Improved handling of nonstandard nucleotides

pdbfixer.py

@@ -273,8 +273,12 @@ class PDBFixer(object):
         for structChain, topChain in zip(self.structureChains, self.topology.chains()):
             for structResidue, topResidue in zip(structChain.iter_residues(), topChain.residues()):
                 key = (structChain.chain_id, structResidue.number, structResidue.name)
-                if key in modres and modres[key] in self.templates:
-                    nonstandard[topResidue] = modres[key]
+                if key in modres:
+                    replacement = modres[key]
+                    if replacement == 'DU':
+                        replacement = 'DT'
+                    if replacement in self.templates:
+                        nonstandard[topResidue] = replacement
         self.nonstandardResidues = [(r, nonstandard[r]) for r in sorted(nonstandard, key=lambda r: r.index)]
     
     def replaceNonstandardResidues(self):

ui.py

@@ -134,10 +134,15 @@ def displayConvertResiduesPage():
         for structResidue, topResidue in zip(structChain.iter_residues(), topChain.residues()):
             indexInChain[topResidue] = structResidue.number
     table = ''
+    nucleotides = ['DA', 'DC', 'DG', 'DT', 'A', 'C', 'G', 'T']
     for i in range(len(fixer.nonstandardResidues)):
         residue, replaceWith = fixer.nonstandardResidues[i]
+        if replaceWith in proteinResidues:
+            replacements = proteinResidues
+        else:
+            replacements = nucleotides
         options = ''
-        for res in proteinResidues:
+        for res in replacements:
             selected = ''
             if res == replaceWith:
                 selected = ' selected'