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 06_Prot/Stats.ipynb notebook.

How to do it...

Take a look at the following steps:

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

   from __future__ import print_function
   from Bio import PDB
   repository = PDB.PDBList()
   parser = PDB.PDBParser()
   repository.retrieve_pdb_file('1TUP', pdir='.')
   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...