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 Chapter08/Distance.py Notebook file.

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 comparisons later:

   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...