Computing molecular distances on a PDB file

Here, we will find atoms closer to three zincs in the 1TUP model. We will consider several distances to these zincs. We will take this opportunity to discuss the performance of algorithms.

Getting ready

You can find this content in the Chapter07/Distance.ipynb Notebook file. Take a look at the Introducing Bio.PDB recipe in this chapter for more information.

How to do it...

Take a look at the following steps:

1. Let's load our model, 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. We will now get our zincs, against which we will perform later comparisons:

zns = []for atom in p53_1tup.get_atoms():
if atom.element == 'ZN':
zns.append(atom)
for zn in zns:
    print(zn, zn.coord)

You should see three zinc atoms.

3. Now, let's define a function to get the distance between one atom and a set of other atoms, as follows...