Add notebook to run quantum calculation container

[bnmajor]

No description provided.

[cjh1]

@bnmajor I am seeing the follow error when I try to run the second cell:

--------------------------------------------------------------------------
HttpError                                 Traceback (most recent call last)
<ipython-input-3-dac8a8c38b02> in <module>
----> 1 mol = oc.find_structure('InChI=1S/2Li')
      2 mol.structure.show()

~/openchemistrypy/openchemistry/api.py in find_structure(identifier, image_name, input_parameters, input_geometry, inchi, smiles)
    130 
    131 def find_structure(identifier=None, image_name=None, input_parameters=None, input_geometry=None, inchi=None, smiles=None):
--> 132     molecule = find_molecule(identifier, inchi, smiles)
    133 
    134     # If we have been provided basis, theory or functional it means the user is

~/openchemistrypy/openchemistry/api.py in find_molecule(identifier, inchi, smiles)
    118 
    119 def find_molecule(identifier=None, inchi=None, smiles=None):
--> 120     molecule = _find_molecule(identifier, inchi, smiles)
    121     if molecule is None:
    122         raise Exception('Unable to find a molecule with the provided identifiers.')

~/openchemistrypy/openchemistry/api.py in _find_molecule(identifier, inchi, smiles)
     32     # Finally, if identifier is something else (a name), try cactus
     33     if identifier:
---> 34         return _find_molecule_using_cactus(identifier)
     35 
     36     return None

~/openchemistrypy/openchemistry/api.py in _find_molecule_using_cactus(identifier)
     61         'cactus': identifier
     62     }
---> 63     res = GirderClient().get('molecules/search', parameters=params)
     64     # Just pick the first
     65     if 'results' in res and len(res['results']) > 0:

/opt/conda/lib/python3.8/site-packages/girder_client/__init__.py in get(self, path, parameters, jsonResp)
    469         Convenience method to call :py:func:`sendRestRequest` with the 'GET' HTTP method.
    470         """
--> 471         return self.sendRestRequest('GET', path, parameters, jsonResp=jsonResp)
    472 
    473     def post(self, path, parameters=None, files=None, data=None, json=None, headers=None,

/opt/conda/lib/python3.8/site-packages/girder_client/__init__.py in sendRestRequest(self, method, path, parameters, data, files, json, headers, jsonResp, **kwargs)
    461                 return result
    462         else:
--> 463             raise HttpError(
    464                 status=result.status_code, url=result.url, method=method, text=result.text,
    465                 response=result)

HttpError: HTTP error 500: GET http://girder:8080/api/v1/molecules/search?cactus=InChI%3D1S%2F2Li
Response text: {"message": "KeyError: KeyError('bonds')", "trace": ["<FrameSummary file /girder/girder/api/rest.py, line 629 in endpointDecorator>", "<FrameSummary file /girder/girder/api/rest.py, line 1190 in GET>", "<FrameSummary file /girder/girder/api/rest.py, line 946 in handleRoute>", "<FrameSummary file /mongochemserver/girder/molecules/molecules/molecule.py, line 490 in search>", "<FrameSummary file /mongochemserver/girder/molecules/molecules/utilities/molecules.py, line 47 in create_molecule>"], "type": "internal", "uid": "a77fe3ed-490c-4af8-92eb-8953a432eae7"}

It is possible that the catus seach is failing? Or something else has changed?

[bnmajor]

@cjh1 I've update find_molecule to use the InChiKey instead, the search should work now.