PolarSolvationPotential Class Reference

This class implements a knowledge-based solvation with polar/hydrophobic information potential. More...

Inheritance diagram for PolarSolvationPotential:

Collaboration diagram for PolarSolvationPotential:

Public Member Functions
	PolarSolvationPotential ()
virtual long double	calculateEnergy (Spacer &sp, unsigned int index1, unsigned int index2)
long double	calculateSolvation (Spacer &sp)
long double	calculateSolvation (AminoAcid &aa, Spacer &sp, unsigned int start=0, unsigned int end=9999)

Detailed Description

This class implements a knowledge-based solvation with polar/hydrophobic information potential.

The likelihood for each of the 20 amino acids to adopt a given relative solvent accessibility is used to derive the pseudo-energy. The relative solvent accessibility is estimated as the number of other Cβ atoms within a sphere of radius 7 Å centered on the residue’s Cβ atom. See also SolvationPotential.

Constructor & Destructor Documentation

PolarSolvationPotential

(

)

Basic constructor, allocate the information from the solv.par file

Member Function Documentation

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

virtual

Calculates energy the energy for a portion of the amino acids in the spacer. considering the portion from start(index 1) to en(Index2).

Parameters

spacer

reference(Spacer&), start and end of the Spacer portion (unsigned int, unsigned int)

Returns

the sum of all the solvation of each amino acid in the spacer portion(long double)

Implements Potential.

long double calculateSolvation

(

Spacer &

sp

)

Calculates the maximum energy for the amino acids in the spacer

Parameters

spacer

reference(Spacer&)

Returns

the corresponding value( double)

long double calculateSolvation	(	AminoAcid &	aa,
		Spacer &	sp,
		unsigned int	start = 0,
		unsigned int	end = 9999
	)

Calculates solvation for a portion of amino acids in the spacer considering one specific amino acid

Parameters

amino

acid reference(AminoAcid&), spacer reference(Spacer&), start and end of the Spacer portion(unsigned int, unsigned int)

Returns

corresponding value of solvation (long double)

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

• Energy/Sources/PolarSolvationPotential.h
• Energy/Sources/PolarSolvationPotential.cc