biu::ContactEnergyFunction Class Reference
#include <DistanceEnergyFunction.hh>
Inheritance diagram for biu::ContactEnergyFunction:
Detailed Description
This class implements a contact based energy function.It provides the contact energy for elements of a specified alphabet.
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] |
bool biu::ContactEnergyFunction::operator== | ( | const DistanceEnergyFunction & | ef2 | ) | const [virtual] |
Field Documentation
const Alphabet* const biu::ContactEnergyFunction::alphabet [private] |
stores the allowed sequence elements to evaluate
Definition at line 107 of file DistanceEnergyFunction.hh.
const EnergyMatrix* const biu::ContactEnergyFunction::energyMat [private] |
the energy table that contains the energy contributions of contacts
Definition at line 110 of file DistanceEnergyFunction.hh.
const double biu::ContactEnergyFunction::firstBaseVecLength [private] |
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.
const LatticeModel* const biu::ContactEnergyFunction::lattice [private] |
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:
- src/biu/DistanceEnergyFunction.hh
- src/biu/DistanceEnergyFunction.cc