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 Chapter08/Stats.py Notebook file.

How to do it...

We’ll get started, using 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') 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...