType matchV;
std::vector< MatchVectType > matches;
unsigned int n;
RWMol *m,*q1;
m = new RWMol();
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(8));
m->addBond(0,1,Bond::SINGLE);
m->addBond(1,2,Bond::SINGLE);
q1 = new RWMol();
q1->addAtom(new QueryAtom(6));
q1->addAtom(new QueryAtom(8));
q1->addBond(0,1,Bond::SINGLE);
n = SubstructMatch(*m,*q1,matchV);
TEST_ASSERT(n);
TEST_ASSERT(matchV.size()==2);
TEST_ASSERT(matchV[0].first==0);
TEST_ASSERT(matchV[0].second==1);
TEST_ASSERT(matchV[1].first==1);
TEST_ASSERT(matchV[1].second==2);
n = SubstructMatch(*m,*q1,matches,false);
CHECK_INVARIANT(n==1,"");
CHECK_INVARIANT(matches.size()==n,"");
CHECK_INVARIANT(matches[0].size()==2,"");
n = SubstructMatch(*m,*q1,matches,true);
CHECK_INVARIANT(n==1,"");
CHECK_INVARIANT(matches.size()==n,"");
CHECK_INVARIANT(matches[0].size()==2,"");
CHECK_INVARIANT(SubstructMatch(*m,*q1,matchV),"");
CHECK_INVARIANT(matchV.size()==2,"");
delete m;
m = new RWMol();
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(8));
m->addBond(0,1,Bond::SINGLE);
m->addBond(1,2,Bond::DOUBLE);
matches.clear();
n = SubstructMatch(*m,*q1,matches,false);
CHECK_INVARIANT(n==0,"");
CHECK_INVARIANT(matches.size()==n,"");
n = SubstructMatch(*m,*q1,matches,true);
CHECK_INVARIANT(n==0,"");
CHECK_INVARIANT(matches.size()==n,"");
CHECK_INVARIANT(!SubstructMatch(*m,*q1,matchV),"");
std::cout << "Done\n" << std::endl;
}
void test3(){
std::cout << " ----------------- Test 3" << std::endl;
MatchVectType matchV;
std::vector< MatchVectType > matches;
unsigned int n;
RWMol *m,*q1;
m = new RWMol();
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(8));
m->addBond(0,1,Bond::SINGLE);
m->addBond(1,2,Bond::SINGLE);
q1 = new RWMol();
q1->addAtom(new QueryAtom(6));
q1->addAtom(new QueryAtom(8));
q1->addBond(0,1,Bond::UNSPECIFIED);
n = SubstructMatch(*m,*q1,matches,false);
CHECK_INVARIANT(n==1,"");
CHECK_INVARIANT(matches.size()==n,"");
CHECK_INVARIANT(matches[0].size()==2,"");
n = SubstructMatch(*m,*q1,matches,true);
CHECK_INVARIANT(n==1,"");
CHECK_INVARIANT(matches.size()==n,"");
CHECK_INVARIANT(matches[0].size()==2,"");
CHECK_INVARIANT(SubstructMatch(*m,*q1,matchV),"");
CHECK_INVARIANT(matchV.size()==2,"");
delete m;
m = new RWMol();
m->addAtom(new Atom(6));
m->addAtom(new Atom(6));
m->addAtom(new Atom(8));
m->addBond(0,1,Bond::SINGLE);
m->addBond(1,2,Bond::DOUBLE);
matches.clear();
n = SubstructMatch(*m,*q1,matches,false);
CHECK_INVARIANT(n==1,"");
CHECK_INVARIANT(matches.size()==n,"");
CHECK_INVARIANT(matches[0].size()==2,"");
n = SubstructMatch(*m,*q1,matches,true);
CHECK_INVARIANT(n==1,"");
CHECK_INVARIANT(matches.size()==n,"");
CHECK_INVARIANT(matches[0].size()==2,"");
CHECK_INVARIANT(SubstructMatch(*m,*q1,matchV),"");
CHECK_INVARIANT(matchV.size()==2,"");
std::cout << "Done\n" << std::endl;
}
void test4(){
std::cout << " ----------------- Test 4" << std::endl;
MatchVectType matchV;
std::vector< MatchVectType > matches;
int n;
RWMol *m,*q1,*q2;
Atom *a6 = new Atom(6);
Atom *a8 = new Atom(8);
m = new RWMol();
m->addAtom(a6);
m->addAtom(a6);
m->addAtom(a8);
m->addAtom(a6);
m->addAtom(a6);
m->addBond(1,0,Bond::SINGLE);
m->addBond(1,2,Bond::SINGLE);
m->addBond(1,3,Bond::SINGLE);
m->addBond(2,4,Bond::SINGLE);
// this will be the recursive query
q1 = new RWMol();
q1->addAtom(new QueryAtom(6),true);
q1->addAtom(new QueryAtom(8),true);
q1->addBond(0,1,Bond::UNSPECIFIED);
// here's the main query
