PDBxFile replaces nonstandard names with standard ones (#3659)

wrappers/python/openmm/app/data/pdbNames.xml

@@ -129,7 +129,7 @@
   <Atom name="HE1" alt1="HE"/>
   <Atom name="HE2" alt1="HNE" alt2="HNE2"/>
  </Residue>
- <Residue name="ASP" type="Protein">
+ <Residue name="ASP" type="Protein" alt1="ASH">
   <Atom name="HB2" alt1="2HB"/>
   <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
  </Residue>
@@ -141,7 +141,7 @@
   <Atom name="HD21" alt1="1HD2" alt2="HND1"/>
   <Atom name="HD22" alt1="2HD2" alt2="HND2"/>
  </Residue>
- <Residue name="GLU" type="Protein">
+ <Residue name="GLU" type="Protein" alt1="GLH">
   <Atom name="HB2" alt1="2HB"/>
   <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
   <Atom name="HG2" alt1="2HG"/>

wrappers/python/openmm/app/pdbxfile.py

@@ -66,6 +66,7 @@ class PDBxFile(object):
         ## The Topology read from the PDBx/mmCIF file
         self.topology = top
         self._positions = []
+        PDBFile._loadNameReplacementTables()
 
         # Load the file.
 
@@ -152,7 +153,14 @@ class PDBxFile(object):
                     # The start of a new residue.
                     resId = (None if resNumCol == -1 else row[resNumCol])
                     resIC = insertionCode
-                    res = top.addResidue(row[resNameCol], chain, resId, resIC)
+                    resName = row[resNameCol]
+                    if resName in PDBFile._residueNameReplacements:
+                        resName = PDBFile._residueNameReplacements[resName]
+                    res = top.addResidue(resName, chain, resId, resIC)
+                    if resName in PDBFile._atomNameReplacements:
+                        atomReplacements = PDBFile._atomNameReplacements[resName]
+                    else:
+                        atomReplacements = {}
                     lastResId = row[resNumCol]
                     lastInsertionCode = insertionCode
                     atomsInResidue.clear()
@@ -161,9 +169,12 @@ class PDBxFile(object):
                     element = elem.get_by_symbol(row[elementCol])
                 except KeyError:
                     pass
-                atom = top.addAtom(row[atomNameCol], element, res, row[atomIdCol])
+                atomName = row[atomNameCol]
+                if atomName in atomReplacements:
+                    atomName = atomReplacements[atomName]
+                atom = top.addAtom(atomName, element, res, row[atomIdCol])
                 atomTable[atomKey] = atom
-                atomsInResidue.add(row[atomNameCol])
+                atomsInResidue.add(atomName)
             else:
                 # This row defines coordinates for an existing atom in one of the later models.