void Molecule::removeBond(unsigned long id)
{
if (id < m_bonds.size()) {
Q_D(Molecule);
if (m_bonds[id] == 0)
return;
d->invalidRings = true;
m_invalidPartialCharges = true;
m_invalidAromaticity = true;
Bond *bond = m_bonds[id];
m_bonds[id] = 0;
// Delete the bond from the list and reorder the remaining bonds
int index = bond->index();
m_bondList.removeAt(index);
for (int i = index; i < m_bondList.size(); ++i) {
m_bondList[i]->setIndex(i);
}
// Also delete the bond from the attached atoms
if (m_atoms.size() > bond->beginAtomId()) {
if (m_atoms[bond->beginAtomId()])
m_atoms[bond->beginAtomId()]->removeBond(id);
}
if (m_atoms.size() > bond->endAtomId()) {
if (m_atoms[bond->endAtomId()])
m_atoms[bond->endAtomId()]->removeBond(id);
}
disconnect(bond, SIGNAL(updated()), this, SLOT(updateBond()));
emit bondRemoved(bond);
bond->deleteLater();
}
}
TEST_F(MoleculeTest, addBond)
{
Molecule molecule;
EXPECT_EQ(molecule.bondCount(), static_cast<Index>(0));
Atom a = molecule.addAtom(1);
Atom b = molecule.addAtom(1);
Bond bondAB = molecule.addBond(a, b);
EXPECT_TRUE(bondAB.isValid());
EXPECT_EQ(bondAB.molecule(), &molecule);
EXPECT_EQ(molecule.bondCount(), static_cast<Index>(1));
EXPECT_EQ(bondAB.index(), static_cast<Index>(0));
EXPECT_EQ(bondAB.atom1().index(), a.index());
EXPECT_EQ(bondAB.atom2().index(), b.index());
EXPECT_EQ(bondAB.order(), static_cast<unsigned char>(1));
Atom c = molecule.addAtom(1);
Bond bondBC = molecule.addBond(b, c, 2);
EXPECT_TRUE(bondBC.isValid());
EXPECT_EQ(molecule.bondCount(), static_cast<Index>(2));
EXPECT_EQ(bondBC.index(), static_cast<Index>(1));
EXPECT_EQ(bondBC.order(), static_cast<unsigned char>(2));
// try to lookup nonexistant bond
Bond bond = molecule.bond(a, c);
EXPECT_FALSE(bond.isValid());
// try to lookup bond between a and b
bond = molecule.bond(a, b);
EXPECT_TRUE(bond.isValid());
EXPECT_EQ(bond.molecule(), &molecule);
EXPECT_EQ(bond.atom1().index(), a.index());
EXPECT_EQ(bond.atom2().index(), b.index());
// try to lookup bond between b and c by index
bond = molecule.bond(1);
EXPECT_TRUE(bond.isValid());
EXPECT_EQ(bond.molecule(), &molecule);
EXPECT_EQ(bond.atom1().index(), b.index());
EXPECT_EQ(bond.atom2().index(), c.index());
}
TEST_F(MoleculeTest, findBond)
{
Molecule molecule;
Atom a1 = molecule.addAtom(5);
Atom a2 = molecule.addAtom(6);
Bond b = molecule.addBond(a1, a2, 1);
EXPECT_EQ(molecule.bond(a1, a2).index(), b.index());
EXPECT_EQ(molecule.bond(a2, a1).index(), b.index());
Array<Bond> bonds = molecule.bonds(a1);
EXPECT_EQ(bonds.size(), 1);
Atom a3 = molecule.addAtom(7);
molecule.addBond(a1, a3, 1);
EXPECT_EQ(molecule.bonds(a1).size(), 2);
EXPECT_EQ(molecule.bonds(a3).size(), 1);
}
