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

Distance restraints. More...

#include <DistanceRestraints.hh>

Inheritance diagram for prf::DistanceRestraints:
Inheritance graph

Public Member Functions

 DistanceRestraints ()
 Default constructor.
void set_pars (std::string xmlfilename)
 Set parameters from an XML file.
double evaluate ()
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
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

This is an extra energy term which can be used to encourage the formation of structures with particular pairs of atoms at given distances. The choice of atoms as well as the functional form of the distance dependence is fairly general. How to use this class to impose distance restraints in Monte Carlo simulations is described in Simulations with distance restraints .

See Also
Simulations with distance restraints

Member Function Documentation

double DistanceRestraints::evaluate ( )

do a new ab initio calculation

Reimplemented from prf::Energy.

void DistanceRestraints::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