#!/usr/bin/env python
# coding: utf-8

# py3Dmol
# =======
# 
# A simple [IPython/Jupyter](http://jupyter.org/) widget to
# embed an interactive [3Dmol.js](http://3dmol.csb.pitt.edu) viewer in a notebook.
# 
# The widget is completely static, which means the viewer doesn't need a running
# IPython kernel to be useful and web pages and presentations generated from
# the notebook will work as expected.  However, this also means there is only
# one-way communication between the notebook and the viewer.
# 
# Installation
# ------------
# 
# From PyPI:
# 
#     pip install py3Dmol
#     
# API
# ---
# 
# The returned view object has the exact same API as [3Dmol.GLViewer](http://3dmol.csb.pitt.edu/doc/$3Dmol.GLViewer.html)
# with the exception that functions return None.
# 
# 

# In[1]:


import py3Dmol


# In[2]:


p = py3Dmol.view(query='pdb:1ycr')
p.setStyle({'cartoon': {'color':'spectrum'}})
p.show()


# In[3]:


xyz = '''4
* (null), Energy   -1000.0000000
N     0.000005    0.019779   -0.000003   -0.157114    0.000052   -0.012746
H     0.931955   -0.364989    0.000003    1.507100   -0.601158   -0.004108
H    -0.465975   -0.364992    0.807088    0.283368    0.257996   -0.583024
H    -0.465979   -0.364991   -0.807088    0.392764    0.342436    0.764260
'''


# In[4]:


xyzview = py3Dmol.view(width=400,height=400)
xyzview.addModel(xyz,'xyz',{'vibrate': {'frames':10,'amplitude':1}})
xyzview.setStyle({'stick':{}})
xyzview.setBackgroundColor('0xeeeeee')
xyzview.animate({'loop': 'backAndForth'})
xyzview.zoomTo()
xyzview.show()


# Display local file.

# In[5]:


benz='''
     RDKit          3D

  6  6  0  0  0  0  0  0  0  0999 V2000
   -0.9517    0.7811   -0.6622 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2847    1.3329   -0.3121 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2365    0.5518    0.3512 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9517   -0.7811    0.6644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2847   -1.3329    0.3144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2365   -0.5518   -0.3489 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  1  1  0
M  END
$$$$'''
view = py3Dmol.view()
view.addModel(benz,'sdf')
view.setStyle({'stick':{}})
view.setStyle({'model':0},{'stick':{'colorscheme':'cyanCarbon'}})
view.zoomTo()


# You can create a single canvas object with multiple viewers arrayed in a grid (3Dmol.createViewerGrid).

# In[6]:


view = py3Dmol.view(query='pdb:1dc9',linked=False,viewergrid=(2,2))
view.setViewStyle({'style':'outline','color':'black','width':0.1})
view.setStyle({'cartoon':{'arrows':True, 'tubes':True, 'style':'oval', 'color':'white'}},viewer=(0,1))
view.setStyle({'stick':{'colorscheme':'greenCarbon'}},viewer=(1,0))
view.setStyle({'cartoon':{'color':'spectrum'}},viewer=(1,1))
view.removeAllModels(viewer=(0,0))
view.addModel(benz,'sdf',viewer=(0,0))
view.setStyle({'stick':{}},viewer=(0,0))
view.zoomTo(viewer=(0,0))
view.render()


# In[7]:


view = py3Dmol.view(query='pdb:1ycr')
chA = {'chain':'A'}
chB = {'chain':'B'}
view.setStyle(chA,{'cartoon': {'color':'spectrum'}})
view.addSurface(py3Dmol.VDW,{'opacity':0.7,'color':'white'}, chA)
view.setStyle(chB,{'stick':{}})
view.show()


# In[8]:


view = py3Dmol.view(query='pdb:5ire',options={'doAssembly':True})
view.setStyle({'cartoon':{'color':'spectrum'}})
view.show()


# Color by temperature factors

# In[9]:


view = py3Dmol.view(query='pdb:1ycr')
view.setStyle({'cartoon': {'color':'white'}})
view.addSurface(py3Dmol.VDW,{'opacity':0.7,'colorscheme':{'prop':'b','gradient':'sinebow','min':0,'max':70}})


# Generate an inline image of what is currently in the viewer (all white if the structure hasn't loaded yet).

# In[11]:


png = view.png()
png


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