EffectiveSolvationPotential Class Reference

Implements a knowledge-based solvation with polar/hydrophobic information potential. A coefficient is used to normalize the propensity. More...

Inheritance diagram for EffectiveSolvationPotential:

Collaboration diagram for EffectiveSolvationPotential:

Public Member Functions
	EffectiveSolvationPotential ()
virtual long double	calculateEnergy (Spacer &sp)
virtual long double	calculateEnergy (Spacer &sp, unsigned int index1, unsigned int index2)
virtual long double	calculateEnergy (AminoAcid &aa, Spacer &sp)

Protected Member Functions
bool	isPolar (AminoAcid &aa)
double	pCalcFracBuried (unsigned int index, Spacer &sp)

Detailed Description

Implements a knowledge-based solvation with polar/hydrophobic information potential. A coefficient is used to normalize the propensity.

This class implements a knowledge-based solvation with polar/hydrophobic information potential. The final values are normalized by an hardcoded coefficient (see source)

Constructor & Destructor Documentation

EffectiveSolvationPotential

(

)

Basic constructor, sets the efective solvation potential for a chain.

Member Function Documentation

long double calculateEnergy ( Spacer &  sp )

virtual

Calculates Energy from the amino acids in the spacer

Parameters

spacer

reference (spacer&)

Returns

energy value (long double)

Implements Potential.

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

virtual

Calculates Energy

Parameters

spacer

reference(spacer&),positions of the start and eend of the amino acids portion of the spacer(unsigned int,unsigned int)

Returns

energy value(long double)

Implements Potential.

long double calculateEnergy ( AminoAcid &  aa, Spacer &  sp  )

virtual

Calculates the energy for the amino acids in the Spacer

Parameters

amino

acid reference(not used AminoAcid&),spacer reference(Spacer&),

Returns

energy value (long double)

Implements Potential.

bool isPolar ( AminoAcid &  aa )

protected

Verifies if the amino acid is a polar one

Parameters

reference

of the aa(aminoAcid&)

Returns

result of the validation(bool)

double pCalcFracBuried ( unsigned int  index, Spacer &  sp  )

protected

Calculates Fraction of the amino acids Buried in the spacer

Parameters

central

amino acid position to considers,(unsigned int ),spacer reference(spacer&)

Returns

the fraction of the amino acids buried (double)

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

• Energy/Sources/EffectiveSolvationPotential.h
• Energy/Sources/EffectiveSolvationPotential.cc