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

Third-neighbour excluded volume contribution. More...

#include <LocExVol.hh>

Inheritance diagram for prf::LocExVol:
Inheritance graph

Public Member Functions

void rangeEstimate (double &x1, double &x2)
 Estimate a range in which values of this observable are expected.
double evaluate ()
double deltaE (Update *)
 do a new delta calculation optimized for the given kind of update
void Accept (Update *)
 Accept a proposed update.
- Public Member Functions inherited from prf::Energy
void Connect (Population *pl)
 Connect the energy term with one population.
virtual void set_pars (std::string pars)
 Set some adjustible parameters.
void refresh ()
 Overrides the virtual member from the Observable class.
double value ()
 return result from last calculation
double deltaE ()
 return result from the last energy change calculation
double delta (Update *)
 Quick estimate of the change in an Observable due to an update.
virtual double deltaEwithlimit (Update *updt, double maxde)
 Calculate energy change for an update, but with a stop condition.
virtual void Revert (Update *)
 Reject a proposed update.
int init_obs ()
 All observables must implement one initialize routine.
- Public Member Functions inherited from prf::Observable
void set (std::string cmd)
 Give the object an instruction to process during initialization.
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

Contribution to excluded volume from "all" atom pairs separated by three covalent bonds. "All" excludes pairs with fixed distance, like in phenyl rings. All such pairs are listed during initialization, and calculation proceeds by a straight forward summation over such pairs. During an update of a single angle, at most 9 such pairs are affected. What pairs would be affected by different kinds of updates is also pre-calculated and stored. Very little needs to be done to get deltaE after an update.

In an equilibrated system this term contributes the lion's share of excluded volume energy. Because the atom pairs involved in this term can not fly apart. This term has the biggest influence on the Ramachandran angle distributions and also the side chain chi angle distributions.

By definition this term always involves atoms from the same peptide. So, it does not need to use the periodic distance measure. By design, the size of the periodic box is sufficiently large so that the different parts of a chain can not reach out and interact with their copies in a different periodic box. And atoms of one chain are always kept together, so that separation between them can not exceed the box length.

Member Function Documentation

void prf::LocExVol::Accept ( Update updt)

PROFASI uses many local contribution matrices and backup variables to quickly evaluate the change caused to any energy term by a given update. Those backup variables and the contribution matrices need to be kept in sync with the current system configuration. So, each energy class has an accept and a reject method, which are called when an update is accepted or rejected. What is done inside these functions depends on the energy term and optimization trick used therein.

Reimplemented from prf::Energy.

double prf::LocExVol::evaluate ( )

do a new ab initio calculation

Reimplemented from prf::Energy.

void prf::LocExVol::rangeEstimate ( double &  x1,
double &  x2 

The default is between 0 and 1. So, for observables with values always between 0 and 1, you need not over-write this virtual function. Sometimes the observable will have a different fixed range, determined by its definition. Sometimes the range can not be determined perfectly. In such a case, let this function just return something reasonable.

Reimplemented from prf::Energy.

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