Clipper
Public Types | Public Member Functions | List of all members
clipper::Ramachandran Class Reference

Ramachandran plot class. More...

#include <ramachandran.h>

Inheritance diagram for clipper::Ramachandran:
clipper::Prob_phi_2d

Public Types

enum  TYPE {
  Gly, Pro, NonGlyPro, NonGly,
  All
}
 enumeration of built-in Ramachandran tables
 

Public Member Functions

 Ramachandran ()
 null constructor
 
 Ramachandran (TYPE type)
 constructor: from standard plot More...
 
void init (TYPE type)
 initialise: from standard plot More...
 
void set_thresholds (ftype prob_favored=0.01, ftype prob_allowed=0.0005)
 change threshholds to different values More...
 
ftype probability (const ftype &phi, const ftype &psi) const
 get probability for a particular pair of angles
 
bool favored (const ftype &phi, const ftype &psi) const
 test if a pair of angles are in the favored region
 
bool allowed (const ftype &phi, const ftype &psi) const
 test if a pair of angles are in the allowed region
 

Additional Inherited Members

- Private Member Functions inherited from clipper::Prob_phi_2d
void init (const int &size)
 initialise: with sampling
 
void accumulate (const ftype32 table[])
 accumulate new table of samples to probability
 
void accumulate (const ftype &phi1, const ftype &phi2, ftype wgt=1.0)
 accumulate new sample to probability More...
 
void normalise ()
 normalise to integrate to 1/(2pi)^2 More...
 
ftype probability (const ftype &phi1, const ftype &phi2) const
 get probability for a particular pair of angles More...
 
String format () const
 formatted string representation (as C++ code)
 
const ftypedata (const int &i, const int &j) const
 2d read access
 
ftypedata (const int &i, const int &j)
 2d write access
 

Detailed Description

Ramachandran plot class.

This class provides a reference Ramachandran plot for Gly, Pro, other, and combinations of those types of residues. The source data comes from the best residues from the 'top500' best-determined structures list of D. C. and J. S. Richardson, http://kinemage.biochem.duke.edu/index.html

The Ramachandran plot is normalised in inverse radians squared, so the mean value of a probability is 1/(2 pi)2.

Constructor & Destructor Documentation

clipper::Ramachandran::Ramachandran ( TYPE  type)

constructor: from standard plot

Construct a Ramachandran plot of a given type.

Parameters
typeThe residue type of the plot. Options include: Ramachandran::Gly, Ramachandran::Pro, Ramachandran::NonGlyPro, Ramachandran::NonGly, Ramachandran::All

Member Function Documentation

void clipper::Ramachandran::init ( TYPE  type)

initialise: from standard plot

Construct a Ramachandran plot of a given type.

Parameters
typeThe residue type of the plot. Options include: Ramachandran::Gly, Ramachandran::Pro, Ramachandran::NonGlyPro, Ramachandran::NonGly, Ramachandran::All
void clipper::Ramachandran::set_thresholds ( ftype  prob_favored = 0.01,
ftype  prob_allowed = 0.0005 
)

change threshholds to different values

Set thresholds for favorable and allowed regions of the Ramachandran plot. The US spelling is used because it is the same length as 'allowed'. I should get out more. Sorry.

Parameters
prob_favoredThe probability threshold for the favored region.
prob_allowedThe probability threshold for the allowed region.

The documentation for this class was generated from the following files: