/// Removes atom from the molecule. This will also remove any bonds
/// to/from the atom.
void Molecule::removeAtom(Atom *atom)
{
if(!contains(atom)){
return;
}
// remove all bonds to/from the atom first
std::vector<Bond *> bonds = atom->bonds();
foreach(Bond *bond, bonds){
removeBond(bond);
}
void Molecule::removeAtom(Atom *atom)
{
if(atom) {
// When deleting an atom this also implicitly deletes any bonds to the atom
foreach (unsigned long bond, atom->bonds()) {
removeBond(bond);
}
m_atoms[atom->id()] = 0;
// 1 based arrays stored/shown to user
int index = atom->index();
m_atomList.removeAt(index);
for (int i = index; i < m_atomList.size(); ++i)
m_atomList[i]->setIndex(i);
atom->deleteLater();
disconnect(atom, SIGNAL(updated()), this, SLOT(updateAtom()));
emit atomRemoved(atom);
}
}
bool Molecule::removeAtom(Index index)
{
if (index >= atomCount())
return false;
Index uniqueId = findAtomUniqueId(index);
if (uniqueId == MaxIndex)
return false;
// Unique ID of an atom that was removed:
m_atomUniqueIds[uniqueId] = MaxIndex;
// Before removing the atom we must first remove any bonds to it.
Core::Array<BondType> atomBonds = Core::Molecule::bonds(atom(index));
while (atomBonds.size()) {
removeBond(atomBonds.back());
atomBonds = Core::Molecule::bonds(atom(index));
}
Index newSize = static_cast<Index>(m_atomicNumbers.size() - 1);
if (index != newSize) {
// We need to move the last atom to this position, and update its unique ID.
m_atomicNumbers[index] = m_atomicNumbers.back();
if (m_positions2d.size() == m_atomicNumbers.size())
m_positions2d[index] = m_positions2d.back();
if (m_positions3d.size() == m_atomicNumbers.size())
m_positions3d[index] = m_positions3d.back();
// Find any bonds to the moved atom and update their index.
atomBonds = Core::Molecule::bonds(atom(newSize));
foreach (const BondType& currentBond, atomBonds) {
std::pair<Index, Index> pair = m_bondPairs[currentBond.index()];
if (pair.first == newSize)
pair.first = index;
else if (pair.second == newSize)
pair.second = index;
m_bondPairs[currentBond.index()] = pair;
}
void Molecule::removeBond(Bond *bond)
{
if(bond) {
removeBond(bond->id());
}
}