Example code with iteration over pdb file chains with sliding window

example.py

from prody import *

pdb = parsePDB("1QS3")

def sliding_window(aminoacids, width=3):
    """
    iterates over residues in given chain, returns iterator 
    with arrays containing each width elements (as a sliding window)
    """
    index = 1 # prody starts iteration from 1, or at least it seems
    aa_list = [ aminoacids[index + offset] for offset in xrange(width) ]
    yield aa_list
    offset = 0
    while width+offset < len(aminoacids):
        aa_list.pop(0)
        aa_list.append(aminoacids[width + offset])
        yield aa_list
        offset += 1


def get_angles(fragment):
    """
    gets list of Aminoacid elements as an input
    returns list of torsion angles (phi, psi) for all atoms except first and last in list
    """
    return [
        (prody.measure.measure.calcPhi(x), prody.measure.measure.calcPsi(x))
        for x in fragment[1:len(fragment) - 1] 
    ]
    
    
def get_aminoacid_sequence(fragment):
    """
    gets list of Aminoacid elements as an input
    returns aminoacid sequence as a string containing 1-letter IUPAC codes
    """
    get = prody.atomic.chain.AAMAP.get
    return ''.join([get(res.getResname(), 'X') for res in fragment])
    

print(pdb)
for chain in pdb.getHierView():
    for fragment in sliding_window(chain):
        print(fragment)
        print(get_aminoacid_sequence(fragment)) # this should be converted to smiles string
        print(get_angles(fragment))