Merge 504f52d into 971aeda

nglview/adaptor.py

@@ -22,7 +22,7 @@
     'BiopythonStructure',
     'IOTBXStructure',
     'IODataStructure',
-    'QCelementalStructure',
+    'QCElementalStructure',
     'Psi4Structure',
     'OpenbabelStructure',
     'RosettaStructure',
@@ -137,22 +137,17 @@ def get_structure_string(self):
             return ASEStructure(ase.io.read(fh.name)).get_structure_string()
 
 
-class QCelementalStructure(Structure):
+class QCElementalStructure(Structure):
     def __init__(self, obj):
         super().__init__()
         self._obj = obj
+        self.ext = 'sdf'
 
     def get_structure_string(self):
-        """Require `ase` package
-        """
-        import ase.io
-        with NamedTemporaryFile(suffix='.xyz') as fh:
-            with open(fh.name, 'w') as fh2:
-                fh2.write(self._obj.to_string('xyz'))
-            return ASEStructure(ase.io.read(fh.name)).get_structure_string()
+        return self._obj.orient_molecule().to_string('nglview-sdf')
 
 
-class Psi4Structure(QCelementalStructure):
+class Psi4Structure(QCElementalStructure):
     pass
 
 

nglview/show.py

@@ -6,7 +6,7 @@
                       IOTBXStructure, MDAnalysisTrajectory, MDTrajTrajectory,
                       OpenbabelStructure, ParmEdTrajectory, PdbIdStructure,
                       ProdyStructure, ProdyTrajectory, PyTrajTrajectory,
-                      QCelementalStructure, RosettaStructure,
+                      QCElementalStructure, RosettaStructure,
                       SchrodingerStructure, SchrodingerTrajectory,
                       RdkitStructure,
                       TextStructure)
@@ -100,7 +100,7 @@ def show_iodata(obj, **kwargs):
 
 
 def show_qcelemental(obj, **kwargs):
-    """Show QCelemental's Molecule (require `ase` package).
+    """Show QCElemental's Molecule.
 
     Examples
     --------
@@ -110,11 +110,11 @@ def show_qcelemental(obj, **kwargs):
     ... view = nv.show_qcelemental(mol)
     ... view
     """
-    return NGLWidget(QCelementalStructure(obj), **kwargs)
+    return NGLWidget(QCElementalStructure(obj), **kwargs)
 
 
 def show_psi4(obj, **kwargs):
-    """Show psi4's Molecule (require `ase` package)
+    """Show Psi4's Molecule.
 
     Examples
     --------
@@ -124,7 +124,7 @@ def show_psi4(obj, **kwargs):
     ... view = nv.show_psi4(mol)
     ... view
     """
-    return NGLWidget(QCelementalStructure(obj), **kwargs)
+    return NGLWidget(QCElementalStructure(obj), **kwargs)
 
 
 def show_openbabel(obj, **kwargs):

nglview/tests/test_show.py

@@ -87,6 +87,9 @@ class MockMol:
         def to_string(self, format):
             return '1\nHe\nHe                    0.000000000000     0.000000000000     0.000000000000\n'
 
+        def orient_molecule(self):
+            return self
+
     v = nglview.show_qcelemental(MockMol())
     v
     nglview.show_psi4(MockMol())

nglview/tests/test_widget.py

@@ -79,6 +79,12 @@
 except ImportError:
     has_bio = False
 
+try:
+    import qcelemental
+    has_qcelemental = True
+except ImportError:
+    has_qcelemental = False
+
 
 def default_view():
     traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
@@ -512,6 +518,15 @@ def test_show_pymatgen():
     view
 
 
+@unittest.skipUnless(has_qcelemental, 'skip if not having qcelemental')
+def test_show_qcelemental():
+    import qcelemental as qcel
+
+    mol = qcel.models.Molecule.from_data("He 0 0 0") 
+    view = nv.show_qcelemental(mol)
+    view
+
+
 @unittest.skipUnless(has_bio, 'skip if not having biopython')
 def test_show_biopython():
     from Bio.PDB import PDBParser

setup.py

@@ -193,6 +193,7 @@ def run(self):
         "rdkit": ["rdkit"],
         "ase": ["ase"],
         "htmd": ["htmd"],
+        "qcelemental": ["qcelemental"],
     },
     'packages': set(find_packages() + 
                 ['nglview',