Bioinformatics with Python Cookbook - Second Edition

How to do it...

Let's take a look at the following steps:

1. First, let's retrieve the data:

from Bio import PDBrepository = 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, let's recall the type of residues that we have with the following code:

my_residues = set()for residue in p53_1tup.get_residues():    my_residues.add(residue.id[0])print(my_residues)

So, we have H_ ZN (zinc) and W (water), which are HETATMs; the vast majority are standard PDB atoms.

3. Let's compute the masses for all chains, zincs, and waters using the following code:

def get_mass(atoms, accept_fun=lambda atom: atom.parent.id[0] != 'W'): return sum([atom.mass ...