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