Handle hex values for atom and residue numbers

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

@@ -141,6 +141,8 @@ class PdbStructure(object):
         self.sequences = []
         self.modified_residues = []
         # read file
+        self._atom_numbers_are_hex = False
+        self._residue_numbers_are_hex = False
         self._load(input_stream)
 
     def _load(self, input_stream):
@@ -148,7 +150,7 @@ class PdbStructure(object):
         for pdb_line in input_stream:
             # Look for atoms
             if (pdb_line.find("ATOM  ") == 0) or (pdb_line.find("HETATM") == 0):
-                self._add_atom(Atom(pdb_line))
+                self._add_atom(Atom(pdb_line, self))
             # Notice MODEL punctuation, for the next level of detail
             # in the structure->model->chain->residue->atom->position hierarchy
             elif (pdb_line.find("MODEL") == 0):
@@ -653,7 +655,7 @@ class Residue(object):
 class Atom(object):
     """Atom represents one atom in a PDB structure.
     """
-    def __init__(self, pdb_line):
+    def __init__(self, pdb_line, pdbstructure=None):
         """Create a new pdb.Atom from an ATOM or HETATM line.
 
         Example line:
@@ -688,10 +690,17 @@ class Atom(object):
         self.is_first_atom_in_chain = False
         self.is_final_atom_in_chain = False
         self.is_first_residue_in_chain = False
-        self.is_final_residue_in_chain = False
+        self.is_final_residue_in_chain = False 
         # Start parsing fields from pdb line
         self.record_name = pdb_line[0:6].strip()
-        self.serial_number = int(pdb_line[6:11])
+        if pdbstructure is not None and pdbstructure._atom_numbers_are_hex:
+            self.serial_number = int(pdb_line[6:11], 16)
+        else:
+            try:
+                self.serial_number = int(pdb_line[6:11])
+            except:
+                self.serial_number = int(pdb_line[6:11], 16)
+                pdbstructure._atom_numbers_are_hex = True
         self.name_with_spaces = pdb_line[12:16]
         alternate_location_indicator = pdb_line[16]
 
@@ -707,7 +716,14 @@ class Atom(object):
         self.residue_name = self.residue_name_with_spaces.strip()
 
         self.chain_id = pdb_line[21]
-        self.residue_number = int(pdb_line[22:26])
+        if pdbstructure is not None and pdbstructure._residue_numbers_are_hex:
+            self.residue_number = int(pdb_line[22:26], 16)
+        else:
+            try:
+                self.residue_number = int(pdb_line[22:26])
+            except:
+                self.residue_number = int(pdb_line[22:26], 16)
+                pdbstructure._residue_numbers_are_hex = True
         self.insertion_code = pdb_line[26]
         # coordinates, occupancy, and temperature factor belong in Atom.Location object
         x = float(pdb_line[30:38])