void
Selection::printInfo(FILE *fp) const
{
fprintf(fp, "\"%s\" (%d position%s, %d atom%s%s)", name(),
posCount(), posCount() == 1 ? "" : "s",
atomCount(), atomCount() == 1 ? "" : "s",
isDynamic() ? ", dynamic" : "");
fprintf(fp, "\n");
}
/// Returns a list of all the bonds in the residue.
std::vector<Bond *> Residue::bonds() const
{
std::vector<Bond *> bonds;
for(size_t i = 0; i < atomCount(); i++){
for(size_t j = i + 1; j < atomCount(); j++){
Bond *bond = d->atoms[i]->bondTo(d->atoms[j]);
if(bond){
bonds.push_back(bond);
}
}
}
return bonds;
}
Molecule::AtomType Molecule::addAtom(unsigned char number, Index uniqueId)
{
if (uniqueId >= static_cast<Index>(m_atomUniqueIds.size()) ||
m_atomUniqueIds[uniqueId] != MaxIndex) {
return AtomType();
}
m_atomUniqueIds[uniqueId] = atomCount();
AtomType a = Core::Molecule::addAtom(number);
return a;
}
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;
}
Molecule::AtomType Molecule::addAtom(unsigned char number)
{
m_atomUniqueIds.push_back(atomCount());
AtomType a = Core::Molecule::addAtom(number);
return a;
}
// --- Properties ---------------------------------------------------------- //
/// Returns the number of atoms in the moiety.
int Moiety::size() const
{
return atomCount();
}
