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 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 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; }
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; }