lastrnum = group.getResno();
}
seq[len] = group.getGroup1();
+
+ /*
+ * JAL-1828 replace a modified amino acid with its standard
+ * equivalent (e.g. MSE with MET->M) to maximise sequence matching
+ */
+ String threeLetterCode = group.getGroup3();
+ String canonical = ResidueProperties.getCanonicalAminoAcid(threeLetterCode);
+ if (canonical != null
+ && !canonical.equalsIgnoreCase(threeLetterCode))
+ {
+ seq[len] = ResidueProperties
+ .getSingleCharacterCode(canonical);
+ }
switch (group.getProteinStructureSubType())
{
case HELIX310: