public PDBChain(String pdbid, String id)
{
- this.pdbid = pdbid.toLowerCase();
+ this.pdbid = pdbid == null ? pdbid : pdbid.toLowerCase();
this.id = id;
}
if (as.astr1.charAt(i) == as.astr2.charAt(i))
{
+ if (pdbpos >= residues.size())
+ {
+ continue;
+ }
Residue res = residues.elementAt(pdbpos);
for (Atom atom : res.atoms)
{
status = PDBChain.IEASTATUS;
}
SequenceFeature[] features = sequence.getSequenceFeatures();
+ if (features == null)
+ {
+ return null;
+ }
for (int i = 0; i < features.length; i++)
{
if (features[i].getFeatureGroup().equals(pdbid))
else
{
- // 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));
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
|| ResidueProperties.nucleotideIndex[nucname
.charAt((deoxyn ? 1 : 0))] == -1)
{
- seq.append("X");
- // System.err.println("PDBReader:Null aa3Hash for " +
- // tmpat.resName);
+ char r = ResidueProperties
+ .getSingleCharacterCode(ResidueProperties
+ .getCanonicalAminoAcid(tmpat.resName));
+ seq.append(r == '0' ? 'X' : r);
+ // System.err.println("PDBReader:Null aa3Hash for " +
+ // tmpat.resName);
}
else
{