private int getInternalNr(Group atomG) { if ( atomG.getType().equals(GroupType.AMINOACID)) { AminoAcidImpl aa = (AminoAcidImpl) atomG; return new Long(aa.getId()).intValue(); } else if ( atomG.getType().equals(GroupType.NUCLEOTIDE)) { NucleotideImpl nu = (NucleotideImpl) atomG; return new Long(nu.getId()).intValue(); } else { HetatomImpl he = (HetatomImpl) atomG; return new Long(he.getId()).intValue(); } }