/**
* Adds the atom oAtom without specifying a {@link IMonomer} or a Strand. Therefore the atom to
* this AtomContainer, but not to a certain Strand or {@link IMonomer} (intended e.g. for
* HETATMs).
*
* @param oAtom The {@link IPDBAtom} to add
*/
@Override
public void addAtom(IPDBAtom oAtom) {
super.addAtom(oAtom);
}
/**
* Adds the atom oAtom to a specified Monomer. Additionally, it keeps record of the iCode.
*
* @param oAtom The IPDBAtom to add
* @param oMonomer The monomer the atom belongs to
*/
public void addAtom(IPDBAtom oAtom, IMonomer oMonomer) {
super.addAtom(oAtom, oMonomer);
if (!sequentialListOfMonomers.contains(oMonomer.getMonomerName()))
sequentialListOfMonomers.add(oMonomer.getMonomerName());
}
/**
* Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand. Additionally, it keeps
* record of the iCode.
*
* @param oAtom The IPDBAtom to add
* @param oMonomer The monomer the atom belongs to
*/
@Override
public void addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand) {
super.addAtom(oAtom, oMonomer, oStrand);
if (!sequentialListOfMonomers.contains(oMonomer.getMonomerName()))
sequentialListOfMonomers.add(oMonomer.getMonomerName());
}
