If a PDB file specifies elements, use them (see bug 1773)

wrappers/python/simtk/openmm/app/internal/pdbstructure.py

@@ -708,28 +708,10 @@ class Atom(object):
         except ValueError: self.formal_charge = None
         # figure out atom element
         try:
-            # First try to find a sensible element symbol from columns 76-77
+            # Try to find a sensible element symbol from columns 76-77
             self.element = element.get_by_symbol(self.element_symbol)
         except KeyError:
-            # otherwise, deduce element from first two characters of atom name
-            # remove digits found in some hydrogen atom names
-            symbol = self.name_with_spaces[0:2].strip().lstrip("0123456789")
-            try:
-                # Some molecular dynamics PDB files, such as gromacs with ffamber force
-                # field, include 4-character hydrogen atom names beginning with "H".
-                # Hopefully elements like holmium (Ho) and mercury (Hg) will have fewer than four
-                # characters in the atom name.  This problem is the fault of molecular
-                # dynamics code authors who feel the need to make up their own atom
-                # nomenclature because it is too tedious to read that provided by the PDB.
-                # These are the same folks who invent their own meanings for biochemical terms
-                # like "dipeptide".  Clowntards.
-                if len(self.name) == 4 and self.name[0:1] == "H":
-                    self.element = element.hydrogen
-                else:
-                    self.element = element.get_by_symbol(symbol)
-            except KeyError:
-                # OK, I give up
-                self.element = None
+            self.element = None
 
     def iter_locations(self):
         """

wrappers/python/simtk/openmm/app/pdbfile.py

@@ -92,30 +92,30 @@ class PDBFile(object):
                     if atomName in atomReplacements:
                         atomName = atomReplacements[atomName]
                     atomName = atomName.strip()
-                    element = None
-
-                    # Try to guess the element.
-                    
-                    upper = atomName.upper()
-                    if upper.startswith('CL'):
-                        element = elem.chlorine
-                    elif upper.startswith('NA'):
-                        element = elem.sodium
-                    elif upper.startswith('MG'):
-                        element = elem.magnesium
-                    elif upper.startswith('BE'):
-                        element = elem.beryllium
-                    elif upper.startswith('LI'):
-                        element = elem.lithium
-                    elif upper.startswith('K'):
-                        element = elem.potassium
-                    elif( len( residue ) == 1 and upper.startswith('CA') ):
-                        element = elem.calcium
-                    else:
-                        try:
-                            element = elem.get_by_symbol(atomName[0])
-                        except KeyError:
-                            pass
+                    element = atom.element
+                    if element is None:
+                        # Try to guess the element.
+                        
+                        upper = atomName.upper()
+                        if upper.startswith('CL'):
+                            element = elem.chlorine
+                        elif upper.startswith('NA'):
+                            element = elem.sodium
+                        elif upper.startswith('MG'):
+                            element = elem.magnesium
+                        elif upper.startswith('BE'):
+                            element = elem.beryllium
+                        elif upper.startswith('LI'):
+                            element = elem.lithium
+                        elif upper.startswith('K'):
+                            element = elem.potassium
+                        elif( len( residue ) == 1 and upper.startswith('CA') ):
+                            element = elem.calcium
+                        else:
+                            try:
+                                element = elem.get_by_symbol(atomName[0])
+                            except KeyError:
+                                pass
                     newAtom = top.addAtom(atomName, element, r)
                     atomByNumber[atom.serial_number] = newAtom
         self._positions = []