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

Inheritance diagram for PhiPsiOmega:

Collaboration diagram for PhiPsiOmega:

Public Member Functions
	PhiPsiOmega (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 &diheds, AminoAcidCode code)

virtual double	calculateMaxEnergy (Spacer &sp)

virtual double	calculateMaxEnergy (unsigned int amino)

virtual double	calculateMinEnergy (Spacer &sp)

virtual double	calculateMinEnergy (unsigned int amino)

virtual vector< vector< ANGLES > > *	getOrderedEnergyTable ()

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 double	getOmegaAngle (int prop, long RANGE_OMEGA)

virtual double	getPhiPsiAngle (int prop, long SIZE_TABLE, int ARC_STEP)

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 z)

int	sGetPropBin (double p)

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 phi , psi and omega angles.

Constructor & Destructor Documentation

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

Constructor that sets the arc steps for the table's size

Parameters

arc	values for table 1 and 2(int ,int), file name where torsion angles are, usually data/tor.par(string)

Member Function Documentation

long double calculateEnergy ( Spacer & sp )

virtual

calculates energy for a protein

Parameters

reference to the spacer containing the protein (Spacer&)

Returns: energy value for the set of amino acids in the spacer (long double)

Implements TorsionPotential.

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

virtual

calculates energy for part of the protein

Parameters

reference to the spacer that contains the protein(Spacer&) , start and end position of the protein part (unsigned int , unsigned int)

Returns: energy value for the set of amino acids in the selected section (long double)

Implements TorsionPotential.

long double calculateEnergy ( AminoAcid & aa )

virtual

calculates energy for a specific amino acid

Parameters

aminoacid reference (AminoAcid&)

Returns: energy value for given amino acid (long double)

Implements TorsionPotential.

long double calculateEnergy	(	AminoAcid &	diheds,
		AminoAcidCode	code
	)

virtual

Parameters

diheds a (phi, psi, omega) triple of dihedral angles. code: an amino acid type. phi-psi-omega torsional energy of the amino acid whose (phi, psi, omega) triple is specified by 'diheds' and whose type is specified by code.

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)

double getOmegaAngle	(	int	prop,
		long	RANGE_OMEGA
	)

protectedvirtual

obtains the Omega angle for a given propensity value and Omega range

Parameters

propensity value (int), Omega range(long)

Returns: corresponding omega angle (double)

Reimplemented from TorsionPotential.

vector< vector< Potential::ANGLES > > * getOrderedEnergyTable ( )

virtual

Returns asort energy table

Parameters

none

Returns: pointer to new ordered table (vector< vector<Potential::ANGLES> >*)

double getPhiPsiAngle	(	int	prop,
		long	SIZE_TABLE,
		int	ARC_STEP
	)

protectedvirtual

Calculates the value os the psi , phi angle

Parameters

propensity value(int), long(not used),arc step(int)

Returns

Reimplemented from TorsionPotential.

void pConstructData ( )

protectedvirtual

Method that using the torsion file, creates the structure

Parameters

none

Returns: changes are made internally(void)

Implements TorsionPotential.

void pConstructMaxPropensities ( )

protectedvirtual

Parameters

@return

void pConstructMinPropensities ( )

protectedvirtual

computes and stores the minimum propensities based on the max propensities based on knowledge

Parameters

none

Returns: changes are made internally(void)

double pGetMaxPropensities ( int amino )

protectedvirtual

obtains the maximum propensity value for an amino acid type considering all the granularities

Parameters

amino acid code(int)

Returns: corresponding propensity value(double)

double pGetMinPropensities ( int amino )

protectedvirtual

Parameters

amino the code of an amino acid type. value: minimum (phi, psi, omega) propensity of that type according to kwnowledge.

void pResetData ( )

protectedvirtual

Resets all the propensities set previously

Parameters

none

Returns: changes are made internally(void)

Implements TorsionPotential.

double pReturnMaxPropensities ( int amino )

virtual

obtains the maximum propensity value for an amino acid type knowledge based

Parameters

amino acid code(int)

Returns: corresponding propensity value(double)

Implements TorsionPotential.

double pReturnMinPropensities ( int amino )

virtual

obtains the minimum propensity value for an amino acid type considering a given phi and psi values knowledge based

Parameters

amino acid code(int), values for the previous phi and psi angles(int , int)

Returns: corresponding propensity value(double)

Reimplemented from TorsionPotential.

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

protected

Adds propensity value for a amino acid type

Parameters

corresponding amino acid code(int), corresponding propensity values(int, int, int, int, int))

Returns: changes are made internally(void)

void setArcStep ( int n )

virtual

Parameters

@return

int setRange_Omega ( int n )

virtual

Sets the range for omega

Parameters

parameter for omega range, only 1,2, and 3 are posible(int)

Returns: corresponding range for omega (int)

int sGetPropBin ( double p )

protected

Returns the propensity binding value using table 1(granularity) for a specific angle

Parameters

angle in degrees

Returns: corresponding prop value (int)

int sGetPropOmegaBin ( double p )

protected

Parameters

@return

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

Energy/Sources/TorsionPotential/PhiPsiOmega.h
Energy/Sources/TorsionPotential/PhiPsiOmega.cc

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation