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

A measure of nativeness based on local environment of residues. More...

#include <NativenessQ.hh>

Inheritance diagram for prf::NativenessQ:
Inheritance graph
[legend]

Public Member Functions

int init_obs ()
 All observables must implement one initialize routine.
 
double evaluate ()
 Actual calculation of the value of the observable.
 
- Public Member Functions inherited from prf::Observable
void set (std::string cmd)
 Give the object an instruction to process during initialization.
 
virtual void refresh ()
 Necessary before an observable value is used.
 
virtual double delta (Update *u)
 Quick estimate of the change in an Observable due to an update.
 
virtual void rangeEstimate (double &x1, double &x2)
 Estimate a range in which values of this observable are expected.
 
double operator() ()
 Retrieve the value of the observable.
 
double Value ()
 Retrieve the value of the observable.
 
void disable_stats ()
 Stop collecting statistical data like averages and histograms.
 
void enable_stats ()
 Start collecting statistical data like averages and histograms.
 
- Public Member Functions inherited from prf::Named
 Named ()
 Create an object with name "unnamed".
 
 Named (const char *st)
 Create an object with name st given as a C string.
 
 Named (std::string st)
 Create an object with a name given as a string.
 
std::string Name () const
 Retrive the name of an object.
 
void Name (std::string gnm)
 Assign a new name to an object.
 

Detailed Description

This class implements the nativeness parameter Q introduced in S. Takada, Z.A. Luthey-Schulten, P.G. Wolynes, J. Chem. Phys. 110 (1999) 11616. The definition of the local version of the measure is taken from G. Chikenji, Y. Fujitsuka and S. Takada, Chem. Phys. 307 (2004) 157.

This measure is only concerned with Calpha distances. For each residue, a list is made of all the other residues which are within 6 Angstroms CA distance from it in the native state. To assess the nativeness of a given new state, each residue's new distance from those in its native neighbourhood list is evaluated. For each pair, the quantity exp(-(r_{ij}-r0_{ij})^2 / d^2) is calculated. These are then averaged over all neighbours of a residue to define its local "nativeness": how similar its environment in the current state is, compared to the native state. The average over all unique pairs over the entire protein is the value returned by the observable.

Member Function Documentation

int NativenessQ::init_obs ( )
virtual

Even if it seems that one particular observable might need additional arguments during initialization, it is advantageous to have a uniform syntax for all of them. So, when additional arguments are needed, one should provide them in a separate function called before initialization, and then call init_obs without arguments. The name init_obs instead of a more natural "init" or "initialize" is because an Observable often inherits from other classes which represent its character more fundamentally. So, the names such as "init" are kept free for such base classes.

Reimplemented from prf::Observable.


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