RamachandranPlot Class Reference

The class RamachandranPlot is used to initialize and store database for Ramachandran plot, sample backbone dihedral angles according to residue type and evaluate the probability of one conformation according to backbone structure. More...

#include <RamachandranPlot.h>

Public Member Functions
	RamachandranPlot (int size=36, char *file_pro="../Data/RamachandranPlot/pro.txt", char *file_pre_pro="../Data/RamachandranPlot/pre_pro.txt", char *file_gly="../Data/RamachandranPlot/gly.txt", char *file_generic="../Data/RamachandranPlot/gen.txt")
	Constructor. More...
virtual	~RamachandranPlot ()
	Destructor.
DihedralAngle *	getRandomDihedralAngle (int type)
	Randomly generate a pair of backbone dihedral angles of specific type. More...
DihedralAngle *	getRandomDihedralAngle (string name, string name_next)
	Randomly generate a pair of backbone dihedral angles given residue name. More...
double	getResidueAngleProbability (PChain *chain, int index)
	Evaluate the probability of a residue's structure according to Ramachandran plot. More...

Static Public Attributes
static const int	PRO = 0
static const int	PRE_PRO = 1
static const int	GLY = 2
static const int	GENERIC = 3

Private Member Functions
double *	construct (char *filename)
	Construct the Ramachandran plot. More...

Private Attributes
double *	pro_acc
double *	pre_pro_acc
double *	gly_acc
double *	gen_acc
double *	pro
double *	pre_pro
double *	gly
double *	gen
int	size
int	gridnum
double	gridlength

Detailed Description

The class RamachandranPlot is used to initialize and store database for Ramachandran plot, sample backbone dihedral angles according to residue type and evaluate the probability of one conformation according to backbone structure.

Constructor & Destructor Documentation

RamachandranPlot::RamachandranPlot	(	int	size = 36,
		char *	file_pro = "../Data/RamachandranPlot/pro.txt",
		char *	file_pre_pro = "../Data/RamachandranPlot/pre_pro.txt",
		char *	file_gly = "../Data/RamachandranPlot/gly.txt",
		char *	file_generic = "../Data/RamachandranPlot/gen.txt"
	)

Constructor.

Parameters

size	number of grids to discretize the angle space [-180.0, 180.0]. By default, 10-degree is the width of a grid.
file_pro	library location for Proline
file_pre_pro	library location for pre-Prolines
file_gly	library location for Glycine
file_generic	library location for generic residues

Member Function Documentation

double * RamachandranPlot::construct ( char *  filename )

private

Construct the Ramachandran plot.

Parameters

filename

data file

Returns

a database

DihedralAngle * RamachandranPlot::getRandomDihedralAngle

(

int

type

)

Randomly generate a pair of backbone dihedral angles of specific type.

Parameters

type	residue type {PRO, PRE_PRO, GLY, GENERIC}

Returns

a pair of dihedral angles

DihedralAngle * RamachandranPlot::getRandomDihedralAngle	(	string	name,
		string	name_next
	)

Randomly generate a pair of backbone dihedral angles given residue name.

Parameters

name	name of the residue
name_next	name of the succeeding residue (for pre-Pro residues)

Returns

a pair of dihedral angles

double RamachandranPlot::getResidueAngleProbability	(	PChain *	chain,
		int	index
	)

Evaluate the probability of a residue's structure according to Ramachandran plot.

Parameters

chain	the chain which contains the residue
index	the index of the residue in the chain

Returns

probability of the residue structure

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

• RamachandranPlot.h
• RamachandranPlot.cc