Molecule Visualization Error

[obrien951]

I was given an error when trying to visualize the molecule. My error and conda list message are below.

Does anyone recognize this error? Are there any changes I might need to make to my environment or to some of the requirements?

Thank you in advance for any help.

Error Message

Connecting to docker host at unix://var/run/docker.sock... done
{}
---------------------------------------------------------------------------
ConnectionError                           Traceback (most recent call last)
<ipython-input-2-0385c2af8f06> in <module>()
      5 
      6 h2 = mdt.Molecule([atom1,atom2], name='H2', charge=0)
----> 7 h2.draw(height=300)

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/moldesign/molecules/atomcollections.pyc in draw(self, width, height, show_2dhydrogens, display)
    246                                 show_hydrogens=show_2dhydrogens)
    247             viz3d = self.draw3d(width=width, height=height,
--> 248                                 display=False)
    249             views = ipy.HBox([viz2d, viz3d])
    250         else:

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/moldesign/molecules/atomcollections.pyc in draw3d(self, highlight_atoms, **kwargs)
    267         """
    268         from moldesign import viewer
--> 269         self.viz3d = viewer.GeometryViewer(self, **kwargs)
    270         if highlight_atoms is not None:
    271             self.viz3d.highlight_atoms(highlight_atoms)

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/moldesign/viewer/viewer3d.pyc in __init__(self, mol, style, display, render, **kwargs)
     69         self._colored_as = {}
     70         if mol:
---> 71             self.add_molecule(mol, render=False)
     72             self._frame_positions.append(self.get_positions())
     73             if style is None:

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/nbmolviz/drivers3d.pyc in add_molecule(self, mol, render)
     54         # javascript: glviewer.addModel(moldata, format, {'keepH': true});
     55         self.mol = mol
---> 56         moldata, format = self.get_input_file()
     57         self.viewer('addModel', args=[moldata, format, {'keepH': True}])
     58         self.set_style('sphere', render=False)

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/moldesign/viewer/viewer3d.pyc in get_input_file(self)
    184         else:
    185             writemol = self.mol
--> 186         instring = writemol.write(format=fmt)
    187         return instring, fmt
    188 

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/moldesign/molecules/molecule.pyc in write(self, filename, **kwargs)
   1118         """
   1119         # TODO: make it easier to do the right thing, which is write to .pkl.bz2
-> 1120         return mdt.write(self, filename=filename, **kwargs)
   1121 
   1122     @property

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/moldesign/fileio.pyc in write(obj, filename, format, mode)
    127         WRITERS[format](obj, fileobj)
    128     else:
--> 129         fileobj.write(openbabel_interface.write_string(obj, format))
    130 
    131     # Return a string if necessary

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/moldesign/compute/runsremotely.pyc in wrapper(*args, **kwargs)
     97                                 python_call,
     98                                 name=self.jobname,
---> 99                                 sendsource=self.sendsource)
    100 
    101             if self.display:

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/pyccc/python.pyc in __init__(self, engine, image, command, interpreter, sendsource, **kwargs)
     97 
     98         super(PythonJob, self).__init__(engine, image, command,
---> 99                                         **kwargs)
    100 
    101     @staticmethod

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/pyccc/job.pyc in __init__(self, engine, image, command, name, submit, inputs, requirements, numcpus, runtime, on_status_update, when_finished)
    104 
    105         if submit and self.engine and self.image:
--> 106             self.submit()
    107 
    108     def _reset(self):

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/pyccc/job.pyc in submit(self, wait, resubmit)
    159                 raise ValueError('This job has already been submitted')
    160 
--> 161         self.engine.submit(self)
    162         self._submitted = True
    163         if wait: self.wait()

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/pyccc/engines/dockerengine.pyc in submit(self, job)
     73             job.workingdir = self.default_wdir
     74         job.imageid = du.create_provisioned_image(self.client, job.image,
---> 75                                                   job.workingdir, job.inputs)
     76         cmdstring = "sh -c '%s'" % job.command
     77 

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/pyccc/docker_utils.pyc in create_provisioned_image(client, image, wdir, inputs, pull)
     32     build_context = create_build_context(image, inputs, wdir)
     33     tarobj = make_tar_stream(build_context)
---> 34     imageid = build_dfile_stream(client, tarobj, is_tar=True, pull=pull)
     35     return imageid
     36 

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/pyccc/docker_utils.pyc in build_dfile_stream(client, dfilestream, is_tar, **kwargs)
     60                             rm=True,
     61                             custom_context=is_tar,
---> 62                             **kwargs)
     63 
     64     # this blocks until the image is done building

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/docker/api/build.pyc in build(self, path, tag, quiet, fileobj, nocache, rm, stream, timeout, custom_context, encoding, pull, forcerm, dockerfile, container_limits, decode, buildargs, gzip, shmsize, labels, cache_from)
    213             headers=headers,
    214             stream=stream,
--> 215             timeout=timeout,
    216         )
    217 

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/docker/utils/decorators.pyc in inner(self, *args, **kwargs)
     45             else:
     46                 kwargs['headers'].update(self._auth_configs['HttpHeaders'])
---> 47         return f(self, *args, **kwargs)
     48     return inner

