optional infer_bonds for convert and writeMMTF

prody/atomic/atomic.py

@@ -291,6 +291,8 @@ def toBioPythonStructure(self, header=None, **kwargs):
 
         :arg csets: coordinate set indices, default is all coordinate sets
         
+        :arg infer_bonds: whether to infer new bonds
+        :type infer_bonds: bool
         """ 
         try:
             from Bio.PDB.Structure import Structure
@@ -308,6 +310,10 @@ def toBioPythonStructure(self, header=None, **kwargs):
         if csets is None:
             csets = range(self.numCoordsets())
 
+        infer_bonds = kwargs.get('infer_bonds', False)
+        if infer_bonds:
+            self.inferBonds()
+
         structure_builder = StructureBuilder()
         structure_builder.init_structure(self.getTitle())
         if header is not None:

prody/proteins/mmtffile.py

@@ -387,12 +387,14 @@ def writeMMTF(filename, atoms, csets=None, autoext=True, **kwargs):
             'to solve the problem.')
 
     header = kwargs.get('header', None)
+    infer_bonds = kwargs.get('infer_bonds', False)
 
     if autoext and not filename.lower().endswith('.mmtf'):
         filename += '.mmtf'
 
-    structure = atoms.toBioPythonStructure(header=header, csets=csets)
+    structure = atoms.toBioPythonStructure(header=header, csets=csets,
+                                           infer_bonds=infer_bonds)
     io=MMTFIO()
     io.set_structure(structure)
-    io.save(filename)
+    io.save(filename, num_bonds=atoms.numBonds())
     return filename