class manages the angle qualities and the energy More...

Inheritance diagram for PhiPsiOmegaChi1Chi2:

Collaboration diagram for PhiPsiOmegaChi1Chi2:

Public Member Functions
	PhiPsiOmegaChi1Chi2 (int SET_ARC1=10, string knownledge="data/tor.par")

virtual long double	calculateEnergy (Spacer &sp)

virtual long double	calculateEnergy (Spacer &sp, unsigned int index1, unsigned int index2)

virtual long double	calculateEnergy (AminoAcid &aa)

virtual double	calculateMaxEnergy (Spacer &sp)

virtual double	calculateMaxEnergy (unsigned int amino)

virtual double	calculateMinEnergy (Spacer &sp)

virtual double	calculateMinEnergy (unsigned int amino)

virtual double	pReturnMaxPropensities (int amino)

virtual double	pReturnMinPropensities (int amino)

virtual void	setArcStep (int n)

virtual int	setRange_Omega (int n)

Protected Member Functions
virtual void	pConstructData ()

virtual void	pConstructMaxPropensities ()

virtual void	pConstructMinPropensities ()

virtual double	pGetMaxPropensities (int amino)

virtual double	pGetMinPropensities (int amino)

virtual void	pResetData ()

virtual void	sAddProp (int code, int x, int y, int z, int m, int n)

virtual int	sGetPropBin (double p)

virtual int	sGetPropChiBin (double p)

virtual int	sGetPropOmegaBin (double p)

Detailed Description

class manages the angle qualities and the energy

This class implements a simple torsion potential based on the statistical preference of aminoacid types for certain phi, psi, chi1, chi2 and omega angles.

Constructor & Destructor Documentation

PhiPsiOmegaChi1Chi2	(	int	SET_ARC1 = `10`,
		string	knownledge = `"data/tor.par"`
	)

Basic constructor

Member Function Documentation

long double calculateEnergy ( Spacer & sp )

virtual

calculates the total energy for the amino acids in the spacer

Parameters

spacer reference(Sapcer(&)

Returns: value of the total energy(long double)

Implements TorsionPotential.

long double calculateEnergy	(	Spacer &	sp,
		unsigned int	index1,
		unsigned int	index2
	)

virtual

calculates the total energy for the amino acids in a portion of the spacer

Parameters

spacer reference(Sapcer(&), positions for start and end of the Sapcer portion (unsigned int, unsigned int)

Returns: value of the total energy for the aminoacids in the given spacer portion(long double)

Implements TorsionPotential.

long double calculateEnergy ( AminoAcid & aa )

virtual

calculates the total energy for the amino acid

Parameters

the	amino acid reference (AminoAcir&)

Returns: corresponding energy value(long double)

Implements TorsionPotential.

double calculateMaxEnergy ( Spacer & sp )

virtualinherited

Calculates the maximum energy for the amino acids in the spacer

Parameters

spacer reference(Spacer&)

Returns: the corresponding value( double)

double calculateMaxEnergy ( unsigned int amino )

virtualinherited

Calculates the maximum energy for an amino acid

Parameters

index of the amino acid, consider the enum list(unsigned int)

Returns: the corresponding value( double)

double calculateMinEnergy ( Spacer & sp )

virtualinherited

Calculates the minimum energy for the amino acids in the spacer

Parameters

spacer reference(Spacer&)

Returns: the corresponding value( double)

double calculateMinEnergy ( unsigned int amino )

virtualinherited

Calculates the minimum energy for an amino acid

Parameters

index of the amino acid, consider the enum list(unsigned int)

Returns: the corresponding value( double)

void pConstructData ( )

protectedvirtual

Sets all the information need for the class

Parameters

none

Returns: changes the object internally (void)

Implements TorsionPotential.

void pConstructMaxPropensities ( )

protectedvirtual

Defines the values for the maximum propensities for each amino acid type

Parameters

none

Returns: changes the object internally (void)

void pConstructMinPropensities ( )

protectedvirtual

Defines the values for the minimum propensities for each amino acid type

Parameters

none

Returns: changes the object internally (void)

double pGetMaxPropensities ( int amino )

protectedvirtual

Calculates the Maximum propensities value for the Chi, and Omega Range of the amino acid

Parameters

amino acid index corresponding to the enum (int)

Returns: corresponding value (double)

double pGetMinPropensities ( int amino )

protectedvirtual

Calculates the minimum propensities value for the Chi, and Omega Range of the amino acid

Parameters

amino acid index corresponding to the enum (int)

Returns: corresponding value (double)

void pResetData ( )

protectedvirtual

Clears all the set data

Parameters

none

Returns: changes the object internally (void)

Implements TorsionPotential.

double pReturnMaxPropensities ( int amino )

virtual

returns the maximum propensities for the corresponding amino

Parameters

amino index from the enum (int)

Returns: the corresponding value(double)

Implements TorsionPotential.

double pReturnMinPropensities ( int amino )

virtual

returns the minimum propensities for the corresponding amino

Parameters

amino index from the enum (int)

Returns: the corresponding value(double)

Reimplemented from TorsionPotential.

void sAddProp	(	int	code,
		int	x,
		int	y,
		int	z,
		int	m,
		int	n
	)

protectedvirtual

Adds a propensity for a specific amino acid type

Parameters

code	of the amion acid(int), coordinates (int,int,int), values to set (int, int)

Returns: changes the object internally (void)

void setArcStep ( int n )

virtual

Sets the step for the arc

Parameters

the	step value(int)

Returns: changes the object internally (void)

int setRange_Omega ( int n )

virtual

Sets the value for the Omega range

Parameters

value for the index range( int)

Returns: the corresponding value for the Range Omega( int)

int sGetPropBin ( double p )

protectedvirtual

obtains and return the propensity binding value

Parameters

angle value(double )

Returns: the corresponding value ( int)

int sGetPropChiBin ( double p )

protectedvirtual

Calculates the chi angles index

Parameters

an	angle(double)

Returns: the index for the angle ( int)

int sGetPropOmegaBin ( double p )

protectedvirtual

obtains and return the propensity Omega binding value

Parameters

angle value(double )

Returns: the corresponding value ( int)

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

Energy/Sources/TorsionPotential/PhiPsiOmegaChi1Chi2.h
Energy/Sources/TorsionPotential/PhiPsiOmegaChi1Chi2.cc

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation