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PhiPsiOmega Class Reference

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
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.

long double calculateEnergy ( AminoAcid diheds,
AminoAcidCode  code 
)
virtual
Parameters
dihedsa (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
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)
double getOmegaAngle ( int  prop,
long  RANGE_OMEGA 
)
protectedvirtual

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

Parameters
propensityvalue (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
propensityvalue(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
aminoacid code(int)
Returns
corresponding propensity value(double)
double pGetMinPropensities ( int  amino)
protectedvirtual
Parameters
aminothe 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
aminoacid 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
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 
)
protected

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
Parameters
@return
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)
protected

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

Parameters
anglein degrees
Returns
corresponding prop value (int)
int sGetPropOmegaBin ( double  p)
protected
Parameters
@return

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