biu::LatticeProtein Class Reference
#include <LatticeProtein.hh>
Inheritance diagram for biu::LatticeProtein:
Detailed Description
The abstract LatticeProtein interface represents a backbone protein representation in an energy landscape whereby all backbone edges are placed on integer lattice points and consecutive positions are neighbored in the lattice.Such a structure is valid, if and only if it is selfavoiding walk in the lattice.
The energy calulation is based on a DistanceEnergyFunction object. A contact is formed, if two structure positions are neighbored and not consecutive in sequence.
Definition at line 26 of file LatticeProtein.hh.
Public Member Functions | |
| virtual DPointVec | get3Ddata () const=0 |
| virtual double | getDRMSD (const BackboneStructure3D &other) const=0 |
| virtual double | getEnergy () const=0 |
| virtual const DistanceEnergyFunction * | getEnergyFunction () const=0 |
| virtual const LatticeModel * | getLatticeModel () const=0 |
| virtual size_t | getLength () const=0 |
| virtual MoveSequence | getMoveSeqAbs () const=0 |
| virtual MoveSequence | getMoveSeqRel () const=0 |
| virtual std::string | getMoveStrAbs () const=0 |
| virtual std::string | getMoveStrRel () const=0 |
| virtual IPointVec | getPoints () const=0 |
| virtual Sequence | getSequence () const=0 |
| virtual const Sequence * | getSequenceRef () const=0 |
| virtual std::string | getStringRepresentation () const=0 |
| virtual Structure | getStructure () const=0 |
| virtual bool | isConnected () const=0 |
| virtual bool | isSelfAvoiding () const=0 |
| virtual bool | isSequenceShared () const=0 |
| virtual bool | isValid () const=0 |
| LatticeProtein () | |
| virtual bool | operator!= (const LatticeProtein &latProt2) const=0 |
| virtual bool | operator== (const LatticeProtein &latProt2) const=0 |
| virtual | ~LatticeProtein () |
Constructor & Destructor Documentation
| biu::LatticeProtein::LatticeProtein | ( | ) | [inline] |
| virtual biu::LatticeProtein::~LatticeProtein | ( | ) | [inline, virtual] |
Member Function Documentation
| virtual DPointVec biu::BackboneStructure3D::get3Ddata | ( | ) | const [pure virtual, inherited] |
Returns the consecutive point representation of the backbone.
Implemented in biu::LatticeProtein_Ipnt, and biu::OffLatticeProtein.
| virtual double biu::BackboneStructure3D::getDRMSD | ( | const BackboneStructure3D & | other | ) | const [pure virtual, inherited] |
Returns the distance root mean square deviation (DRMSD) to an other BackboneStructure3D
Implemented in biu::LatticeProtein_Ipnt, and biu::OffLatticeProtein.
| virtual double biu::BioMolecule::getEnergy | ( | ) | const [pure virtual, inherited] |
Returns the specific energy of the BioMolecule.
Implemented in biu::LatticeProtein_Ipnt, and biu::RNAStructure_TB.
| virtual const DistanceEnergyFunction* biu::LatticeProtein::getEnergyFunction | ( | ) | const [pure virtual] |
Returns the energy function this lattice protein is basing on.
Implemented in biu::LatticeProtein_I.
| virtual const LatticeModel* biu::LatticeProtein::getLatticeModel | ( | ) | const [pure virtual] |
| virtual size_t biu::BioMolecule::getLength | ( | ) | const [pure virtual, inherited] |
Returns the length of the Biomolecule, i.e. the number of monomers.
Implemented in biu::LatticeProtein_I, biu::RNAStructure, and biu::RNAStructure_TB.
| virtual MoveSequence biu::LatticeProtein::getMoveSeqAbs | ( | ) | const [pure virtual] |
Returns the absolute move sequence of the lattice protein structure.
Implemented in biu::LatticeProtein_Ipnt.
| virtual MoveSequence biu::LatticeProtein::getMoveSeqRel | ( | ) | const [pure virtual] |
Returns the relative move sequence of the lattice protein structure.
Implemented in biu::LatticeProtein_Ipnt.
| virtual std::string biu::LatticeProtein::getMoveStrAbs | ( | ) | const [pure virtual] |
Returns the absolute move string representation of the lattice protein structure.
Implemented in biu::LatticeProtein_Ipnt.
| virtual std::string biu::LatticeProtein::getMoveStrRel | ( | ) | const [pure virtual] |
Returns the relative move string representation of the lattice protein structure.
Implemented in biu::LatticeProtein_Ipnt.
| virtual IPointVec biu::LatticeProtein::getPoints | ( | ) | const [pure virtual] |
Returns the successive 3D coordinates of the lattice protein structure.
Implemented in biu::LatticeProtein_Ipnt.
| virtual Sequence biu::BioMolecule::getSequence | ( | ) | const [pure virtual, inherited] |
Implemented in biu::LatticeProtein_I, biu::RNAStructure, and biu::RNAStructure_TB.
| virtual const Sequence* biu::LatticeProtein::getSequenceRef | ( | ) | const [pure virtual] |
Returns the pointer to the sequence if shared and a new sequence object otherwise.
NOTE: This object has to be deleted by the user manually!
Implemented in biu::LatticeProtein_I.
| virtual std::string biu::BioMolecule::getStringRepresentation | ( | ) | const [pure virtual, inherited] |
Returns a specific std::string representation of this BioMolecule.
Implemented in biu::LatticeProtein_Ipnt, biu::RNAStructure, and biu::RNAStructure_TB.
| virtual Structure biu::BioMolecule::getStructure | ( | ) | const [pure virtual, inherited] |
Implemented in biu::LatticeProtein_Ipnt, biu::RNAStructure, and biu::RNAStructure_TB.
| virtual bool biu::LatticeProtein::isConnected | ( | ) | const [pure virtual] |
Tests whether or not consecutive structure elements are neighbored in the lattice.
Implemented in biu::LatticeProtein_Ipnt.
| virtual bool biu::LatticeProtein::isSelfAvoiding | ( | ) | const [pure virtual] |
| virtual bool biu::LatticeProtein::isSequenceShared | ( | ) | const [pure virtual] |
Returns whether or not the sequence is shared among several LatticeProtein objects.
Implemented in biu::LatticeProtein_I.
| virtual bool biu::BioMolecule::isValid | ( | ) | const [pure virtual, inherited] |
Returns whether or not the BioMolecule is valid concerning some internal criterias (e.g. selfavoidingness of lattice proteins).
Implemented in biu::LatticeProtein_Ipnt, biu::RNAStructure, and biu::RNAStructure_TB.
| virtual bool biu::LatticeProtein::operator!= | ( | const LatticeProtein & | latProt2 | ) | const [pure virtual] |
Implemented in biu::LatticeProtein_Ipnt.
| virtual bool biu::LatticeProtein::operator== | ( | const LatticeProtein & | latProt2 | ) | const [pure virtual] |
Implemented in biu::LatticeProtein_Ipnt.
The documentation for this class was generated from the following file:
- src/biu/LatticeProtein.hh