Merge pull request #352 from summeraz/use_parmed

Use Parmed loaders by default, remove Mdtraj dependency

mbuild/compound.py

@@ -11,7 +11,6 @@
 import tempfile
 from warnings import warn
 
-import mdtraj as md
 import numpy as np
 from oset import oset as OrderedSet
 import parmed as pmd
@@ -21,7 +20,6 @@
 
 from mbuild.bond_graph import BondGraph
 from mbuild.box import Box
-from mbuild.coordinate_transform import translate
 from mbuild.exceptions import MBuildError
 from mbuild.formats.hoomdxml import write_hoomdxml
 from mbuild.formats.lammpsdata import write_lammpsdata
@@ -32,7 +30,7 @@
 
 
 def load(filename, relative_to_module=None, compound=None, coords_only=False,
-         rigid=False, use_parmed=False, **kwargs):
+         rigid=False, use_mdtraj=False, **kwargs):
     """Load a file into an mbuild compound.
 
     Files are read using the MDTraj package unless the `use_parmed` argument is
@@ -55,8 +53,8 @@ def load(filename, relative_to_module=None, compound=None, coords_only=False,
         Only load the coordinates into an existing compoint.
     rigid : bool, optional, default=False
         Treat the compound as a rigid body
-    use_parmed : bool, optional, default=False
-        Use readers from ParmEd instead of MDTraj.
+    use_mdtraj : bool, optional, default=False
+        Use readers from MDTraj instead of Parmed.
     **kwargs : keyword arguments
         Key word arguments passed to mdTraj for loading.
 
@@ -76,12 +74,14 @@ def load(filename, relative_to_module=None, compound=None, coords_only=False,
     if compound is None:
         compound = Compound()
 
-    if use_parmed:
-        structure = pmd.load_file(filename, structure=True)
-        compound.from_parmed(structure)
-    else:
-        traj = md.load(filename, **kwargs)
+    if use_mdtraj:
+        mdtraj = import_('mdtraj')
+
+        traj = mdtraj.load(filename, **kwargs)
         compound.from_trajectory(traj, frame=-1, coords_only=coords_only)
+    else:
+        structure = pmd.load_file(filename, structure=True)
+        compound.from_parmed(structure, coords_only=coords_only)
 
     if rigid:
         compound.label_rigid_bodies()
@@ -1478,6 +1478,7 @@ def to_trajectory(self, show_ports=False, chains=None,
         _to_topology
 
         """
+        mdtraj = import_('mdtraj')
         atom_list = [particle for particle in self.particles(show_ports)]
 
         top = self._to_topology(atom_list, chains, residues)
@@ -1496,7 +1497,7 @@ def to_trajectory(self, show_ports=False, chains=None,
             else:
                 unitcell_lengths[dim] = box.lengths[dim]
 
-        return md.Trajectory(xyz, top, unitcell_lengths=unitcell_lengths,
+        return mdtraj.Trajectory(xyz, top, unitcell_lengths=unitcell_lengths,
                              unitcell_angles=np.array([90, 90, 90]))
 
     def _to_topology(self, atom_list, chains=None, residues=None):
@@ -1640,7 +1641,7 @@ def from_parmed(self, structure, coords_only=False):
             for parmed_atom, particle in atoms_particles:
                 particle.pos = np.array([parmed_atom.xx,
                                          parmed_atom.xy,
-                                         parmed_atom.xz])
+                                         parmed_atom.xz]) / 10
             return
 
         atom_mapping = dict()
@@ -1657,7 +1658,7 @@ def from_parmed(self, structure, coords_only=False):
                 chain_compound = self
             for residue in residues:
                 for atom in residue.atoms:
-                    pos = np.array([atom.xx, atom.xy, atom.xz])
+                    pos = np.array([atom.xx, atom.xy, atom.xz]) / 10
                     new_atom = Particle(name=str(atom.name), pos=pos)
                     chain_compound.add(new_atom, label='{0}[$]'.format(atom.name))
                     atom_mapping[atom] = new_atom

mbuild/tests/test_compound.py

@@ -30,12 +30,15 @@ def test_save_box(self, ch3):
         box_attributes = ['mins', 'maxs', 'lengths']
         custom_box = mb.Box([.8, .8, .8])
         for ext in extensions:
+            use_mdtraj = False
+            if ext == '.hoomdxml':
+                use_mdtraj = True
             outfile_padded = 'padded_methyl' + ext
             outfile_custom = 'custom_methyl' + ext
             ch3.save(filename=outfile_padded, box=None, overwrite=True)
             ch3.save(filename=outfile_custom, box=custom_box, overwrite=True)
-            padded_ch3 = mb.load(outfile_padded)
-            custom_ch3 = mb.load(outfile_custom)
+            padded_ch3 = mb.load(outfile_padded, use_mdtraj=use_mdtraj)
+            custom_ch3 = mb.load(outfile_custom, use_mdtraj=use_mdtraj)
             for attr in box_attributes:
                 pad_attr = getattr(padded_ch3.boundingbox, attr)
                 custom_attr = getattr(custom_ch3.boundingbox, attr)
@@ -559,14 +562,10 @@ def test_charge_neutrality_warn(self, benzene):
         with pytest.warns(UserWarning):
             benzene.save('charge-test.mol2')
 
-        with pytest.warns(ValidationWarning):
-            benzene.save('charge-test.mol2', forcefield_name='oplsaa',
-                         overwrite=True)
-
-        with pytest.warns(None) as record_warnings:
+        with pytest.warns(None) as record_warnings, pytest.warns(ValidationWarning) as validation_warnings:
             benzene.save('charge-test.mol2', forcefield_name='oplsaa', 
                          overwrite=True)
-        assert len(record_warnings) - 1 == 0
+        assert len(record_warnings) - len(validation_warnings) == 0
 
     @pytest.mark.skipif(not has_openbabel, reason="Open Babel package not installed")
     def test_energy_minimization(self, octane):
@@ -623,7 +622,7 @@ def test_clone_outside_containment(self, ch2, ch3):
         with pytest.raises(MBuildError):
             ch3_clone = mb.clone(ch3)
 
-    def test_load_mol2_parmed(self):
+    def test_load_mol2_mdtraj(self):
         with pytest.raises(KeyError):
-            mb.load(get_fn('benzene-nonelement.mol2'))
-        mb.load(get_fn('benzene-nonelement.mol2'), use_parmed=True)
+            mb.load(get_fn('benzene-nonelement.mol2'), use_mdtraj=True)
+        mb.load(get_fn('benzene-nonelement.mol2'))

mbuild/utils/io.py

@@ -124,6 +124,12 @@ def import_(module):
 except ImportError:
     has_gsd = False
 
+try:
+    import mdtraj
+    has_mdtraj = True
+except ImportError:
+    has_mdtraj = False
+
 try:
     import openbabel
     has_openbabel = True