add removeBondsToMetals argument

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

@@ -59,7 +59,7 @@ class PDBFile(object):
     _residueNameReplacements = {}
     _atomNameReplacements = {}
 
-    def __init__(self, file):
+    def __init__(self, file, removeBondsToMetals=False):
         """Load a PDB file.
 
         The atom positions and Topology can be retrieved by calling getPositions() and getTopology().
@@ -68,6 +68,9 @@ class PDBFile(object):
         ----------
         file : string
             the name of the file to load
+        removeBondsToMetals : bool
+            if True, those inter-residue CONECT bonds that indicate coordination to metals 
+            (cf. metalc connectivity in mmCIF/PDBx) are not added to the topology
         """
         
         metalElements = ['Al','As','Ba','Ca','Cd','Ce','Co','Cs','Cu','Dy','Fe','Gd','Hg','Ho','In','Ir','K','Li','Mg',
@@ -161,7 +164,9 @@ class PDBFile(object):
         for connect in pdb.models[-1].connects:
             i = connect[0]
             for j in connect[1:]:
-                if i in atomByNumber and j in atomByNumber:
+                if i in atomByNumber and j in atomByNumber and not removeBondsToMetals:
+                    connectBonds.append((atomByNumber[i], atomByNumber[j]))  
+                elif i in atomByNumber and j in atomByNumber and removeBondsToMetals:    
                     if atomByNumber[i].element is not None and atomByNumber[j].element is not None:
                         if atomByNumber[i].element.symbol in metalElements or atomByNumber[j].element.symbol in metalElements:
                             if atomByNumber[i].residue == atomByNumber[j].residue: