#include <InteractionEnergyVrna.h>

Inheritance diagram for IntaRNA::InteractionEnergyVrna:

Collaboration diagram for IntaRNA::InteractionEnergyVrna:

[legend]

Public Member Functions
	InteractionEnergyVrna (const Accessibility &accS1, const ReverseAccessibility &accS2, VrnaHandler &vrnaHandler, const size_t maxInternalLoopSize1=16, const size_t maxInternalLoopSize2=16, const bool initES=false, const E_type energyAdd=Ekcal_2_E(0.0), const bool energyWithDangles=true, const bool internalLoopGU=true)

virtual	~InteractionEnergyVrna ()

virtual E_type	getES1 (const size_t i1, const size_t j1) const

virtual E_type	getES2 (const size_t i2, const size_t j2) const

virtual E_type	getE_multiUnpaired (const size_t numUnpaired) const

virtual E_type	getE_multiHelix (const size_t j1, const size_t j2) const

virtual E_type	getE_multiClosing () const

virtual E_type	getE_init () const

virtual E_type	getE_interLeft (const size_t i1, const size_t j1, const size_t i2, const size_t j2) const

virtual E_type	getE_danglingLeft (const size_t i1, const size_t i2) const

virtual E_type	getE_danglingRight (const size_t j1, const size_t j2) const

virtual E_type	getE_endLeft (const size_t i1, const size_t i2) const

virtual E_type	getE_endRight (const size_t j1, const size_t j2) const

virtual E_type	getEall1 () const

virtual E_type	getEall2 () const

virtual Z_type	getRT () const

Public Member Functions inherited from IntaRNA::InteractionEnergy
	InteractionEnergy (const Accessibility &accS1, const ReverseAccessibility &accS2, const size_t maxInternalLoopSize1, const size_t maxInternalLoopSize2, const E_type energyAdd, const bool energyWithDangle, const bool internalLoopGU)

virtual	~InteractionEnergy ()

virtual E_type	getE (const size_t i1, const size_t j1, const size_t i2, const size_t j2, const E_type hybridE) const

virtual E_type	getE (const Z_type Z) const

virtual EnergyContributions	getE_contributions (const Interaction &interaction) const

virtual bool	areComplementary (const size_t i1, const size_t i2) const

virtual bool	isGU (const size_t i1, const size_t i2) const

virtual size_t	size1 () const

virtual size_t	size2 () const

virtual E_type	getED1 (const size_t i1, const size_t j1) const

virtual E_type	getED2 (const size_t i2, const size_t j2) const

virtual bool	isAccessible1 (const size_t i) const

virtual bool	isAccessible2 (const size_t i) const

virtual E_type	getE_multi (const size_t i1, const size_t j1, const size_t i2, const size_t j2, const ES_multi_mode ES_mode) const

virtual Z_type	getPr_danglingLeft (const size_t i1, const size_t j1, const size_t i2, const size_t j2) const

virtual Z_type	getPr_danglingRight (const size_t i1, const size_t j1, const size_t i2, const size_t j2) const

virtual const Accessibility &	getAccessibility1 () const

virtual const ReverseAccessibility &	getAccessibility2 () const

const size_t	getMaxInternalLoopSize1 () const

const size_t	getMaxInternalLoopSize2 () const

virtual Z_type	getBoltzmannWeight (const E_type energy) const

virtual Z_type	getBoltzmannWeight (const Z_type energy) const

virtual Interaction::BasePair	getBasePair (const size_t i1, const size_t i2) const

virtual size_t	getIndex1 (const Interaction::BasePair &bp) const

virtual size_t	getIndex2 (const Interaction::BasePair &bp) const

virtual E_type	getEnergyAdd () const

virtual bool	isValidInternalLoop (const size_t i1, const size_t j1, const size_t i2, const size_t j2) const

bool	isInternalLoopGUallowed () const

Protected Types
typedef UpperTriangularMatrix< E_type >	EsMatrix
	matrix to store ES values (upper triangular matrix)

Protected Member Functions
bool	isGC (const size_t i1, const size_t i2) const

void	computeES (const Accessibility &acc, EsMatrix &esToFill)

E_type	computeIntraEall (const Accessibility &acc) const

Protected Attributes
vrna_md_t	foldModel
	Vienna RNA package : folding model to be used for the energy computation.

vrna_param_t *	foldParams

Z_type	RT
	the RT constant to be used for Boltzmann weight computations

const int	bpCG
	base pair code for (C,G)

const int	bpGC
	base pair code for (G,C)

EsMatrix *	esValues1
	the ES values for seq1 if computed (otherwise NULL)

EsMatrix *	esValues2
	the ES values for seq2 if computed (otherwise NULL)

