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

#include <DihedralRestraints.hh>

Inheritance diagram for prf::DihedralRestraints:

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:

model/Energy/Extras/DihedralRestraints.hh
model/Energy/Extras/DihedralRestraints.cc

Public Member Functions

Detailed Description

Member Function Documentation