Bioinformatics with Python Cookbook - Second Edition

How to do it...

Take a look at the following steps:

1. First, let's retrieve 1TUP, as follows:

from Bio import PDBrepository = PDB.PDBList()parser = PDB.PDBParser()repository.retrieve_pdb_file('1TUP', pdir='.', file_format='pdb') #XXXp53_1tup = parser.get_structure('P 53', 'pdb1tup.ent')

2. Then, extract some atom-related statistics:

from collections import defaultdictatom_cnt = defaultdict(int)atom_chain = defaultdict(int)atom_res_types = defaultdict(int)for atom in p53_1tup.get_atoms():    my_residue = atom.parent    my_chain = my_residue.parent    atom_chain[my_chain.id] += 1    if my_residue.resname != 'HOH':        atom_cnt[atom.element] += 1    atom_res_types[my_residue.resname] += 1print(dict(atom_res_types))print(dict(atom_chain))print(dict(atom_cnt))