Merge pull request #798 from hainm/show-prody

ADD: show_prody

nglview/adaptor.py

@@ -27,7 +27,9 @@
     'IODataStructure', 'QCelementalStructure', 'Psi4Structure',
     'OpenbabelStructure',
     'RosettaStructure',
+    'ProdyStructure',
     'SimpletrajTrajectory',
+    'ProdyTrajectory',
     'MDTrajTrajectory', 'PyTrajTrajectory', 'ParmEdTrajectory',
     'MDAnalysisTrajectory', 'HTMDTrajectory', 'ASETrajectory',
     'register_backend',
@@ -207,6 +209,38 @@ def get_structure_string(self):
         return _get_structure_string(self._mol.dump_pdb)
 
 
+@register_backend('prody')
+class ProdyStructure(Structure):
+    def __init__(self, obj):
+        super(ProdyStructure, self).__init__()
+        self._obj = obj
+        self.ext = 'pdb'
+        self.params = {}
+
+    def get_structure_string(self):
+        import prody
+        def write(fname):
+            if isinstance(self._obj, prody.Ensemble):
+                st = self._obj[0]
+            else:
+                st = self._obj
+            prody.writePDB(fname, st)
+        return _get_structure_string(write)
+
+
+@register_backend('prody')
+class ProdyTrajectory(Trajectory, ProdyStructure):
+    def __init__(self, obj):
+        ProdyStructure.__init__(self, obj)
+
+    @property
+    def n_frames(self):
+        return self._obj.numConfs()
+
+    def get_coordinates(self, index):
+        return self._obj.getConformation(index).getCoords()
+
+
 @register_backend('simpletraj')
 class SimpletrajTrajectory(Trajectory, Structure):
     '''simpletraj adaptor.

nglview/show.py

@@ -13,6 +13,8 @@
                       IODataStructure,
                       QCelementalStructure,
                       OpenbabelStructure,
+                      ProdyStructure,
+                      ProdyTrajectory,
                       MDTrajTrajectory,
                       PyTrajTrajectory, ParmEdTrajectory, MDAnalysisTrajectory,
                       HTMDTrajectory, ASETrajectory, SchrodingerStructure, SchrodingerTrajectory)
@@ -32,6 +34,7 @@
     'show_rosetta',
     'show_asetraj',
     'show_simpletraj',
+    'show_prody',
     'show_mdtraj',
     'show_pytraj',
     'show_mdanalysis',
@@ -249,6 +252,27 @@ def show_simpletraj(traj, **kwargs):
     return NGLWidget(traj, **kwargs)
 
 
+def show_prody(obj, **kwargs):
+    """
+
+    Examples
+    --------
+    >>> import nglview as nv # doctest: +SKIP
+    ... import prody
+    ... structure = prody.parsePDB('what.pdb')
+    ... ensemble = prody.parseDCD('what.dcd')
+    ... ensemble.setAtoms(structure)
+    ... nv.show_prody(ensemble)
+    ... # nv.show_prody(structure)
+    """
+    import prody
+    if isinstance(obj, prody.Ensemble):
+        view_obj = ProdyTrajectory(obj)
+    else:
+        view_obj = ProdyStructure(obj)
+    return NGLWidget(view_obj, **kwargs)
+
+
 def show_mdtraj(mdtraj_trajectory, **kwargs):
     '''Show mdtraj trajectory.
 

nglview/tests/test_show.py

@@ -103,3 +103,33 @@ def test_show_openbabel():
     b.SetOutFormat.assert_called_with('pdb')
     assert b.WriteFile.called
     assert len(b.WriteFile.call_args_list[0]) == 2
+
+
+def test_show_prody():
+    import types
+    prody = types.ModuleType('prody')
+    sys.modules['prody'] = prody
+
+    class MockEnsemble:
+        def __getitem__(self, index):
+            return 0
+
+        def numConfs(self):
+            return 1
+
+        def getConformation(self, index):
+            class Struct:
+                def getCoords(self):
+                    return
+
+    prody.Ensemble = MockEnsemble
+    prody.writePDB = MagicMock()
+    ens = MockEnsemble()
+    nglview.show_prody(ens)
+    assert prody.writePDB.called
+    prody.writePDB.reset_mock()
+    assert not prody.writePDB.called
+
+    st = MagicMock()
+    nglview.show_prody(st)
+    assert prody.writePDB.called