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biu::LatticeProtein_I Class Reference

#include <LatticeProtein_I.hh>

Inheritance diagram for biu::LatticeProtein_I:

[legend]

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Detailed Description

A partial LatticeProtein implementation providing storage and access to the underlying lattice and energy function. Further the protein objects sequence, encoded using the alphabet of the energy function, is handled.

Definition at line 13 of file LatticeProtein_I.hh.

Public Member Functions
virtual LatticeProtein_I *	clone ()=0
virtual LatticeProtein_I *	fromString (const std::string &stringRep) const =0
virtual DPointVec	get3Ddata () const=0
virtual double	getDRMSD (const BackboneStructure3D &other) const=0
virtual double	getEnergy () const=0
virtual const DistanceEnergyFunction *	getEnergyFunction () const
virtual const LatticeModel *	getLatticeModel () const
size_t	getLength () const
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 IPointVec *	getPointsRef ()=0
virtual const IPointVec *const	getPointsRef () const=0
Sequence	getSequence () const
virtual const Sequence *	getSequenceRef () const
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
virtual bool	isValid () const=0
	LatticeProtein_I (const LatticeProtein_I &toCopy)
	LatticeProtein_I (const LatticeModel *lattice, const DistanceEnergyFunction *energyFunc, const Sequence *seq, const bool seqShared)
virtual bool	operator!= (const LatticeProtein &latProt2) const=0
virtual LatticeProtein_I &	operator= (const LatticeProtein_I &latProt2)
virtual bool	operator== (const LatticeProtein &latProt2) const=0
virtual void	setMoveStrAbs (const std::string &moveString)=0
virtual	~LatticeProtein_I ()
Protected Attributes
DistanceEnergyFunction const *	energyFunc
LatticeModel const *	lattice
bool	seqShared
Sequence const *	sequence

---

Constructor & Destructor Documentation

biu::LatticeProtein_I::LatticeProtein_I	(	const LatticeModel *	lattice,
		const DistanceEnergyFunction *	energyFunc,
		const Sequence *	seq,
		const bool	seqShared
	)

Constructs a new lattice protein object and initializes some internal data structures.

Parameters:

	lattice	the lattice model the protein structure is basing on
	energyFunc	the energy function inclusive the alphabet for the sequence
	seq	the sequence encoded using the alphabet of the energy function object
	seqShared	false if a local copy of seq should be generated; true if seq is shared among several LatticeProtein objects using the provided seq pointer

Definition at line 7 of file LatticeProtein_I.cc.

biu::LatticeProtein_I::LatticeProtein_I

(

const LatticeProtein_I &

toCopy

)

Definition at line 28 of file LatticeProtein_I.cc.

biu::LatticeProtein_I::~LatticeProtein_I

(

)

[virtual]

destruction

Definition at line 38 of file LatticeProtein_I.cc.

---

Member Function Documentation

virtual LatticeProtein_I* biu::LatticeProtein_I::clone

(

)

[pure virtual]

Implemented in biu::LatticeProtein_Ipnt.

virtual LatticeProtein_I* biu::LatticeProtein_I::fromString

(

const std::string &

stringRep

)

const [pure virtual]

Implemented in biu::LatticeProtein_Ipnt.

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.

const biu::DistanceEnergyFunction * biu::LatticeProtein_I::getEnergyFunction

(

)

const [virtual]

Returns the energy function this lattice protein is basing on.

Implements biu::LatticeProtein.

Definition at line 57 of file LatticeProtein_I.cc.

const biu::LatticeModel * biu::LatticeProtein_I::getLatticeModel

(

)

const [virtual]

Returns the lattice model this lattice protein is basing on.

Implements biu::LatticeProtein.

Definition at line 51 of file LatticeProtein_I.cc.

size_t biu::LatticeProtein_I::getLength

(

)

const [virtual]

Returns the length of the Biomolecule, i.e. the number of monomers.