q2 = new RWMol();
QueryAtom *qA = new QueryAtom(6);
RecursiveStructureQuery *rsq = new RecursiveStructureQuery(q1);
qA->expandQuery(rsq,Queries::COMPOSITE_AND);
//std::cout << "post expand: " << qA->getQuery() << std::endl;
q2->addAtom(qA,true,true);
//std::cout << "mol: " << q2->getAtomWithIdx(0)->getQuery() << std::endl;
q2->addAtom(new QueryAtom(6),true,true);
q2->addBond(0,1,Bond::UNSPECIFIED);
bool found = SubstructMatch(*m,*q2,matchV);
CHECK_INVARIANT(found,"");
CHECK_INVARIANT(matchV.size()==2,"");
TEST_ASSERT(matchV[0].first==0);
TEST_ASSERT(matchV[0].second==1);
TEST_ASSERT(matchV[1].first==1);
TEST_ASSERT(matchV[1].second==0||matchV[1].second==3);
n = SubstructMatch(*m,*q2,matches,true);
CHECK_INVARIANT(n==2,"");
CHECK_INVARIANT(matches[0].size()==2,"");
std::cout << "Done\n" << std::endl;
}
void test5(){
std::cout << " ----------------- Test 5" << std::endl;
MatchVectType matchV;
std::vector< MatchVectType > matches;
int n;
RWMol *m,*q1,*q2;
Atom *a6 = new Atom(6);
Atom *a8 = new Atom(8);
// CC(OC)C
m = new RWMol();
m->addAtom(a6);
m->addAtom(a6);
m->addAtom(a8);
m->addAtom(a6);
m->addAtom(a6);
m->addBond(0,1,Bond::SINGLE);
m->addBond(1,2,Bond::SINGLE);
m->addBond(1,4,Bond::SINGLE);
m->addBond(2,3,Bond::SINGLE);
// this will be the recursive query
q1 = new RWMol();
q1->addAtom(new QueryAtom(6),true);
q1->addAtom(new QueryAtom(8),true);
q1->addBond(0,1,Bond::UNSPECIFIED);
// here's the main query
q2 = new RWMol();
QueryAtom *qA = new QueryAtom();
RecursiveStructureQuery *rsq = new RecursiveStructureQuery(q1);
qA->setQuery(rsq);
//std::cout << "post expand: " << qA->getQuery() << std::endl;
q2->addAtom(qA,true,true);
//std::cout << "mol: " << q2->getAtomWithIdx(0)->getQuery() << std::endl;
q2->addAtom(new QueryAtom(6),true,true);
q2->addBond(0,1,Bond::UNSPECIFIED);
bool found = SubstructMatch(*m,*q2,matchV);
CHECK_INVARIANT(found,"");
CHECK_INVARIANT(matchV.size()==2,"");
n = SubstructMatch(*m,*q2,matches,true);
CHECK_INVARIANT(n==2,"");
CHECK_INVARIANT(matches[0].size()==2,"");
std::cout << "Done\n" << std::endl;
}
void test6(){
std::cout << " ----------------- Test 6 (Issue71 related)" << std::endl;
MatchVectType matchV;
std::vector< MatchVectType > matches;
int n;
RWMol *m,*q1;
Atom *a6 = new Atom(6);
m = new RWMol();
m->addAtom(a6);
m->addAtom(a6);
m->addAtom(a6);
m->addBond(0,1,Bond::SINGLE);
m->addBond(1,2,Bond::SINGLE);
m->addBond(0,2,Bond::SINGLE);
q1 = new RWMol();
q1->addAtom(new QueryAtom(6),true);
q1->addAtom(new QueryAtom(6),true);
q1->addAtom(new QueryAtom(6),true);
q1->addBond(0,1,Bond::UNSPECIFIED);
q1->addBond(1,2,Bond::UNSPECIFIED);
bool found = SubstructMatch(*m,*q1,matchV);
CHECK_INVARIANT(found,"");
CHECK_INVARIANT(matchV.size()==3,"");
n = SubstructMatch(*m,*q1,matches,true);
CHECK_INVARIANT(n==1,"");
CHECK_INVARIANT(matches[0].size()==3,"");
// close the loop and try again (we should still match)
q1->addBond(0,2,Bond::UNSPECIFIED);
found = SubstructMatch(*m,*q1,matchV);
CHECK_INVARIANT(found,"");
CHECK_INVARIANT(matchV.size()==3,"");
n = SubstructMatch(*m,*q1,matches,true);
CHECK_INVARIANT(n==1,"");
CHECK_INVARIANT(matches[0].size()==3,"");
std::cout << "Done\n" << std::endl;
}
void test7(){
std::cout << " ----------------- Test 7 (leak check)" << std::endl;
MatchVectType matchV;
int n;
RWMol *m,*q1;
Atom *a6 = new Atom(6);
m = new RWMol();
m->addAtom(a6);
m->addAtom(a6);
m->addAtom(a6);
m->addBond(0,1,Bond::SINGLE);
