PROFASI  Version 1.5
Public Member Functions | List of all members
prf::Proximity Class Reference

A ContactFunction based on spatial proximity. More...

#include <ContactFunctions.hh>

Inheritance diagram for prf::Proximity:
Inheritance graph

Public Member Functions

void minimum_links (int nlnk)
 Minimum number of close pairs of heavy atoms for a contact, default=2.

Detailed Description

This contact function returns true if the two concerned amino acids are close in space. The closeness is defined in this way: If a heavy atom in amino acid i is closer than a certain given cutoff distance to any heavy atom in amino acid j, there is said to be a link between the two residues. The residues are said to be in contact if there is at least two (or some other number specified by the minimum_links(int) function) links between them. The cutoff distance is tunable. This contact function needs an initialization with a Population * as the argument.

Member Function Documentation

void prf::Proximity::minimum_links ( int  nlnk)

If you set minimum links to 1, this contact function will work like a simple heavy atom contact function.

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