PROFASI
Version 1.5
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Root mean square deviation of Ramachandran angles. More...
#include <RCAngleRMSD.hh>
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. | |
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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. | |
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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. | |
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.
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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.
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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.