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

# # [Prody](http://prody.csb.pitt.edu) is an open-source Python package for protein structural dynamics analysis with expansive and well-written API.

# In[1]:


import prody
prot = prody.parsePDB('3UB5')


# The default visualization in ProDy uses matplotlib.

# In[2]:


get_ipython().run_line_magic('matplotlib', 'inline')
prody.showProtein(prot)


# With the latest version of ProDy, `py3Dmol` will be used if it has been imported.

# In[3]:


prody.checkUpdates()


# In[4]:


import py3Dmol
prody.showProtein(prot)


# # Configuration
# 
# A number of keyword arguments are supported.

# The background color is configurable.

# In[5]:


prody.showProtein(prot,backgroundColor="black")


# The height and width of the viewer can be changed.

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prody.showProtein(prot, height=400, width=200,backgroundcolor='gray')


# The viewer can be zoomed and centered on a given [AtomSelectionSpec](http://3dmol.csb.pitt.edu/doc/types.html#AtomSelectionSpec).

# In[7]:


prody.showProtein(prot, zoomto={'resn':'ATP'})


# # Styles
# 
# Custom styles can be applied by providing [AtomSelectionSpec](http://3dmol.csb.pitt.edu/doc/types.html#AtomSelectionSpec) and [AtomStyleSpec](http://3dmol.csb.pitt.edu/doc/types.html#AtomStyleSpec) objects.
# 
# A single style may be applied.

# In[8]:


prody.showProtein(prot,style={'cartoon':{'colorscheme':'chain'},'stick':{'colorscheme':'chain'}})


# For more complex styling, generate and manipulate the py3Dmol view object directly.

# In[9]:


view = prody.view3D(prot)
view.setStyle({'cartoon':{'colorscheme':'chain'}})
view.setStyle({'hetflag':True},{'stick':{'colorscheme':'magentaCarbon'}})
view.setStyle({'bonds': 0},{'sphere':{'radius':0.5}})
view.addLabel('Chain A',{'inFront':True,'showBackground':False,'fontColor':'blue'},{'chain':'A'})
view.addLabel('Chain P',{'inFront':True,'showBackground':False,'fontColor':'green'},{'chain':'P'})

view.show()


# # GNM/ANM
# 
# Squared fluctuations (or any other alpha-carbon length numerical vector) can be visualized in a RWB colorscheme.  Red values are larger.

# In[10]:


gnm, sel = prody.calcGNM(prot)


# In[16]:


prody.showProtein(prot,flucts=prody.calcSqFlucts(gnm))


# Individual modes may be visualized.

# In[12]:


prody.showProtein(prot,flucts=gnm[0].getArray())


# Styles can still be applied.

# In[13]:


prody.showProtein(prot,flucts=gnm[1].getArray(),style={'cartoon':{}})


# # Motions
# 
# It is also possible to provide an array of vectors (one per a calpha) that can be used to animate motions.  The animate kwarg takes the 3Dmol.js animate options.

# In[14]:


anm, sel = prody.calcANM(prot)


# In[15]:


prody.showProtein(prot,vecs=anm[0].getArray(),
                  flucts=prody.calcSqFlucts(anm[0]),
                  style={'cartoon':{}})


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