In [1]:

    

from chemlab.notebook import load_remote_system, load_remote_molecule, display_system
from chemview.render import render_povray


    

    




:0: FutureWarning: IPython widgets are experimental and may change in the future.
/home/gabriele/anaconda/envs/py3/lib/python3.4/site-packages/IPython/utils/path.py:290: UserWarning: Ignoring ~/.config/ipython in favour of ~/.ipython. Remove ~/.config/ipython to get rid of this message
  'get rid of this message').format(cu(xdg_ipdir), cu(ipdir)))






    




HDF backend is not available because pytables is not installed

In [2]:

    

pdb = load_remote_system('http://www.rcsb.org/pdb/files/3B75.pdb', format='pdb')


    

    




/tmp/tmpu2r0p53y /tmp/tmpu2r0p53y  pdb

In [5]:

    

mv = display_system(pdb)
mv


    

    




/home/gabriele/anaconda/envs/py3/lib/python3.4/site-packages/IPython/utils/traitlets.py:438: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  silent = bool(old_value == new_value)

In [6]:

    

# SLOW: render_povray(mv.get_scene(), extra_opts={'radiosity':True})


    

    




---------------------------------------------------------------------------
KeyboardInterrupt                         Traceback (most recent call last)
<ipython-input-6-09009f2b2f3a> in <module>()
----> 1 render_povray(mv.get_scene(), extra_opts={'radiosity':True})

/home/gabriele/workspace/chemview/chemview/render.py in render_povray(scene, filename, width, height, antialiasing, extra_opts)
     90 
     91     return scene.render(filename, width=width, height=height,
---> 92                         antialiasing = antialiasing)
     93 
     94 def _generate_objects(representations):

/home/gabriele/anaconda/envs/py3/lib/python3.4/site-packages/vapory/vapory.py in render(self, outfile, height, width, quality, antialiasing, remove_temp, auto_camera_angle, show_window, tempfile)
     80 
     81         return render_povstring(str(self), outfile, height, width,
---> 82                                 quality, antialiasing, remove_temp, show_window, tempfile)
     83 
     84 

/home/gabriele/anaconda/envs/py3/lib/python3.4/site-packages/vapory/io.py in render_povstring(string, outfile, height, width, quality, antialiasing, remove_temp, show_window, tempfile)
    110                                     stdout=subprocess.PIPE)
    111 
--> 112     out, err = process.communicate(string.encode('ascii'))
    113 
    114     if remove_temp:

/home/gabriele/anaconda/envs/py3/lib/python3.4/subprocess.py in communicate(self, input, timeout)
    958 
    959             try:
--> 960                 stdout, stderr = self._communicate(input, endtime, timeout)
    961             finally:
    962                 self._communication_started = True

/home/gabriele/anaconda/envs/py3/lib/python3.4/subprocess.py in _communicate(self, input, endtime, orig_timeout)
   1615                         raise TimeoutExpired(self.args, orig_timeout)
   1616 
-> 1617                     ready = selector.select(timeout)
   1618                     self._check_timeout(endtime, orig_timeout)
   1619 

/home/gabriele/anaconda/envs/py3/lib/python3.4/selectors.py in select(self, timeout)
    365             ready = []
    366             try:
--> 367                 fd_event_list = self._poll.poll(timeout)
    368             except InterruptedError:
    369                 return ready

KeyboardInterrupt: 

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