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9cabf873744329ad09f77bbffdc7b2c9cef192d6
rdkit/Code/GraphMol/querytest.cpp
Greg Landrum 9cabf87374 remove vflib from Jamfiles 
remove const specifiers from return values in DataStructs
add initial pass at query-query matching for Atoms and Bonds
fix and test for sf.net issu 2738320
add Mol.AddRecursiveQuery() method to Mol
2009-06-29 11:47:38 +00:00

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// $Id$
//
// Copyright (C) 2002-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <iostream>
using namespace RDKit;
using namespace std;
typedef class RWMol Mol;
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);
qA = new QueryAtom(6);
qA->expandQuery(makeAtomNumEqualsQuery(8),Queries::COMPOSITE_OR);
qM.addAtom(qA);
qM.addAtom(new QueryAtom(8));
//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);
qB = new QueryBond(Bond::DOUBLE);
qB->setOwningMol(qM);
qB->setBeginAtomIdx(1);
qB->setEndAtomIdx(2);
qM.addBond(qB);
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;
}
void test2(){
BOOST_LOG(rdErrorLog) << "---------------------- Test2" << 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);
m.addAtom(a);
delete a;
m.addBond(0,1,Bond::TRIPLE);
m.addBond(1,2,Bond::SINGLE);
a = new Atom(8);
m.addAtom(a);
delete a;
m.addBond(2,3,Bond::DOUBLE);
MolOps::sanitizeMol(m);
QueryBond *qB;
qB = new QueryBond(Bond::SINGLE);
CHECK_INVARIANT(!qB->Match(m.getBondWithIdx(0)),"");
CHECK_INVARIANT(qB->Match(m.getBondWithIdx(1)),"");
CHECK_INVARIANT(!qB->Match(m.getBondWithIdx(2)),"");
BOND_EQUALS_QUERY *newQ = makeBondOrderEqualsQuery(Bond::DOUBLE);
qB->expandQuery(newQ,Queries::COMPOSITE_OR);
CHECK_INVARIANT(!qB->Match(m.getBondWithIdx(0)),"");
CHECK_INVARIANT(qB->Match(m.getBondWithIdx(1)),"");
CHECK_INVARIANT(qB->Match(m.getBondWithIdx(2)),"");
BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}
void test3(){
BOOST_LOG(rdErrorLog) << "---------------------- Test3" << std::endl;
Mol m;
Atom *a = new Atom(6);
// we copy in addAtom, so this is safe
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
delete a;
m.addBond(0,1,Bond::SINGLE);
m.addBond(1,2,Bond::DOUBLE);
m.addBond(2,3,Bond::SINGLE);
m.addBond(3,4,Bond::DOUBLE);
m.addBond(4,5,Bond::SINGLE);
m.addBond(5,0,Bond::DOUBLE);
m.addBond(5,6,Bond::SINGLE);
MolOps::sanitizeMol(m);
ATOM_EQUALS_QUERY *aeq = makeAtomExplicitDegreeQuery(3);
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
delete aeq;
aeq = makeAtomExplicitDegreeQuery(2);
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
delete aeq;
aeq = makeAtomHCountQuery(1);
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
delete aeq;
aeq = makeAtomInNRingsQuery(1);
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
delete aeq;
aeq = makeAtomInNRingsQuery(0);
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)),"");
delete aeq;
aeq = makeAtomAromaticQuery();
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
delete aeq;
aeq = makeAtomAliphaticQuery();
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)),"");
delete aeq;
aeq = makeAtomInRingQuery();
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
aeq->setNegation(true);
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)),"");
delete aeq;
aeq = makeAtomInRingOfSizeQuery(6);
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
aeq->setNegation(true);
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)),"");
delete aeq;
aeq = makeAtomInRingOfSizeQuery(5);
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)),"");
CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
