simplified wrapping of mdtraj top/traj with added proper exceptions; …

…data. .lmp and .lammps all recognized as lammps data files

mbuild/topology.py

@@ -28,7 +28,13 @@ def __init__(self, topology=None):
 
     def __getattr__(self, attr_name):
         """Redirect attribute access to the wrapped topology. """
-        return getattr(self.__dict__['_w_topology'], attr_name)
+        return getattr(self._w_topology, attr_name)
+
+    def __setattr__(self, key, value):
+        try:
+            self._w_topology.__setattr__(key, value)
+        except KeyError:
+            self.__dict__[key] = value
 
     @classmethod
     def from_dataframe(cls, atoms, bonds=None):
@@ -239,8 +245,8 @@ def from_compound(cls, compound, bond_list=None, show_ports=False,
             # Add the actual atoms
             try:
                 ele = elem.get_by_symbol(atom.kind)
-            except:
-               ele = Element(1000, atom.kind, atom.kind, 1.0)
+            except KeyError:
+                ele = Element(1000, atom.kind, atom.kind, 1.0)
             at = out.add_atom(atom.kind, ele, last_residue)
             at.charge = atom.charge
 

mbuild/trajectory.py

@@ -248,7 +248,7 @@ def save(self, filename, **kwargs):
             save_xyz(traj=self, filename=filename, **kwargs)
         elif filename.endswith(".mol2"):
             save_mol2(traj=self, filename=filename, **kwargs)
-        elif filename.startswith("data.") or filename.startswith(".lmp"):
+        elif filename.startswith("data.") or filename.endswith((".lmp", ".lammps")):
             save_lammps_data(traj=self, filename=filename, **kwargs)
         else:
             self._w_trajectory.save(filename, **kwargs)
@@ -257,9 +257,10 @@ def __getattr__(self, attr_name):
         return getattr(self._w_trajectory, attr_name)
 
     def __setattr__(self, key, value):
-        if key in ['unitcell_vectors', 'unitcell_lengths', 'unitcell_angles', 'xyz', 'time']:
+        try:
             self._w_trajectory.__setattr__(key, value)
-        self.__dict__[key] = value
+        except KeyError:
+            self.__dict__[key] = value
 
     def __getitem__(self, key):
         """Get a slice of this trajectory"""
@@ -277,12 +278,3 @@ def _string_summary_basic(self):
         value = "mbuild.Trajectory with %d frames, %d atoms, %d residues, %s" % (
                     self.n_frames, self.n_atoms, self.n_residues, unitcell_str)
         return value
-
-
-if __name__ == "__main__":
-    import pdb
-    from testing.tools import get_fn
-    traj = Trajectory.load(get_fn('ecer2.hoomdxml'))
-    comp = traj.to_compound()
-
-    pdb.set_trace()