RapdfPotential Class Reference

Distance-dependent residue-specific all-atom probability discriminatory function. More...

Inheritance diagram for RapdfPotential:

Collaboration diagram for RapdfPotential:

Public Member Functions
	RapdfPotential ()
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)
virtual long double	calculateEnergy (AminoAcid &aa, AminoAcid &aa2)
virtual long double	calculateEnergy (Atom &at1, Atom &at2, string aaType, string aaType2)

Protected Member Functions
unsigned int	pGetDistanceBinOne (double distance)
unsigned int	pGetGroupBin (const char *group_name)

Detailed Description

Distance-dependent residue-specific all-atom probability discriminatory function.

The RAPDF potential (Samudrala and Moult, 1998) is a distance-dependent residue-specific all-atom probability discriminatory function. It discriminates between 167 protein heavy atom types, meaning that different types are assigned to each common atom of the 20 amino acids. E.g. the Cα of an isoleucine is a different type from the Cα of a glycine. Interactions are divided based on distance (d) into 18 bins (b), covering distances of up to 20 Å (d → b := [0,..., 3]→ 1, (3,..., 4]→ 2,(4,..., 5]→ 3,...,(19,..., 20]→ 18). The originally published parameters (Samudrala et al., 1998), as downloaded from the ProStar website (URL: http://prostar.carb.nist.gov/) were used.

Constructor & Destructor Documentation

RapdfPotential

(

)

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

Member Function Documentation

long double calculateEnergy ( Spacer &  sp )

virtual

Calculates the energy for 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 the energy for a group of amino acids in the Spacer limited by the index values as start and end

Parameters

spacer

reference(Spacer&), start and end positions (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 that are different to the given aa

Parameters

amino

acid reference(AminoAcid&),spacer reference(Spacer&),

Returns

energy value (long double)

Implements Potential.

long double calculateEnergy ( AminoAcid &  aa, AminoAcid &  aa2  )

virtual

Calculates the energy between 2 amino acids

Parameters

amino

acids references( AminoAcid&,AminoAcid&)

Returns

energy value (long double)

long double calculateEnergy ( Atom &  at1, Atom &  at2, string  aaType, string  aaType2  )

virtual

calculates the energy between two atoms

Parameters

the	references to the atoms (Atom&,Atom&)the amino acid types(string,string)

Returns

the value of maximum propensity(long double)

unsigned int pGetDistanceBinOne ( double  distance )

protected

Retrieves the corresponding index for the given distance

Parameters

distance

(double)

Returns

corresponding index (unsigned int)

unsigned int pGetGroupBin ( const char *  group_name )

protected

Retrieves the corresponding index for the given group(AAtype_AtomType)

Parameters

group

name (char*)

Returns

corresponding index (unsigned int)

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

• Energy/Sources/RapdfPotential.h
• Energy/Sources/RapdfPotential.cc