public class PDBChain
{
+ public static final String RESNUM_FEATURE = "RESNUM";
+
/**
* SequenceFeature group for PDB File features added to sequences
*/
pdbpos++;
}
- boolean sameResidue = Comparison.compareChars(as.astr1.charAt(i),
+ boolean sameResidue = Comparison.isSameResidue(as.astr1.charAt(i),
as.astr2.charAt(i), false);
if (sameResidue)
{
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
+ SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, tmpat.resName
+ ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
+ count, offset + count, pdbid);
resFeatures.addElement(sf);
try
{
index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
- b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+ b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0),
+ 0, null, null, 0f);
index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
- b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+ b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
+ null, null, 0f);
} catch (Exception e)
{