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Bioinformatics with Python Cookbook

Bioinformatics with Python Cookbook

By : Tiago R Antao, Tiago Antao
4.7 (6)
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Bioinformatics with Python Cookbook

Bioinformatics with Python Cookbook

4.7 (6)
By: Tiago R Antao, Tiago Antao

Overview of this book

If you have intermediate-level knowledge of Python and are well aware of the main research and vocabulary in your bioinformatics topic of interest, this book will help you develop your knowledge further.
Table of Contents (11 chapters)
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10
Index

Performing geometric operations


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

Getting ready

You can find this content in the 06_Prot/Mass.ipynb notebook.

How to do it...

Take a look at the following steps:

  1. First, let's retrieve the data:

    from __future__ import print_function
    import numpy as np
    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')
  2. Then, remember 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) that are HETATMs and the vast majority that 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...

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