README.md

BioPhysics

Source codes and data for BioPhysics course on Bioinformatics

polarcontacts.py

Code for listing polar contacts ans interaction energies from a PDB file

StructureWrapper.py

Convenient wrapper classes for Bio.PDB classes

ForceField.py

Module for vdw parameters management

ResLib.py

Module for Residue Library management

data/vdwprm

Simple vdw parameters (based on AMBER ff)

data/aaLib.lib

Library for obtaining amino acid atom types and partial charges (based on AMBER ff)

Usage:

python3 polarContacts.py [-h] [--backonly] [--nowats] pdb_path

External dependencies

Bio.PDB.NeighborSearch (BioPython)
Bio.PDB.PDBParser (Biopython)

prob217.py

Simple script to solve Exercise 7 form 2.1 collection