aeq->setNegation(true);
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)),"");
delete aeq;
BOND_EQUALS_QUERY *beq = makeBondIsInRingQuery();
CHECK_INVARIANT(beq->Match(m.getBondWithIdx(0)),"");
CHECK_INVARIANT(!beq->Match(m.getBondWithIdx(6)),"");
CHECK_INVARIANT(beq->Match(m.getBondBetweenAtoms(0,1)),"");
CHECK_INVARIANT(beq->Match(m.getBondBetweenAtoms(1,0)),"");
CHECK_INVARIANT(!beq->Match(m.getBondBetweenAtoms(5,6)),"");
CHECK_INVARIANT(!beq->Match(m.getBondBetweenAtoms(6,5)),"");
BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}
void test4(){
BOOST_LOG(rdErrorLog) << "---------------------- Test4" << std::endl;
Mol m;
Atom *a = new Atom(6);
// we copy in addAtom, so this is safe
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
delete a;
m.addBond(0,1,Bond::SINGLE);
m.addBond(1,2,Bond::DOUBLE);
m.addBond(2,3,Bond::SINGLE);
m.addBond(3,4,Bond::DOUBLE);
m.addBond(4,5,Bond::SINGLE);
m.addBond(5,0,Bond::DOUBLE);
m.addBond(5,6,Bond::SINGLE);
MolOps::sanitizeMol(m);
ATOM_NULL_QUERY *aeq = makeAtomNullQuery();
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)),"");
CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)),"");
delete aeq;
BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}
void test5(){
BOOST_LOG(rdErrorLog) << "---------------------- Test5" << std::endl;
Mol m;
Atom *a = new Atom(6);
// we copy in addAtom, so this is safe
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
m.addAtom(a);
delete a;
m.addBond(0,1,Bond::SINGLE);
m.addBond(1,2,Bond::DOUBLE);
m.addBond(2,3,Bond::SINGLE);
m.addBond(3,4,Bond::DOUBLE);
m.addBond(4,5,Bond::SINGLE);
m.addBond(5,0,Bond::DOUBLE);
m.addBond(5,6,Bond::SINGLE);
MolOps::sanitizeMol(m);
unsigned int valenceProd;
valenceProd=queryAtomBondProduct(m.getAtomWithIdx(0));
TEST_ASSERT(valenceProd==1681); // aromatic*aromatic = 41 * 41 = 1681
valenceProd=queryAtomBondProduct(m.getAtomWithIdx(1));
TEST_ASSERT(valenceProd==1681);
valenceProd=queryAtomBondProduct(m.getAtomWithIdx(5));
TEST_ASSERT(valenceProd==5043);
valenceProd=queryAtomBondProduct(m.getAtomWithIdx(6));
TEST_ASSERT(valenceProd==3);
valenceProd=queryAtomAllBondProduct(m.getAtomWithIdx(6));
TEST_ASSERT(valenceProd==81);
BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}
void test6(){
BOOST_LOG(rdErrorLog) << "---------------------- Test6" << std::endl;
Mol m;
Atom *a = new Atom(6);
int massVal;
massVal=queryAtomMass(a);
TEST_ASSERT(massVal==static_cast<int>(RDKit::round(12.011*massIntegerConversionFactor)));
a->setMass(13);
massVal=queryAtomMass(a);
TEST_ASSERT(massVal==static_cast<int>(RDKit::round(13.000*massIntegerConversionFactor)));
BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}
void testQueryQueryMatches(){
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "Testing query--query matches" << std::endl;
// =====================================
// ATOMS
// =====================================
{
QueryAtom a1,a2;
a1.setQuery(makeAtomNullQuery());
a2.setQuery(makeAtomNullQuery());
TEST_ASSERT(a1.Match(&a2));
TEST_ASSERT(a2.Match(&a1));
}
{
QueryAtom a1,a2(6);
a1.setQuery(makeAtomNullQuery());
TEST_ASSERT(a1.Match(&a2));
TEST_ASSERT(a2.Match(&a1));
}
{
QueryAtom a1(6),a2(8);
TEST_ASSERT(!a1.Match(&a2));
TEST_ASSERT(!a2.Match(&a1));
}
{
QueryAtom a1(6),a2(6);
TEST_ASSERT(a1.Match(&a2));
TEST_ASSERT(a2.Match(&a1));
}
{
QueryAtom a1,a2;
a1.setQuery(makeAtomAromaticQuery());
a2.setQuery(makeAtomAromaticQuery());
TEST_ASSERT(a1.Match(&a2));
TEST_ASSERT(a2.Match(&a1));
}
{
QueryAtom a1,a2;
a1.setQuery(makeAtomAromaticQuery());
a2.setQuery(makeAtomAliphaticQuery());
