PROFASI  Version 1.5
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prf::HPContact Class Reference

A Contact function for Hydrophobic contacts. More...

#include <ContactFunctions.hh>

Inheritance diagram for prf::HPContact:
Inheritance graph

Public Member Functions

void set_cutoff (double xx)
 Change contact fraction cutoff for hydrophobic contacts.

Detailed Description

This contact function checks if the given residues are in hydrophobic contact. It is not based on the hydrophobic energy, but simply on how many hydrophobic atoms of one non-polar residue are in contact with one or more such atoms of the other. This number is then scaled by its maximum value to obtain a fraction between 0 and 1. When this number is greater than a certain lower cutoff, by default set to 0.1, the residues are regarded as being in contact. The minimum contact fraction can of course be changed with the function set_cutoff(double).

The hydrophobic contact makes sense for amino acids as well as end groups.

The documentation for this class was generated from the following files:

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2