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PhiPsi Class Reference

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
spacerreference(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
spacerreference(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
theamino 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
theamino 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
pairof 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
theamino 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
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 getEnergyFromPhiPsi ( AminoAcidCode  code,
double  phi,
double  psi 
)

calculates the energy from the PhiPsi angles of an amino acid

Parameters
codeof 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
aminoacid 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
aminoacid 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
aminoindex 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
aminoindex 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
codeof 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
thestep value(int)
Returns
changes the object internally (void)
int sGetPropBin ( double  p)
protected

Calculates the propensity binding value for a specific angle

Parameters
anglevalue (double)
Returns
the corresponding value( int)
int sGetPropBinDiff ( double  p,
double &  diff 
)

Calculates the differenciated propensity binding and the

Parameters
anglevalue(double), reference to the calculated diff propensity binding(double&)
Returns
propensity value( int)

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