private boolean hasMacromoleculeChain() {
final StructureModel model = LigandExplorer.sgetModel();
final Structure structure = model.getStructures().get(0);
for (Chain chain : structure.getStructureMap().getChains()) {
if (chain.getClassification() == Residue.Classification.AMINO_ACID
|| chain.getClassification() == Residue.Classification.NUCLEIC_ACID) {
return true;
}
}
return false;
}
private Vector<Chain> getLigandList(final Structure structure) {
final Vector<Chain> ligandList = new Vector<Chain>();
for (Chain chain : structure.getStructureMap().getChains())
if (chain.getClassification() == Residue.Classification.LIGAND
|| chain.getClassification() == Residue.Classification.BIRD
|| chain.hasModifiedResidues()) ligandList.add(chain);
return ligandList;
}
/**
* Returns all residues relate to a BIRD molecule. Since BIRD molecules can span multiple internal
* chains, we need to search all chains with a particular BIRD instance
*
* @param structure
* @param chain
* @return
*/
private Residue[] getBirdResidues(Structure structure, Chain chain) {
List<Residue> residues = new ArrayList<Residue>();
Bird bird = chain.getBird();
for (Chain c : structure.getStructureMap().getChains()) {
Bird b = c.getBird();
if (b != null && b.isSameInstance(bird)) {
residues.addAll(c.getResidues());
}
}
return residues.toArray(new Residue[residues.size()]);
}
