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

A restraint energy term based on dihedral angles. More...

#include <DihedralRestraints.hh>

Inheritance diagram for prf::DihedralRestraints:
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Public Member Functions

 DihedralRestraints ()
 Default constructor.
 
void set_pars (std::string xmlfilename)
 Set parameters from an XML file.
 
double evaluate ()
 
double deltaE (Update *up)
 do a new delta calculation optimized for the given kind of update
 
void rangeEstimate (double &x1, double &x2)
 Estimate a range in which values of this observable are expected.
 
- Public Member Functions inherited from prf::Energy
void Connect (Population *pl)
 Connect the energy term with one population.
 
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 Accept (Update *)
 Accept a proposed update.
 
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

This term provides a way insert an arbitrary energy term that is purely a function of dihedral angles. The term can be inserted using the settings file or the command line. What angles and what functional form to use can be configured with an XML file read in at run time. Efficient delta calculations for this energy term are trivial. How to use this class to restrain simulations is described in Restraining simulations with a torsional angle potential .

See Also
Restraining simulations with a torsional angle potential

Member Function Documentation

double DihedralRestraints::evaluate ( )
virtual

do a new ab initio calculation

Reimplemented from prf::Energy.

void DihedralRestraints::rangeEstimate ( double &  x1,
double &  x2 
)
virtual

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