Performing geometric operations

We will now perform computations with geometry information, including computing the center of the mass of chains and whole models.

Getting ready

You can find this content in the Chapter08/Mass.py Notebook file.

How to do it...

Let’s take a look at the following steps:

1. First, let’s retrieve the data:

   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. 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 HETATM types; the vast majority are standard PDB atoms.

3. Let’s compute the masses for all chains...