Here, we will continue our exploration of the record structure produced by Bio.PDB from PDB files.
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.
Take a look at the following steps:
First, let's retrieve
1TUPas 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')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...