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:
- 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')
- 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...