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PhiPsiOmegaPreAngle Class Reference

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

+ Inheritance diagram for PhiPsiOmegaPreAngle:
+ Collaboration diagram for PhiPsiOmegaPreAngle:

Public Member Functions

 PhiPsiOmegaPreAngle (int SET_ARC1=10, int SET_ARC2=40, 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 pReturnMaxPropensitiesPreAngle (int amino, int prephi, int prepsi)
 
virtual void setArcStep (int n)
 
virtual int setRange_Omega (int n)
 
virtual int sGetPropBin2 (double p)
 

Protected Member Functions

virtual void pConstructData ()
 
virtual void pConstructMaxPropensities ()
 
virtual double pGetMaxPropensities (int amino)
 
virtual double pGetMaxPropensities (int amino, int prephi, int prepsi)
 
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 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 phi, psi, omega, prephi and pre psi angles.

Constructor & Destructor Documentation

PhiPsiOmegaPreAngle ( int  SET_ARC1 = 10,
int  SET_ARC2 = 40,
string  knownledge = "data/tor.par" 
)

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

Parameters
arcvalues 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
referenceto 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
referenceto 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
aminoacidreference (AminoAcid&)
Returns
energy value for given amino acid (long double)

Implements TorsionPotential.

double calculateMaxEnergy ( Spacer sp)
virtualinherited

Calculates the maximum energy for the amino acids in the spacer

Parameters
spacerreference(Spacer&)
Returns
the corresponding value( double)
double calculateMaxEnergy ( unsigned int  amino)
virtualinherited

Calculates the maximum energy for an amino acid

Parameters
indexof 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
spacerreference(Spacer&)
Returns
the corresponding value( double)
double calculateMinEnergy ( unsigned int  amino)
virtualinherited

Calculates the minimum energy for an amino acid

Parameters
indexof the amino acid, consider the enum list(unsigned int)
Returns
the corresponding value( double)
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

Creates the maximum 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
aminoacid code(int)
Returns
corresponding propensity value(double)
double pGetMaxPropensities ( int  amino,
int  prephi,
int  prepsi 
)
protectedvirtual

obtains the maximum propensity value for an amino acid type considering a given phi and psi values considering all the granularities

Parameters
aminoacid code(int), values for the previous phi and psi angles(int , int)
Returns
corresponding propensity value(double)
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
aminoacid code(int)
Returns
corresponding propensity value(double)

Implements TorsionPotential.

double pReturnMaxPropensitiesPreAngle ( int  amino,
int  prephi,
int  prepsi 
)
virtual

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

Parameters
aminoacid 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,
int  m,
int  n 
)
protectedvirtual

Adds propensity value for a amino acid type

Parameters
correspondingamino acid code(int), corresponding propensity values(int, int, int, int, int))
Returns
changes are made internally(void)
void setArcStep ( int  n)
virtual

Sets the arc step, needed to define the Size table

Parameters
quantityof steps(int)
Returns
changes are made internally(void)
int setRange_Omega ( int  n)
virtual

Sets the range for omega

Parameters
parameterfor omega range, only 1,2, and 3 are posible(int)
Returns
corresponding range for omega (int)
int sGetPropBin ( double  p)
protectedvirtual

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

Parameters
anglein degrees
Returns
corresponding prop value (int)
int sGetPropBin2 ( double  p)
virtual

Returns the propensity binding using table 2(granularity for i-1 aa) value for a specific angle

Parameters
anglein degrees(double)
Returns
corresponding prop value (int)

Reimplemented from TorsionPotential.

int sGetPropOmegaBin ( double  p)
protectedvirtual

Returns the propensity Omega binding using

Parameters
omegaangle in degrees(double)
Returns
corresponding prop value (int)

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