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

Inheritance diagram for PhiPsi:

Collaboration diagram for PhiPsi:

Public Member Functions
	PhiPsi (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 long double	calculateEnergy (AminoAcid &aa, double phi, double psi)

virtual long double	calculateEnergy (AminoAcid &diheds, AminoAcidCode code)

virtual long double	calculateEnergySmooth (AminoAcid &aa)

virtual double	calculateMaxEnergy (Spacer &sp)

virtual double	calculateMaxEnergy (unsigned int amino)

virtual double	calculateMinEnergy (Spacer &sp)

virtual double	calculateMinEnergy (unsigned int amino)

double	getEnergyFromPhiPsi (AminoAcidCode code, double phi, double psi)

virtual double	pReturnMaxPropensities (int amino)

virtual double	pReturnMinPropensities (int amino)

virtual void	setArcStep (int n)

int	sGetPropBinDiff (double p, double &diff)

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 ()

void	sAddProp (int code, int x, int y)

int	sGetPropBin (double p)

Detailed Description

class manages the angle qualities and the energy

Includes methods that allow to obtain information about the angle and the energy. This class implements a simple torsion potential based on the statistical preference of aminoacid types for phi and psi angles.

Constructor & Destructor Documentation

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

Parameters

@return

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.

long double calculateEnergy	(	AminoAcid &	aa,
		double	phi,
		double	psi
	)

virtual

calculates the total energy for the amino acid, considering a specific phi an psi value

Parameters

the	amino acid reference (AminoAcir&), values for phi and psi (double)

Returns: corresponding energy value(long double)

long double calculateEnergy	(	AminoAcid &	diheds,
		AminoAcidCode	code
	)

virtual

Calculates the psi-psi torsional energy of the amino acid whose (phi, psi) pair is specified by 'diheds' and whose type is specified by code.

Parameters

pair	of dihedral angles(AminoAcir&), the amino acid code(AminoAcidCode)

Returns: corresponding value(long double)

Implements TorsionPotential.

long double calculateEnergySmooth ( AminoAcid & aa )

virtual

calculates the total energy for the amino acid

Parameters

the	amino acid reference (AminoAcir&)

Returns: corresponding energy value(long double)

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)

double getEnergyFromPhiPsi	(	AminoAcidCode	code,
		double	phi,
		double	psi
	)

calculates the energy from the PhiPsi angles of an amino acid

Parameters

code	of the amino acid(AminoAcidCode), values for phi and psi(double,double)

Returns: 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

fill an array containing max propensities for each amino

Parameters

none

Returns: changes the object internally (void)

void pConstructMinPropensities ( )

protectedvirtual

fill an array containing min propensities for each amino

Parameters

none

Returns: changes the object internally (void)

double pGetMaxPropensities ( int amino )

protectedvirtual

Calculates the Maximum propensities value 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 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
	)

protected

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 sGetPropBin ( double p )

protected

Calculates the propensity binding value for a specific angle

Parameters

angle value (double)

Returns: the corresponding value( int)

int sGetPropBinDiff	(	double	p,
		double &	diff
	)

Calculates the differenciated propensity binding and the

Parameters

angle value(double), reference to the calculated diff propensity binding(double&)

Returns: propensity value( int)

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

Energy/Sources/TorsionPotential/PhiPsi.h
Energy/Sources/TorsionPotential/PhiPsi.cc

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation