void testHasPropMatch() {
QueryAtom qA;
qA.setQuery(makeHasPropQuery<Atom>("foo"));
Atom a1(6);
TEST_ASSERT(!qA.Match(&a1));
a1.setProp<int>("foo", 1);
TEST_ASSERT(qA.Match(&a1));
}
void testRecursiveSerialNumbers(){
std::cout << " ----------------- Testing serial numbers on recursive queries" << 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(new RWMol(*q1),1);
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(8),true,true);
q2->addBond(0,1,Bond::UNSPECIFIED);
qA = new QueryAtom(6);
rsq = new RecursiveStructureQuery(new RWMol(*q1),1);
qA->expandQuery(rsq,Queries::COMPOSITE_AND);
q2->addAtom(qA,true,true);
q2->addBond(1,2,Bond::UNSPECIFIED);
bool found = SubstructMatch(*m,*q2,matchV);
CHECK_INVARIANT(found,"");
CHECK_INVARIANT(matchV.size()==3,"");
n = SubstructMatch(*m,*q2,matches,true);
TEST_ASSERT(n==1);
TEST_ASSERT(matches.size()==1);
TEST_ASSERT(matches[0].size()==3);
delete q1;
delete q2;
}
delete m;
std::cout << "Done\n" << std::endl;
}
void testHasPropWithValueMatch() {
{
QueryAtom qA;
qA.setQuery(makePropQuery<Atom, int>("foo", 2));
Atom a1(6);
TEST_ASSERT(!qA.Match(&a1));
a1.setProp<int>("foo", 1);
TEST_ASSERT(!qA.Match(&a1));
a1.setProp<int>("foo", 2);
TEST_ASSERT(qA.Match(&a1));
a1.clearProp("foo");
a1.setProp<double>("foo", 2);
TEST_ASSERT(!qA.Match(&a1));
}
{
QueryAtom qA;
qA.setQuery(makePropQuery<Atom, std::string>("foo", "bar"));
Atom a1(6);
TEST_ASSERT(!qA.Match(&a1));
a1.setProp<std::string>("foo", "bar");
TEST_ASSERT(qA.Match(&a1));
}
{
QueryBond qA;
qA.setQuery(makePropQuery<Bond, int>("foo", 2));
Bond a1;
TEST_ASSERT(!qA.Match(&a1));
a1.setProp<int>("foo", 1);
TEST_ASSERT(!qA.Match(&a1));
a1.setProp<int>("foo", 2);
TEST_ASSERT(qA.Match(&a1));
a1.clearProp("foo");
a1.setProp<double>("foo", 2);
TEST_ASSERT(!qA.Match(&a1));
}
{
QueryBond qA;
qA.setQuery(makePropQuery<Bond, std::string>("foo", "bar"));
Bond a1;
TEST_ASSERT(!qA.Match(&a1));
a1.setProp<std::string>("foo", "bar");
TEST_ASSERT(qA.Match(&a1));
}
}
void test5QueryRoot(){
std::cout << " ----------------- Test 5 QueryRoot" << 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(8),true);
q1->addAtom(new QueryAtom(6),true);
q1->addBond(0,1,Bond::UNSPECIFIED);
q1->setProp("_queryRootAtom",1);
// here's the main query
q2 = new RWMol();
QueryAtom *qA = new QueryAtom();
RecursiveStructureQuery *rsq = new RecursiveStructureQuery(q1);
qA->setQuery(rsq);
q2->addAtom(qA,true,true);
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 test4() {
string smi = "C1COCCNCOCNSCC1";
unsigned int heteros1[] = {2, 7};
Mol *m = SmilesToMol(smi);
QueryAtom *q = new QueryAtom();
q->setQuery(makeAtomNumQuery(8));
{
unsigned int nSeen = 0;
for (Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
queryIt != m->endQueryAtoms(); queryIt++) {
CHECK_INVARIANT((*queryIt)->getIdx() == heteros1[nSeen], "bad query");
nSeen++;
}
}
{
Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
queryIt++;
queryIt--;
CHECK_INVARIANT((*queryIt)->getIdx() == heteros1[0], "bad query");
CHECK_INVARIANT((*++queryIt)->getIdx() == heteros1[1], "bad query");
CHECK_INVARIANT((*queryIt)->getIdx() == heteros1[1], "bad query");
}
{
Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
queryIt++;
queryIt--;
Mol::QueryAtomIterator queryIt2 = queryIt;
CHECK_INVARIANT((*queryIt2)->getIdx() == heteros1[0], "bad query");
CHECK_INVARIANT((*++queryIt2)->getIdx() == heteros1[1], "bad query");
CHECK_INVARIANT((*queryIt2)->getIdx() == heteros1[1], "bad query");
}
smi = "CC(C)CC(C)CC(C)CC(C)C";
unsigned int heteros2[] = {1, 4, 7, 10};
m = SmilesToMol(smi);
// m->debugMol(cout);
q->setQuery(makeAtomImplicitValenceQuery(1));
{
unsigned int nSeen = 0;
for (Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
queryIt != m->endQueryAtoms(); ++queryIt) {
CHECK_INVARIANT((*queryIt)->getIdx() == heteros2[nSeen], "bad query");
nSeen++;
}
}
BOOST_LOG(rdInfoLog) << "test4 done" << endl;
};
void test8() {
{
string smi = "CC1CC2CC1C2";
Mol *m = SmilesToMol(smi);
QueryAtom *q = new QueryAtom();
q->setQuery(makeAtomExplicitDegreeQuery(3));
q->expandQuery(makeAtomRingBondCountQuery(2));
unsigned int nSeen = 0;
for (Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
queryIt != m->endQueryAtoms(); ++queryIt) {
TEST_ASSERT((*queryIt)->getIdx() == 1);
nSeen++;
}
TEST_ASSERT(nSeen == 1);
delete m;
delete q;
}
BOOST_LOG(rdInfoLog) << "test8 done" << endl;
};
void testHasPropWithDoubleValueMatch() {
{
QueryAtom qA;
qA.setQuery(makePropQuery<Atom, double>("foo", 2));
Atom a1(6);
TEST_ASSERT(!qA.Match(&a1));
a1.setProp<double>("foo", 1);
TEST_ASSERT(!qA.Match(&a1));
a1.setProp<double>("foo", 2);
TEST_ASSERT(qA.Match(&a1));
}
{
QueryBond qA;
qA.setQuery(makePropQuery<Bond, double>("foo", 2));
Bond a1;
TEST_ASSERT(!qA.Match(&a1));
a1.setProp<double>("foo", 1);
TEST_ASSERT(!qA.Match(&a1));
a1.setProp<double>("foo", 2);
TEST_ASSERT(qA.Match(&a1));
}
}
void testExtraAtomQueries() {
BOOST_LOG(rdErrorLog) << "---------------------- Test extra atom queries"
<< std::endl;
{ // radicals
QueryAtom qA;
qA.setQuery(makeAtomNumRadicalElectronsQuery(1));
Atom a1(6);
TEST_ASSERT(!qA.Match(&a1));
a1.setNumRadicalElectrons(1);
TEST_ASSERT(qA.Match(&a1));
a1.setNumRadicalElectrons(2);
TEST_ASSERT(!qA.Match(&a1));
qA.getQuery()->setNegation(true);
TEST_ASSERT(qA.Match(&a1));
a1.setNumRadicalElectrons(0);
TEST_ASSERT(qA.Match(&a1));
a1.setNumRadicalElectrons(1);
TEST_ASSERT(!qA.Match(&a1));
}
{ // chiral tags
QueryAtom qA;
qA.setQuery(makeAtomHasChiralTagQuery());
