Extracting more information from a PDB file

Here, we will continue our exploration of the record structure produced by Bio.PDB from PDB files.

Getting ready

For general information about the PDB models that we are using, refer to the previous recipe.

You can find this content in the Chapter07/Stats.ipynb Notebook file.

How to do it...

Take a look at the following steps:

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

from Bio import PDB
repository = PDB.PDBList()
parser = PDB.PDBParser()
repository.retrieve_pdb_file('1TUP', pdir='.', file_format='pdb') #XXX
p53_1tup = parser.get_structure('P 53', 'pdb1tup.ent')

2. Then, extract some atom-related statistics:

from collections import defaultdict

atom_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...