Ion Environments Project

This repository contains code for the Computational Geometry based analysis of ion environments in three dimensional protein structures, created for the thesis project.

Prerequisites

The scripts are written in Python and use a few other standard libraries and biopython.

• Python
• Biopython

Driver.py

This is the main module which is used to call other modules and perform the analysis. The sequence identity cutoff value is the main variable parameter

PDB.py

This module contains the PDB Class which has methods to:

• Download PDB Files
• Describe PDB Files
• Get unique chains from PDB files, based on ATOM information (not sequence based)
• Extract specific chains from a PDB file
• Create unique PDB entries based on a specific HETATM records for a PDB chain

Subprocess.py

This module uses the subprocess module to call upon a few Java programs.

Calculations.py

This module performs calculations relevent to the computational geometry based analysis.