Atom a1(6);
TEST_ASSERT(!qA.Match(&a1));
a1.setChiralTag(Atom::CHI_TETRAHEDRAL_CW);
TEST_ASSERT(qA.Match(&a1));
a1.setChiralTag(Atom::CHI_TETRAHEDRAL_CCW);
TEST_ASSERT(qA.Match(&a1));
a1.setChiralTag(Atom::CHI_OTHER);
TEST_ASSERT(qA.Match(&a1));
qA.getQuery()->setNegation(true);
a1.setChiralTag(Atom::CHI_UNSPECIFIED);
TEST_ASSERT(qA.Match(&a1));
a1.setChiralTag(Atom::CHI_TETRAHEDRAL_CW);
TEST_ASSERT(!qA.Match(&a1));
a1.setChiralTag(Atom::CHI_TETRAHEDRAL_CCW);
TEST_ASSERT(!qA.Match(&a1));
a1.setChiralTag(Atom::CHI_OTHER);
TEST_ASSERT(!qA.Match(&a1));
}
{ // missing chiral tags
QueryAtom qA;
qA.setQuery(makeAtomMissingChiralTagQuery());
Atom a1(6);
TEST_ASSERT(!qA.Match(&a1));
a1.setChiralTag(Atom::CHI_TETRAHEDRAL_CW);
TEST_ASSERT(!qA.Match(&a1));
a1.setChiralTag(Atom::CHI_TETRAHEDRAL_CCW);
TEST_ASSERT(!qA.Match(&a1));
a1.setChiralTag(Atom::CHI_OTHER);
TEST_ASSERT(!qA.Match(&a1));
a1.setChiralTag(Atom::CHI_UNSPECIFIED);
a1.setProp(common_properties::_ChiralityPossible, 1);
TEST_ASSERT(qA.Match(&a1));
a1.setChiralTag(Atom::CHI_TETRAHEDRAL_CW);
TEST_ASSERT(!qA.Match(&a1));
a1.setChiralTag(Atom::CHI_TETRAHEDRAL_CCW);
TEST_ASSERT(!qA.Match(&a1));
a1.setChiralTag(Atom::CHI_OTHER);
TEST_ASSERT(!qA.Match(&a1));
qA.getQuery()->setNegation(true);
a1.clearProp(common_properties::_ChiralityPossible);
a1.setChiralTag(Atom::CHI_UNSPECIFIED);
TEST_ASSERT(qA.Match(&a1));
a1.setChiralTag(Atom::CHI_TETRAHEDRAL_CW);
TEST_ASSERT(qA.Match(&a1));
a1.setChiralTag(Atom::CHI_TETRAHEDRAL_CCW);
TEST_ASSERT(qA.Match(&a1));
a1.setChiralTag(Atom::CHI_OTHER);
TEST_ASSERT(qA.Match(&a1));
a1.setChiralTag(Atom::CHI_UNSPECIFIED);
a1.setProp(common_properties::_ChiralityPossible, 1);
TEST_ASSERT(!qA.Match(&a1));
}
BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}
void testQualifiedQueries() {
BOOST_LOG(rdErrorLog)
<< "---------------------- Test queries using qualifiers instead of =="
<< std::endl;
RWMol *m = SmilesToMol("CNO");
{
QueryAtom qA;
qA.setQuery(makeAtomNumQuery<ATOM_GREATER_QUERY>(7, "test"));
TEST_ASSERT(qA.Match(m->getAtomWithIdx(0)));
TEST_ASSERT(!qA.Match(m->getAtomWithIdx(1)));
TEST_ASSERT(!qA.Match(m->getAtomWithIdx(2)));
}
{
QueryAtom qA;
qA.setQuery(makeAtomNumQuery<ATOM_GREATEREQUAL_QUERY>(7, "test"));
TEST_ASSERT(qA.Match(m->getAtomWithIdx(0)));
TEST_ASSERT(qA.Match(m->getAtomWithIdx(1)));
TEST_ASSERT(!qA.Match(m->getAtomWithIdx(2)));
}
{
QueryAtom qA;
qA.setQuery(makeAtomNumQuery<ATOM_LESS_QUERY>(7, "test"));
TEST_ASSERT(!qA.Match(m->getAtomWithIdx(0)));
TEST_ASSERT(!qA.Match(m->getAtomWithIdx(1)));
TEST_ASSERT(qA.Match(m->getAtomWithIdx(2)));
}
{
QueryAtom qA;
qA.setQuery(makeAtomNumQuery<ATOM_LESSEQUAL_QUERY>(7, "test"));
TEST_ASSERT(!qA.Match(m->getAtomWithIdx(0)));
