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biu::ContactEnergyFunction Class Reference

#include <DistanceEnergyFunction.hh>

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Detailed Description

This class implements a contact based energy function.

It provides the contact energy for elements of a specified alphabet.

Author:
Martin Mann, Sebastian Will, Andreas Richter

Definition at line 102 of file DistanceEnergyFunction.hh.

Public Member Functions

 ContactEnergyFunction (const Alphabet *const alphabet, const EnergyMatrix *const energyMat, const LatticeModel *const lattice)
virtual const Alphabet *const getAlphabet () const
virtual double getContactEnergy (const Alphabet::AlphElem &first, const Alphabet::AlphElem &second) const
virtual double getEnergy (const Alphabet::AlphElem &seq_i, const Alphabet::AlphElem &seq_j, const DblPoint &cor_i, const DblPoint &cor_j) const
virtual double getEnergy (const Alphabet::AlphElem &seq_i, const Alphabet::AlphElem &seq_j, const IntPoint &cor_i, const IntPoint &cor_j) const
virtual double getEnergy (const Alphabet::AlphElem &seq_i, const Alphabet::AlphElem &seq_j, const double &distance) const
virtual bool operator!= (const DistanceEnergyFunction &ef2) const
virtual bool operator== (const DistanceEnergyFunction &ef2) const
virtual ~ContactEnergyFunction ()

Private Attributes

const Alphabet *const alphabet
const EnergyMatrix *const energyMat
const double firstBaseVecLength
const LatticeModel *const lattice


Constructor & Destructor Documentation

biu::ContactEnergyFunction::ContactEnergyFunction ( const Alphabet *const  alphabet,
const EnergyMatrix *const  energyMat,
const LatticeModel *const  lattice 
)

Constructs a new contact energy function for the given alphabet.

The alphabet elements of type AlphElem are mapped to the EnergyMatrix indices via the getIndex(..) of the Alphabet class.

Parameters:
alphabet the alphabet the energy function supports
energyMat the contact energy matrix used. NOTE: has to have the same dimensions as the alphabet has elements!
lattice the lattice model used to check if two positions are neighbored

Definition at line 17 of file DistanceEnergyFunction.cc.

biu::ContactEnergyFunction::~ContactEnergyFunction (  )  [virtual]

Definition at line 35 of file DistanceEnergyFunction.cc.


Member Function Documentation

virtual const Alphabet* const biu::ContactEnergyFunction::getAlphabet (  )  const [inline, virtual]

Returns the alphabet this energy function is based on.

Implements biu::DistanceEnergyFunction.

Definition at line 187 of file DistanceEnergyFunction.hh.

double biu::ContactEnergyFunction::getContactEnergy ( const Alphabet::AlphElem first,
const Alphabet::AlphElem second 
) const [virtual]

Returns the contact energy of two elements of the alphabet.

Parameters:
first,second have to be elements of the specified alphabet.

Definition at line 40 of file DistanceEnergyFunction.cc.

double biu::ContactEnergyFunction::getEnergy ( const Alphabet::AlphElem seq_i,
const Alphabet::AlphElem seq_j,
const DblPoint cor_i,
const DblPoint cor_j 
) const [virtual]

Returns the energy contribution of two elements of the alphabet with given coordinates.

Parameters:
seq_i,seq_j have to be elements of the specified alphabet.
cor_i,cor_j the corresponding coordinates of the two monomers to evaluate
Returns:
the energy contribution

Implements biu::DistanceEnergyFunction.

Definition at line 72 of file DistanceEnergyFunction.cc.

double biu::ContactEnergyFunction::getEnergy ( const Alphabet::AlphElem seq_i,
const Alphabet::AlphElem seq_j,
const IntPoint cor_i,
const IntPoint cor_j 
) const [virtual]

Returns the energy contribution of two elements of the alphabet with given coordinates.

Parameters:
seq_i,seq_j have to be elements of the specified alphabet.
cor_i,cor_j the corresponding coordinates of the two monomers to evaluate
Returns:
the energy contribution

Implements biu::DistanceEnergyFunction.

Definition at line 60 of file DistanceEnergyFunction.cc.

double biu::ContactEnergyFunction::getEnergy ( const Alphabet::AlphElem seq_i,
const Alphabet::AlphElem seq_j,
const double &  distance 
) const [virtual]

Returns the energy contribution of two elements of the alphabet that are in a certain distance.

Parameters:
seq_i,seq_j have to be elements of the specified alphabet.
distance the distance of the two monomers to evaluate
Returns:
the energy contribution

Implements biu::DistanceEnergyFunction.

Definition at line 49 of file DistanceEnergyFunction.cc.

bool biu::ContactEnergyFunction::operator!= ( const DistanceEnergyFunction ef2  )  const [virtual]

Implements biu::DistanceEnergyFunction.

Definition at line 94 of file DistanceEnergyFunction.cc.

bool biu::ContactEnergyFunction::operator== ( const DistanceEnergyFunction ef2  )  const [virtual]

Implements biu::DistanceEnergyFunction.

Definition at line 82 of file DistanceEnergyFunction.cc.


Field Documentation

stores the allowed sequence elements to evaluate

Definition at line 107 of file DistanceEnergyFunction.hh.

the energy table that contains the energy contributions of contacts

Definition at line 110 of file DistanceEnergyFunction.hh.

the length of the first base vector of the lattice to allow for a distance based contact evaluation

Definition at line 115 of file DistanceEnergyFunction.hh.

the lattice model used to check if two positions are neighbored

Definition at line 112 of file DistanceEnergyFunction.hh.


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