PROFASI  Version 1.5
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prf::CircularNormal Class Reference

Circular normal potential well. More...

#include <RestraintFunction.hh>

Inheritance diagram for prf::CircularNormal:
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Public Member Functions

int set_pars (prf_xml::XML_Node *pars)
 Set parameters for circular normal potential.
 
double operator() (double x)
 Evaluate the function for a given value of the coordinate.
 
double estimate_max (double scale_large)
 Estimate a maximum based on some "large" scale.
 
- Public Member Functions inherited from prf::RestraintFunction
 RestraintFunction ()
 Default constructor.
 
virtual double estimate_min ()
 Estimate a minimum.
 

Detailed Description

This is an adaptation of the circular normal or von Mises distribution for use as a potential well in angle space. The von Mises distribution is given by
$ f(\theta)= \frac{\exp(\kappa \cos(\theta-\mu))}{2\pi I_0 (\kappa)} $ where $I_0$ is the modified Bessel function. The parameter kappa roughly corresponds to the inverse of the square of the width of the distribution. The angle in question does not appear in the denominator. It is therefore convenient to modify the function to :
$ f(\theta)=N \left( 1 - \frac{\exp(\kappa \cos(\theta-\mu))}{\exp(\kappa)} \right) $ This way of writing the function makes sure that the value is 0 when the the angle takes its mean value, and N when it is not. The user can choose the location (mu), width ( roughly inverse square-root of kappa ) and the depth (N) of the potential well.

Member Function Documentation

int CircularNormal::set_pars ( prf_xml::XML_Node pars)
virtual

The XML node passed should be a parameters node with up to 3 child fields called kappa , mean and weight in arbitrary order. Example:

<parameters>
    <mean>1.1342</mean>
    <kappa>8</kappa>
    <weight>10</weight>
<parameters>

Reimplemented from prf::RestraintFunction.


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