clipper::Ramachandran Class Reference

Ramachandran plot class. More...

#include <ramachandran.h>

Inheritance diagram for clipper::Ramachandran:

List of all members.

Public Types
enum	TYPE {   Gly, Pro, NonGlyPro, NonGly,   All, Gly5, Pro5, NonGlyPro5,   NonGly5, All5 }
	enumeration of built-in Ramachandran tables
Public Member Functions
	Ramachandran ()
	null constructor
	Ramachandran (TYPE type)
	constructor: from standard plot
void	init (TYPE type)
	initialise: from standard plot
void	set_thresholds (ftype prob_favored=0.01, ftype prob_allowed=0.0005)
	change threshholds to different values
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

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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.

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Constructor & Destructor Documentation

clipper::Ramachandran::Ramachandran

(

TYPE

type

)

constructor: from standard plot

Construct a Ramachandran plot of a given type.

Parameters:

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

References init().

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Member Function Documentation

void clipper::Ramachandran::init

(

TYPE

type

)

initialise: from standard plot

Construct a Ramachandran plot of a given type.

Parameters:

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

References clipper::Prob_phi_2d::accumulate(), clipper::Prob_phi_2d::normalise(), and set_thresholds().

Referenced by Ramachandran().

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_favored	The probability threshold for the favored region.
prob_allowed	The probability threshold for the allowed region.

Referenced by init().

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

• ramachandran.h
• ramachandran.cpp