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

Distance between two designated atoms. More...

#include <AtomDistance.hh>

Inheritance diagram for prf::AtomDistance:
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Public Member Functions

int init_obs ()
 All observables must implement one initialize routine.
 
void set_atoms (int i1, int i2)
 attach to two atoms given by their unique ids.
 
double evaluate ()
 Actual calculation of the value of the observable.
 
void rangeEstimate (double &xmin, double &xmax)
 Estimate a range in which values of this observable are expected.
 
- Public Member Functions inherited from prf::Observable
void set (std::string cmd)
 Give the object an instruction to process during initialization.
 
virtual void refresh ()
 Necessary before an observable value is used.
 
virtual double delta (Update *u)
 Quick estimate of the change in an Observable due to an update.
 
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

A somewhat more general observable than the end-to-end distance. This could represent the end-to-end distance, if you just initialize it with the two end atoms of the relevant backbone. But end-to-end distance could just be more noisy in some situations, when there are loose unstructured loops at the ends of the chain. One might then want to use the distance between the structured end-points of the chain. This class allows one to use any two atoms for this distance. It knows nothing about atoms however, as it blindly takes the integer id of the atoms, and asks AtomCoordinates class to return the distance between those to ids. It is your responsibility to make sure that the two indices you pass make sense.

Member Function Documentation

int prf::AtomDistance::init_obs ( )
virtual

Even if it seems that one particular observable might need additional arguments during initialization, it is advantageous to have a uniform syntax for all of them. So, when additional arguments are needed, one should provide them in a separate function called before initialization, and then call init_obs without arguments. The name init_obs instead of a more natural "init" or "initialize" is because an Observable often inherits from other classes which represent its character more fundamentally. So, the names such as "init" are kept free for such base classes.

Reimplemented from prf::Observable.

void prf::AtomDistance::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::Observable.


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