previous commit introduced recursion bug in setattr - need to revisit…

… the issue of properly wrapping mdtraj; fixed atom.name usage when atom.atomtype is not specified: No such file or directory; test_hoomdxml now loads into a compound instead of a trajectory; fixed some imports

mbuild/compound.py

@@ -204,7 +204,7 @@ def to_trajectory(self, show_ports=False, **kwargs):
         return Trajectory.from_compound(self, show_ports=show_ports, **kwargs)
 
     @classmethod
-    def load(cls, filename, relative_to_module=None, frame=0):
+    def load(cls, filename, relative_to_module=None, frame=0, **kwargs):
         """Load a file into a Compound.
 
         Args:
@@ -216,7 +216,8 @@ def load(cls, filename, relative_to_module=None, frame=0):
         """
         from mbuild.trajectory import Trajectory
 
-        traj = Trajectory.load(filename, relative_to_module=relative_to_module)
+        traj = Trajectory.load(filename, relative_to_module=relative_to_module,
+                               **kwargs)
         return traj.to_compound(frame=frame)
 
     # Convenience functions

mbuild/formats/lammps_data.py

@@ -1,6 +1,7 @@
-from mdtraj.utils import in_units_of
 import operator
 
+from mdtraj.utils import in_units_of
+
 
 def save_lammps_data(traj, step=-1, filename='data.mbuild', unit_set='real'):
     """Output a Trajectory as a LAMMPS data file.

mbuild/tests/test_hoomdxml.py

@@ -4,10 +4,12 @@
 """Tests for `mbuild.hoomdxmlfile` module. """
 
 import pytest
+import numpy as np
+
+from mbuild.compound import Compound
 from mbuild.examples.ethane.ethane import Ethane
 from mbuild.testing.tools import get_fn
-import numpy as np
-from mbuild.trajectory import Trajectory
+
 from base_test import BaseTest
 
 
@@ -18,12 +20,9 @@ def molecule(self):
         lj_units = {'mass': 72.0,
                     'distance': 0.6, 
                     'energy': 0.4}
-        traj = Trajectory.load(get_fn('ecer2.hoomdxml'), lj_units=lj_units)
-        return traj
+        compound = Compound.load(get_fn('ecer2.hoomdxml'), lj_units=lj_units)
+        return compound
 
-    # def test_load_and_create(self):
-    #     methyl = load_mol2('methyl.mol2')
-    #
     def test_write(self, molecule):
         molecule.save('ecer2-saved.hoomdxml')
 
@@ -46,10 +45,5 @@ def test_units(self, molecule):
              [0.0277806278318, -3.6437664032, 0.310265809298],
              [0.00889551546425, -3.54814314842, -0.252536147833],
              [-0.121015898883, -3.50847649574, -0.732142329216]])
-        loaded = molecule[0].xyz / 0.6
-        assert loaded.all() == positions.all() 
-
-if __name__=="__main__":
-    TestHoomdXml().test_write()
-    TestHoomdXml().test_update_from_file()
-    TestHoomdXml().test_units()
+        loaded = molecule.to_trajectory().xyz / 0.6
+        assert loaded.all() == positions.all()

mbuild/topology.py

@@ -31,9 +31,10 @@ def __getattr__(self, attr_name):
         return getattr(self._w_topology, attr_name)
 
     def __setattr__(self, key, value):
-        try:
+        if key in ['chains', 'n_chains', 'residues', 'n_residues', 'atoms',
+                   'n_atoms', 'bonds', 'n_bonds']:
             self._w_topology.__setattr__(key, value)
-        except KeyError:
+        else:
             self.__dict__[key] = value
 
     @classmethod
@@ -250,11 +251,10 @@ def from_compound(cls, compound, bond_list=None, show_ports=False,
             at = out.add_atom(atom.kind, ele, last_residue)
             at.charge = atom.charge
 
-            if hasattr(atom, 'extras'):
-                if 'atomtype' in atom.extras:
-                    at.atomtype = atom.atomtype
-                else:
-                    at.atomtype = atom.kind
+            try:
+                at.atomtype = atom.atomtype
+            except AttributeError:
+                at.atomtype = atom.kind
             #print("Added {} to residue {} in chain {}".format(atom, last_residue, last_chain))
             atom_mapping[atom] = at
 

mbuild/trajectory.py

@@ -257,9 +257,12 @@ def __getattr__(self, attr_name):
         return getattr(self._w_trajectory, attr_name)
 
     def __setattr__(self, key, value):
-        try:
+        if key in ['n_frames', 'n_atoms', 'n_residues', 'time', 'timestep',
+                   'topology', 'top', 'xyz', 'unitcell_volumes',
+                   'unitcell_vectors', 'unitcell_lengths', 'unitcell_angles',
+                   '_have_unitcell']:
             self._w_trajectory.__setattr__(key, value)
-        except KeyError:
+        else:
             self.__dict__[key] = value
 
     def __getitem__(self, key):