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

This class provides an energy term based on an arbritrary Observable. More...

#include <ObsEnergy.hh>

Inheritance diagram for prf::ObsEnergy:
Inheritance graph

Public Member Functions

 ObsEnergy ()
 Default constructor.
void setScaleFactor (double x)
 Set scale.
double getScaleFactor () const
 Get scale factor.
void connectObs (Observable *o)
 Connect to one Observable.
double evaluate ()
std::string obsName () const
 Name of the observable associated with the energy term.
void setObsName (std::string s)
 Set name of the observable this term should be associated with.
void rangeEstimate (double &x1, double &x2)
 Estimate a range.
void set_pars (std::string pars)
 Configure the ObsEnergy term.
- 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
virtual double deltaE (Update *)
 do a new delta calculation optimized for the given kind of update
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

It is sometimes desirable to be able to use a measurement performed on a structure as a "constraint", or an energy term driving the dynamics towards a larger or smaller values of that Observable. This class helps with one approach towards such constrained simulations. Any Observable, such as RMSD, native contacts, radius of gyration etc. can be used to guide the simulations, through this pseudo-energy term.

See Also

Member Function Documentation

double ObsEnergy::evaluate ( )

do a new ab initio calculation

Reimplemented from prf::Energy.

void ObsEnergy::set_pars ( std::string  pars)

The term can be configured by a string consisting of a comma separated pair of assignments like this: "obs=rg,scale=50".

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