TEST_ASSERT(qA.Match(m->getAtomWithIdx(1)));
TEST_ASSERT(qA.Match(m->getAtomWithIdx(2)));
}
delete m;
BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}
void test1() {
BOOST_LOG(rdErrorLog) << "---------------------- Test1" << std::endl;
Mol qM;
Mol m;
Atom *a = new Atom(6);
// we copy in addAtom, so this is safe
m.addAtom(a);
m.addAtom(a);
delete a;
m.addBond(0, 1, Bond::SINGLE);
a = new Atom(8);
m.addAtom(a);
delete a;
m.addBond(1, 2, Bond::DOUBLE);
MolOps::sanitizeMol(m);
QueryAtom *qA = new QueryAtom(6);
CHECK_INVARIANT(qA->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(qA->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(!qA->Match(m.getAtomWithIdx(2)), "");
qA->expandQuery(makeAtomImplicitValenceQuery(3));
CHECK_INVARIANT(qA->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(!qA->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(!qA->Match(m.getAtomWithIdx(2)), "");
qM.addAtom(qA);
delete qA;
qA = new QueryAtom(6);
qA->expandQuery(makeAtomNumQuery(8), Queries::COMPOSITE_OR);
qM.addAtom(qA);
delete qA;
qM.addAtom(new QueryAtom(8), true, true);
// Atom::ATOM_SPTR qA(new QueryAtom(6));
QueryBond *qB;
qB = new QueryBond(Bond::UNSPECIFIED);
qB->setOwningMol(qM);
qB->setBeginAtomIdx(0);
qB->setEndAtomIdx(1);
CHECK_INVARIANT(qB->Match(m.getBondWithIdx(0)), "");
CHECK_INVARIANT(qB->Match(m.getBondWithIdx(1)), "");
qM.addBond(qB, true);
qB = new QueryBond(Bond::DOUBLE);
qB->setOwningMol(qM);
qB->setBeginAtomIdx(1);
qB->setEndAtomIdx(2);
qM.addBond(qB, true);
CHECK_INVARIANT(qM.getAtomWithIdx(0)->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(!qM.getAtomWithIdx(0)->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(!qM.getAtomWithIdx(0)->Match(m.getAtomWithIdx(2)), "");
CHECK_INVARIANT(qM.getAtomWithIdx(1)->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(qM.getAtomWithIdx(1)->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(qM.getAtomWithIdx(1)->Match(m.getAtomWithIdx(2)), "");
CHECK_INVARIANT(!qM.getAtomWithIdx(2)->Match(m.getAtomWithIdx(0)), "");
CHECK_INVARIANT(!qM.getAtomWithIdx(2)->Match(m.getAtomWithIdx(1)), "");
CHECK_INVARIANT(qM.getAtomWithIdx(2)->Match(m.getAtomWithIdx(2)), "");
CHECK_INVARIANT(qM.getBondWithIdx(0)->Match(m.getBondWithIdx(0)), "");
CHECK_INVARIANT(qM.getBondWithIdx(0)->Match(m.getBondWithIdx(1)), "");
CHECK_INVARIANT(!qM.getBondWithIdx(1)->Match(m.getBondWithIdx(0)), "");
CHECK_INVARIANT(qM.getBondWithIdx(1)->Match(m.getBondWithIdx(1)), "");
BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}
QueryAtom *HasPropQueryAtom(const std::string &propname, bool negate) {
QueryAtom *res = new QueryAtom();
res->setQuery(makeHasPropQuery<Atom>(propname));
if (negate) res->getQuery()->setNegation(true);
return res;
}
