- Atom tmp = (Atom) atoms.elementAt(i);
- resNumber = tmp.resNumber;
- int res = resNumber;
-
- if (i == 0) {
- offset = resNumber;
- }
-
- Vector resAtoms = new Vector();
- //Add atoms to a vector while the residue number
- //remains the same as the first atom's resNumber (res)
- while ((resNumber == res) && (i < atoms.size())) {
- resAtoms.addElement((Atom) atoms.elementAt(i));
- i++;
-
- if (i < atoms.size()) {
- resNumber = ((Atom) atoms.elementAt(i)).resNumber;
- } else {
- resNumber++;
- }
- }
-
- //We need this to keep in step with the outer for i = loop
- i--;
-
- //Make a new Residue object with the new atoms vector
- residues.addElement(new Residue(resAtoms, resNumber - 1, count));
-
- Residue tmpres = (Residue) residues.lastElement();
- Atom tmpat = (Atom) tmpres.atoms.elementAt(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,MCview.PDBChain.PDBFILEFEATURE);
- resFeatures.addElement(sf);
- // Keep totting up the sequence
- if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null)
- {
- seq.append("X") ;
- // System.err.println("PDBReader:Null aa3Hash for " +
- // tmpat.resName);
- } else {
-
- seq.append(ResidueProperties.aa[((Integer) ResidueProperties.getAA3Hash()
- .get(tmpat.resName)).intValue()]);
- }
- count++;
+ b.startCol = Color.red;
+ }
+ else if (b.at1.resName.equalsIgnoreCase("LYS")
+ || b.at1.resName.equalsIgnoreCase("ARG"))
+ {
+ b.startCol = Color.blue;
+ }
+ else if (b.at1.resName.equalsIgnoreCase("CYS"))
+ {
+ b.startCol = Color.yellow;
+ }
+ else
+ {
+ b.startCol = Color.lightGray;