Implements biu::BioMolecule.

Definition at line 87 of file LatticeProtein_I.cc.

virtual MoveSequence biu::LatticeProtein::getMoveSeqAbs

(

)

const [pure virtual, inherited]

Returns the absolute move sequence of the lattice protein structure.

Implemented in biu::LatticeProtein_Ipnt.

virtual MoveSequence biu::LatticeProtein::getMoveSeqRel

(

)

const [pure virtual, inherited]

Returns the relative move sequence of the lattice protein structure.

Implemented in biu::LatticeProtein_Ipnt.

virtual std::string biu::LatticeProtein::getMoveStrAbs

(

)

const [pure virtual, inherited]

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, inherited]

Returns the relative move string representation of the lattice protein structure.

Implemented in biu::LatticeProtein_Ipnt.

virtual IPointVec biu::LatticeProtein::getPoints

(

)

const [pure virtual, inherited]

Returns the successive 3D coordinates of the lattice protein structure.

Implemented in biu::LatticeProtein_Ipnt.

virtual IPointVec* biu::LatticeProtein_I::getPointsRef

(

)

[pure virtual]

Returns a pointer to the integer-point representation of the protein for read-write access. Calling this function sets all calculated properties to an indifferent state.

Implemented in biu::LatticeProtein_Ipnt.

virtual const IPointVec* const biu::LatticeProtein_I::getPointsRef

(

)

const [pure virtual]

Returns a pointer to the integer-point representation of the protein move sequence for read only access.

Implemented in biu::LatticeProtein_Ipnt.

biu::Sequence biu::LatticeProtein_I::getSequence

(

)

const [virtual]

Implements biu::BioMolecule.

Definition at line 78 of file LatticeProtein_I.cc.

const Sequence * biu::LatticeProtein_I::getSequenceRef

(

)

const [virtual]

Returns the pointer to the sequence.

Implements biu::LatticeProtein.

Definition at line 70 of file LatticeProtein_I.cc.

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, inherited]

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, inherited]

Tests whether or not the structure is self avoiding.

Implemented in biu::LatticeProtein_Ipnt.

bool biu::LatticeProtein_I::isSequenceShared

(

)

const [virtual]

Returns whether or not the sequence is shared among several LatticeProtein objects.

Implements biu::LatticeProtein.

Definition at line 64 of file LatticeProtein_I.cc.

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, inherited]

Implemented in biu::LatticeProtein_Ipnt.

LatticeProtein_I & biu::LatticeProtein_I::operator=

(

const LatticeProtein_I &

latProt2

)

[virtual]

Reimplemented in biu::LatticeProtein_Ipnt.

Definition at line 93 of file LatticeProtein_I.cc.

virtual bool biu::LatticeProtein::operator==

(

const LatticeProtein &

latProt2

)

const [pure virtual, inherited]

Implemented in biu::LatticeProtein_Ipnt.

virtual void biu::LatticeProtein_I::setMoveStrAbs

(

const std::string &

moveString

)

[pure virtual]

Sets a new absolute move string.

Implemented in biu::LatticeProtein_Ipnt.

---

Field Documentation

DistanceEnergyFunction const* biu::LatticeProtein_I::energyFunc [protected]

the distance based energy function

Definition at line 21 of file LatticeProtein_I.hh.

LatticeModel const* biu::LatticeProtein_I::lattice [protected]

the lattice model this structure belongs to

Definition at line 18 of file LatticeProtein_I.hh.

bool biu::LatticeProtein_I::seqShared [protected]

whether or not the sequence is shared or has to be copied

Definition at line 27 of file LatticeProtein_I.hh.

Sequence const* biu::LatticeProtein_I::sequence [protected]

the indexed sequence of the lattice protein

Definition at line 24 of file LatticeProtein_I.hh.

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

• src/biu/LatticeProtein_I.hh
• src/biu/LatticeProtein_I.cc