In [1]:

    

from Bio.PDB import *
cutoff = 3.5
parser = PDBParser()
structure = parser.get_structure('4hj2', '4hj2.pdb')
chain = structure.get_chains().next()
searcher = NeighborSearch([atom for atom in chain.get_atoms() if atom.name in ('O','N')])
neighbors = searcher.search_all(cutoff, level='R')


    

In [2]:

    

import numpy as np
contacts = np.zeros([len(chain), len(chain)])
for n in neighbors:
    contacts[n[0].id[1] - 1, n[1].id[1] - 1] = 1
    contacts[n[1].id[1] - 1, n[0].id[1] - 1] = 1
for i in xrange(len(chain)):
    contacts[i,i] = 0
contacts


    

    
Out[2]:





array([[ 0.,  1.,  1., ...,  0.,  0.,  0.],
       [ 1.,  0.,  1., ...,  0.,  0.,  0.],
       [ 1.,  1.,  0., ...,  0.,  0.,  0.],
       ..., 
       [ 0.,  0.,  0., ...,  0.,  1.,  1.],
       [ 0.,  0.,  0., ...,  1.,  0.,  1.],
       [ 0.,  0.,  0., ...,  1.,  1.,  0.]])

In [3]:

    

%matplotlib inline
import matplotlib.pyplot as plt
plt.figure(figsize=(8, 8))
a = plt.imshow(contacts, cmap="Greys")


    

    




/Users/lenny/Envs/assignss/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
  warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')






    

In [4]:

    

helices = []
helix = set()
for i in xrange(len(chain)):
    try:
        if contacts[i][i+3]:
            if abs(chain[i]['O'] - chain[i+3]['N']) <= cutoff:
                helix.add(chain[i])
                continue
    except:
        pass
    
    try:
        if contacts[i][i-3]:
            if abs(chain[i-3]['O'] - chain[i]['N']) <= cutoff:
                helix.add(chain[i])
    except:
        pass
        
    if len(helix) >= 6:
        helix = list(helix)
        helix.sort(key=lambda x: x.id[1])
        helices.append(helix)
        helix = set()
helix_ranges = []
for i in helices:
    helix = "%s-%s" % (str(i[0].id[1]), str(i[-1].id[1]))
    print helix
    helix_ranges.append(helix)


    

    




13-18
19-35
37-42
43-71
74-89
90-97
98-105
108-121
122-136
137-164
165-181
182-193
194-213

In [5]:

    

import nglview
view = nglview.show_structure_file('4hj2.pdb')
view.clear_representations()
view.add_cartoon(selection='protein', color='blue')
for helix in helix_ranges:
    view.add_cartoon(selection=helix, color='red')
view.render_image()
view


    

In [7]:

    

view.get_image()


    

In [ ]: