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BioPhysics

Source codes and data for BioPhysics course on Bioinformatics

forcefield.py

Module for forcefield parameters management

residue_library.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)

ala_scanning_base.py

Base script for Ala Scanning exercise

External dependencies

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

Exercises

prob217.py

Simple script to solve Exercise 7 form 2.1 collection

prob217_noclass.py

Simple script to solve Exercise 7 form 2.1 collection. Version without python classes