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/docker/api/client.pyc in _post(self, url, **kwargs)
    177     @update_headers
    178     def _post(self, url, **kwargs):
--> 179         return self.post(url, **self._set_request_timeout(kwargs))
    180 
    181     @update_headers

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/requests/sessions.pyc in post(self, url, data, json, **kwargs)
    558         """
    559 
--> 560         return self.request('POST', url, data=data, json=json, **kwargs)
    561 
    562     def put(self, url, data=None, **kwargs):

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/requests/sessions.pyc in request(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)
    511         }
    512         send_kwargs.update(settings)
--> 513         resp = self.send(prep, **send_kwargs)
    514 
    515         return resp

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/requests/sessions.pyc in send(self, request, **kwargs)
    621 
    622         # Send the request
--> 623         r = adapter.send(request, **kwargs)
    624 
    625         # Total elapsed time of the request (approximately)

/Users/JosephOBrien/anaconda3/envs/mdtk27/lib/python2.7/site-packages/requests/adapters.pyc in send(self, request, stream, timeout, verify, cert, proxies)
    488 
    489         except (ProtocolError, socket.error) as err:
--> 490             raise ConnectionError(err, request=request)
    491 
    492         except MaxRetryError as e:

ConnectionError: ('Connection aborted.', error(61, 'Connection refused'))

Conda List

appnope                   0.1.0                     <pip>
backports-abc             0.5                       <pip>
backports.shutil-get-terminal-size 1.0.0                     <pip>
backports.ssl-match-hostname 3.5.0.1                   <pip>
biopython                 1.68                np112py27_0  
bleach                    2.0.0                     <pip>
certifi                   2017.4.17                 <pip>
chardet                   3.0.3                     <pip>
configparser              3.5.0                     <pip>
cycler                    0.10.0                    <pip>
decorator                 4.0.11                    <pip>
docker                    2.3.0                     <pip>
docker-py                 1.10.6                    <pip>
docker-pycreds            0.2.1                     <pip>
entrypoints               0.2.2                     <pip>
enum34                    1.1.6                     <pip>
fortranformat             0.2.5                     <pip>
funcsigs                  1.0.2                     <pip>
functools32               3.2.3.post2               <pip>
future                    0.16.0                    <pip>
html5lib                  0.999999999               <pip>
idna                      2.5                       <pip>
ipaddress                 1.0.18                    <pip>
ipykernel                 4.6.1                     <pip>
ipython                   5.3.0                     <pip>
ipython-genutils          0.2.0                     <pip>
ipywidgets                6.0.0                     <pip>
Jinja2                    2.9.6                     <pip>
jsonschema                2.6.0                     <pip>
jupyter-client            5.0.1                     <pip>
jupyter-core              4.3.0                     <pip>
markdown2                 2.3.4                     <pip>
MarkupSafe                1.0                       <pip>
matplotlib                2.0.2                     <pip>
mistune                   0.7.4                     <pip>
mkl                       2017.0.1                      0  
moldesign                 0.7.3                     <pip>
nbconvert                 5.2.1                     <pip>
nbformat                  4.3.0                     <pip>
nbmolviz                  0.6.6                     <pip>
notebook                  5.0.0                     <pip>
numpy                     1.12.1                   py27_0  
numpy                     1.12.1                    <pip>
openssl                   1.0.2l                        0  
pandocfilters             1.4.1                     <pip>
pathlib2                  2.2.1                     <pip>
pexpect                   4.2.1                     <pip>
pickleshare               0.7.4                     <pip>
Pint                      0.8                       <pip>
pip                       9.0.1                    py27_1  
prompt-toolkit            1.0.14                    <pip>
ptyprocess                0.5.1                     <pip>
py                        1.4.33                    <pip>
pyccc                     0.7.4                     <pip>
Pygments                  2.2.0                     <pip>
pyparsing                 2.2.0                     <pip>
pytest                    3.1.1                     <pip>
python                    2.7.13                        0  
python-dateutil           2.6.0                     <pip>
pytz                      2017.2                    <pip>
PyYAML                    3.12                      <pip>
pyzmq                     16.0.2                    <pip>
readline                  6.2                           2  
requests                  2.17.3                    <pip>
scandir                   1.5                       <pip>
scipy                     0.19.0                    <pip>
setuptools                27.2.0                   py27_0  
simplegeneric             0.8.1                     <pip>
singledispatch            3.4.0.3                   <pip>
six                       1.10.0                    <pip>
sqlite                    3.13.0                        0  
subprocess32              3.2.7                     <pip>
tblib                     1.3.2                     <pip>
terminado                 0.6                       <pip>
testpath                  0.3.1                     <pip>
tk                        8.5.18                        0  
tornado                   4.5.1                     <pip>
traitlets                 4.3.2                     <pip>
urllib3                   1.21.1                    <pip>
uuid                      1.30                      <pip>
wcwidth                   0.1.7                     <pip>
webcolors                 1.7                       <pip>
webencodings              0.5.1                     <pip>
websocket-client          0.40.0                    <pip>
wheel                     0.29.0                   py27_0  
widgetsnbextension        2.0.0                     <pip>
zlib                      1.2.8                         3  

[avirshup]

@obrien951 - hey Joseph; do you have the docker engine installed on your machine? I suspect that's what the problem is.

If true, then MDT needs to emit a better error message