m->addBond(1,2,Bond::SINGLE);
m->addBond(0,2,Bond::SINGLE);
q1 = new RWMol();
q1->addAtom(new QueryAtom(6),true);
q1->addAtom(new QueryAtom(6),true);
q1->addAtom(new QueryAtom(6),true);
q1->addBond(0,1,Bond::UNSPECIFIED);
q1->addBond(1,2,Bond::UNSPECIFIED);
bool found = SubstructMatch(*m,*q1,matchV);
CHECK_INVARIANT(found,"");
CHECK_INVARIANT(matchV.size()==3,"");
std::vector< MatchVectType > matches;
for(int i=0;i<300000;i++){
n = SubstructMatch(*m,*q1,matches,true,true);
CHECK_INVARIANT(n==1,"");
CHECK_INVARIANT(matches[0].size()==3,"");
if(! (i%500) ) std::cout << i << std::endl;
}
std::cout << "Done\n" << std::endl;
}
#ifdef CACHE_ARMOLGRAPHS
void test8(){
std::cout << " ----------------- Test 8 (molgraph cache)" << std::endl;
MatchVectType matchV;
int n;
RWMol *m,*q1;
Atom *a6 = new Atom(6);
m = new RWMol();
m->addAtom(a6);
m->addAtom(a6);
m->addAtom(a6);
m->addBond(0,1,Bond::SINGLE);
m->addBond(1,2,Bond::SINGLE);
m->addBond(0,2,Bond::SINGLE);
q1 = new RWMol();
q1->addAtom(new QueryAtom(6),true);
q1->addAtom(new QueryAtom(6),true);
q1->addAtom(new QueryAtom(6),true);
q1->addBond(0,1,Bond::UNSPECIFIED);
q1->addBond(1,2,Bond::UNSPECIFIED);
bool found = SubstructMatch(*m,*q1,matchV);
CHECK_INVARIANT(found,"");
CHECK_INVARIANT(matchV.size()==3,"");
std::vector< MatchVectType > matches;
for(int i=0;i<30000;i++){
n = SubstructMatch(*m,*q1,matches,true,true);
CHECK_INVARIANT(n==1,"");
CHECK_INVARIANT(matches[0].size()==3,"");
if(! (i%500) ) std::cout << i << std::endl;
}
std::cout << "Done\n" << std::endl;
}
#endif
void test9(){
std::cout << " ----------------- Test 9 (chiral searches)" << std::endl;
MatchVectType matchV;
std::vector< MatchVectType > matches;
int n;
RWMol *m,*q1;
Atom *a6 = new Atom(6);
m = new RWMol();
m->addAtom(a6);
m->addAtom(new Atom(6));
m->addAtom(new Atom(7));
m->addAtom(new Atom(8));
m->addAtom(new Atom(9));
m->addBond(0,1,Bond::SINGLE);
m->addBond(0,2,Bond::SINGLE);
m->addBond(0,3,Bond::SINGLE);
m->addBond(0,4,Bond::SINGLE);
m->getAtomWithIdx(0)->setChiralTag(Atom::CHI_TETRAHEDRAL_CW);
q1 = new RWMol();
q1->addAtom(a6);
q1->addAtom(new Atom(6));
q1->addAtom(new Atom(7));
q1->addAtom(new Atom(8));
q1->addAtom(new Atom(9));
q1->addBond(0,1,Bond::SINGLE);
q1->addBond(0,2,Bond::SINGLE);
q1->addBond(0,3,Bond::SINGLE);
q1->addBond(0,4,Bond::SINGLE);
q1->getAtomWithIdx(0)->setChiralTag(Atom::CHI_TETRAHEDRAL_CCW);
MolOps::sanitizeMol(*m);
MolOps::assignAtomChiralCodes(*m);
MolOps::sanitizeMol(*q1);
MolOps::assignAtomChiralCodes(*q1);
bool found;
// test with default options (no chirality):
found = SubstructMatch(*m,*q1,matchV);
TEST_ASSERT(found);
n = SubstructMatch(*m,*q1,matches,true);
TEST_ASSERT(n==1);
// test with chirality
found = SubstructMatch(*m,*q1,matchV,true,true);
TEST_ASSERT(!found);
n = SubstructMatch(*m,*q1,matches,true,true,true);
TEST_ASSERT(n==0);
// self matches:
found = SubstructMatch(*m,*m,matchV,true,true);
TEST_ASSERT(found);
n = SubstructMatch(*m,*m,matches,true,true,true);
TEST_ASSERT(n==1);
found = SubstructMatch(*q1,*q1,matchV,true,true);
TEST_ASSERT(found);
n = SubstructMatch(*q1,*q1,matches,true,true,true);
TEST_ASSERT(n==1);
std::cout << "Done\n" << std::endl;
}
int main(int argc,char *argv[])
{
#if 1
test1();
test2();
test3();
#endif
test4();
test5();
test6();
if(argc>1 && !strcmp(argv[1],"-l"))
test7();
test9();
return 0;
}
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