TEST_ASSERT(!a1.Match(&a2));
TEST_ASSERT(!a2.Match(&a1));
}
{
QueryAtom a1(6),a2(8);
a1.expandQuery(makeAtomNumEqualsQuery(8),Queries::COMPOSITE_OR);
a2.expandQuery(makeAtomNumEqualsQuery(9),Queries::COMPOSITE_OR);
TEST_ASSERT(a1.Match(&a2));
TEST_ASSERT(a2.Match(&a1));
}
{
QueryAtom a1(6),a2(8);
a1.expandQuery(makeAtomNumEqualsQuery(7),Queries::COMPOSITE_OR);
a2.expandQuery(makeAtomNumEqualsQuery(9),Queries::COMPOSITE_OR);
TEST_ASSERT(!a1.Match(&a2));
TEST_ASSERT(!a2.Match(&a1));
}
{
QueryAtom a1(6),a2(6);
a1.expandQuery(makeAtomExplicitValenceQuery(3),Queries::COMPOSITE_AND);
a2.expandQuery(makeAtomExplicitValenceQuery(3),Queries::COMPOSITE_AND);
TEST_ASSERT(a1.Match(&a2));
TEST_ASSERT(a2.Match(&a1));
}
{
QueryAtom a1(6),a2(6);
a1.expandQuery(makeAtomExplicitValenceQuery(3),Queries::COMPOSITE_AND);
a2.expandQuery(makeAtomExplicitValenceQuery(4),Queries::COMPOSITE_AND);
TEST_ASSERT(!a1.Match(&a2));
TEST_ASSERT(!a2.Match(&a1));
}
{
QueryAtom a1(6),a2(8);
a1.expandQuery(makeAtomExplicitValenceQuery(3),Queries::COMPOSITE_AND);
a2.expandQuery(makeAtomExplicitValenceQuery(3),Queries::COMPOSITE_AND);
TEST_ASSERT(!a1.Match(&a2));
TEST_ASSERT(!a2.Match(&a1));
}
{
QueryAtom a1(6),a2(8);
a1.expandQuery(makeAtomNumEqualsQuery(8),Queries::COMPOSITE_OR);
TEST_ASSERT(a1.Match(&a2));
TEST_ASSERT(a2.Match(&a1));
}
// =====================================
// BONDS
// =====================================
{
QueryBond a1,a2;
a1.setQuery(makeBondNullQuery());
a2.setQuery(makeBondNullQuery());
TEST_ASSERT(a1.Match(&a2));
TEST_ASSERT(a2.Match(&a1));
}
{
QueryBond a1,a2(Bond::SINGLE);
a1.setQuery(makeBondNullQuery());
TEST_ASSERT(a1.Match(&a2));
TEST_ASSERT(a2.Match(&a1));
}
{
QueryBond a1(Bond::SINGLE),a2(Bond::SINGLE);
TEST_ASSERT(a1.Match(&a2));
TEST_ASSERT(a2.Match(&a1));
}
{
QueryBond a1(Bond::SINGLE),a2(Bond::DOUBLE);
TEST_ASSERT(!a1.Match(&a2));
TEST_ASSERT(!a2.Match(&a1));
}
{
QueryBond a1(Bond::SINGLE),a2(Bond::DOUBLE);
a1.expandQuery(makeBondOrderEqualsQuery(Bond::DOUBLE),Queries::COMPOSITE_OR);
a2.expandQuery(makeBondOrderEqualsQuery(Bond::AROMATIC),Queries::COMPOSITE_OR);
TEST_ASSERT(a1.Match(&a2));
TEST_ASSERT(a2.Match(&a1));
}
{
QueryBond a1(Bond::SINGLE),a2(Bond::DOUBLE);
a1.expandQuery(makeBondOrderEqualsQuery(Bond::TRIPLE),Queries::COMPOSITE_OR);
a2.expandQuery(makeBondOrderEqualsQuery(Bond::AROMATIC),Queries::COMPOSITE_OR);
TEST_ASSERT(!a1.Match(&a2));
TEST_ASSERT(!a2.Match(&a1));
}
{
QueryBond a1(Bond::SINGLE),a2(Bond::DOUBLE);
a1.expandQuery(makeBondMinRingSizeQuery(4),Queries::COMPOSITE_OR);
a2.expandQuery(makeBondMinRingSizeQuery(4),Queries::COMPOSITE_OR);
TEST_ASSERT(a1.Match(&a2));
TEST_ASSERT(a2.Match(&a1));
}
{
QueryBond a1(Bond::SINGLE),a2(Bond::DOUBLE);
a1.expandQuery(makeBondMinRingSizeQuery(4),Queries::COMPOSITE_AND);
a2.expandQuery(makeBondMinRingSizeQuery(4),Queries::COMPOSITE_AND);
TEST_ASSERT(!a1.Match(&a2));
TEST_ASSERT(!a2.Match(&a1));
}
{
QueryBond a1(Bond::SINGLE),a2(Bond::SINGLE);
a1.expandQuery(makeBondMinRingSizeQuery(5),Queries::COMPOSITE_AND);
a2.expandQuery(makeBondMinRingSizeQuery(4),Queries::COMPOSITE_AND);
TEST_ASSERT(!a1.Match(&a2));
TEST_ASSERT(!a2.Match(&a1));
}
{
QueryBond a1(Bond::SINGLE),a2(Bond::AROMATIC);
a1.expandQuery(makeBondOrderEqualsQuery(Bond::AROMATIC),Queries::COMPOSITE_OR);
TEST_ASSERT(a1.Match(&a2));
TEST_ASSERT(a2.Match(&a1));
}
BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}
int main(){
RDLog::InitLogs();
test1();
test2();
test3();
test4();
test5();
test6();
testQueryQueryMatches();
return 0;
}
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