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

Root mean square deviation of Ramachandran angles. More...

#include <RCAngleRMSD.hh>

Inheritance diagram for prf::RCAngleRMSD:
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Public Member Functions

int init_obs ()
 All observables must implement one initialize routine.
 
double evaluate ()
 Analyze Ramachandran angle differences from reference.
 
double rc_sq_diff (int i) const
 Squared RC angle difference for the i'th residue in the whole system.
 
void rangeEstimate (double &x0, double &x1)
 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

This is a similarity measure based on the backbone degrees of freedom in the model, the Ramachandran phi and psi angles. The return value of the observable is the root mean square difference from a given reference set of angles. Residuewise differences can also be retrieved. The angular differences are of course, modulo pi.

The reference phi and psi angles for each residue can be given in a file, or calculated from a PDB file.

Member Function Documentation

int RCAngleRMSD::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 RCAngleRMSD::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