+ else
+ {
+ tmpchain = new PDBChain(id, tmpatom.chain);
+ chains.addElement(tmpchain);
+ tmpchain.atoms.addElement(tmpatom);
+ }
+ lastID = tmpatom.resNumIns.trim();
+ }
+ index++;
+ }
+
+ makeResidueList();
+ makeCaBondList();
+
+ if (id == null)
+ {
+ id = inFile.getName();
+ }
+ for (int i = 0; i < chains.size(); i++)
+ {
+ SequenceI dataset = chains.elementAt(i).sequence;
+ dataset.setName(id + "|" + dataset.getName());
+ PDBEntry entry = new PDBEntry();
+ entry.setId(id);
+ entry.setProperty(new Hashtable());
+ if (chains.elementAt(i).id != null)
+ {
+ entry.getProperty().put("CHAIN",
+ chains.elementAt(i).id);
+ }
+ if (inFile != null)
+ {
+ entry.setFile(inFile.getAbsolutePath());
+ }
+ else
+ {
+ // TODO: decide if we should dump the datasource to disk
+ entry.setFile(getDataName());
+ }
+ dataset.addPDBId(entry);
+ SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects
+ // maintain reference to
+ // dataset
+ seqs.addElement(chainseq);
+ if (isRNA(chainseq) == true)
+ {
+ rna.add(chainseq);
+ }
+ else
+ {
+ prot.add(chainseq);