- // boolean baseDetected = false;
- // for (Atom resAtom : resAtoms)
- // {
- // if (resAtom.insCode == ' ')
- // {
- // baseDetected = true;
- // }
- // }
- // if (!baseDetected)
- // {
- // continue;
- // }
- // Make a new Residue object with the new atoms vector
- residues.addElement(new Residue(resAtoms, resNumber - 1, count));
-
- Residue tmpres = residues.lastElement();
- Atom tmpat = tmpres.atoms.get(0);
- // Make A new SequenceFeature for the current residue numbering
- SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
- + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
- + count, offset + count, pdbid);
- // MCview.PDBChain.PDBFILEFEATURE);
- resFeatures.addElement(sf);
- resAnnotation.addElement(new Annotation(tmpat.tfactor));
- // Keep totting up the sequence
-
- if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
- {
- String nucname = tmpat.resName.trim();
- // use the aaIndex rather than call 'toLower' - which would take a bit
- // more time.
- deoxyn = nucname.length() == 2
- && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D'];
- if (tmpat.name.equalsIgnoreCase("CA")
- || ResidueProperties.nucleotideIndex[nucname
- .charAt((deoxyn ? 1 : 0))] == -1)