/** * 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()); }