E_type	Eall1
	ensemble energy of intra-molecular structures of seq1

E_type	Eall2
	ensemble energy of intra-molecular structures of seq2

Protected Attributes inherited from IntaRNA::InteractionEnergy
const Accessibility &	accS1
	accessibility values for sequence S1

const ReverseAccessibility &	accS2
	accessibility values for sequence S2 (reversed index order)

const size_t	maxInternalLoopSize1

const size_t	maxInternalLoopSize2

const E_type	energyAdd
	user defined shift of the energy spectrum

const bool	energyWithDangles
	whether or not dangling end energy contributions are to be added

const bool	internalLoopGU
	whether or not GU base pairs allowed in internal loops

Additional Inherited Members
Public Types inherited from IntaRNA::InteractionEnergy
enum	ES_multi_mode { ES_multi_1only , ES_multi_2only , ES_multi_both }

Static Protected Member Functions inherited from IntaRNA::InteractionEnergy
static bool	isAllowedLoopRegion (const RnaSequence &seq, const size_t i, const size_t j, const size_t maxInternalLoopSize)

Detailed Description

Implements an energy interface based on free energy estimates computed with the Vienna RNA package.

Author: Martin Mann 2014

Member Typedef Documentation

◆ EsMatrix

typedef UpperTriangularMatrix<E_type> IntaRNA::InteractionEnergyVrna::EsMatrix

protected

matrix to store ES values (upper triangular matrix)

Constructor & Destructor Documentation

◆ InteractionEnergyVrna()

IntaRNA::InteractionEnergyVrna::InteractionEnergyVrna	(	const Accessibility &	accS1,
		const ReverseAccessibility &	accS2,
		VrnaHandler &	vrnaHandler,
		const size_t	maxInternalLoopSize1 = `16`,
		const size_t	maxInternalLoopSize2 = `16`,
		const bool	initES = `false`,
		const E_type	energyAdd = `Ekcal_2_E(0.0)`,
		const bool	energyWithDangles = `true`,
		const bool	internalLoopGU = `true`
	)

Construct energy utility object given the accessibility ED values for two sequences.

Parameters

accS1	accessibility of the first sequence
accS2	accessibility of the second sequence
vrnaHandler	the VRNA parameter handler to be used
maxInternalLoopSize1	maximal number of enclosed unpaired positions between two intermolecular base pairs in sequence 1, ie it holds for an intermolecular loop closed by base pairs (i1,i2) and (j1,j2) : (j1-i1+1) <= maxInternalLoopSize
maxInternalLoopSize2	maximal number of enclosed unpaired positions between two intermolecular base pairs in sequence 2, ie it holds for an intermolecular loop closed by base pairs (i1,i2) and (j1,j2) : (j2-i2+1) <= maxInternalLoopSize
initES	whether or not ES values are to be computed
energyAdd	when computing the overall energy via getE(), this term is always added; thus it defines a shift of the energy spectrum as e.g. needed when computing predictions with accessibility constraints
energyWithDangles	whether or not dangling end contributions are considered within overall energies
internalLoopGU	whether or not GU base pairs are allowed within internal loops

◆ ~InteractionEnergyVrna()

virtual IntaRNA::InteractionEnergyVrna::~InteractionEnergyVrna ( )

virtual

Member Function Documentation

◆ computeES()

void IntaRNA::InteractionEnergyVrna::computeES	(	const Accessibility &	acc,
		EsMatrix &	esToFill
	)

protected

Computes the ES values and fills esValues container

Parameters

acc	the accessibility object for the sequence to compute the ES values for
esToFill	the container to write the ES values to

◆ computeIntraEall()

E_type IntaRNA::InteractionEnergyVrna::computeIntraEall ( const Accessibility & acc ) const

protected

Computes the ensemble energy of all intra-molecular structures that are conform to the accessibility constraints

Parameters

acc	the Accessibility object to access sequence and constraints

Returns: the computed ensemble energy

◆ getE_danglingLeft()

E_type IntaRNA::InteractionEnergyVrna::getE_danglingLeft	(	const size_t	i1,
		const size_t	i2
	)		const

inlinevirtual

Computes the dangling end energy penalties for the left side (i1-1 and i2-1) of the interaction closed by the intermolecular base pair (i1,i2).

Parameters

i1	the index of the first sequence interacting with i2
i2	the index of the second sequence interacting with i1

Returns: the dangling end penalty for the left side of the interaction

Implements IntaRNA::InteractionEnergy.

◆ getE_danglingRight()

E_type IntaRNA::InteractionEnergyVrna::getE_danglingRight	(	const size_t	j1,
		const size_t	j2
	)		const

inlinevirtual

Computes the dangling end energy penalties for the right side (j1+1 and j2+1) of the interaction closed by the intermolecular base pair (j1,j2).

Parameters

j1	the index of the first sequence interacting with j2
j2	the index of the second sequence interacting with j1

Returns: the dangling end penalty for the right side of the interaction

Implements IntaRNA::InteractionEnergy.

◆ getE_endLeft()

E_type IntaRNA::InteractionEnergyVrna::getE_endLeft	(	const size_t	i1,
		const size_t	i2
	)		const

inlinevirtual

Provides the penalty for closing an interaction with the given base pair on the "left side" (i1 = 5' end of seq1 of the interaction)

Parameters

i1	the index of the first sequence interacting with i2
i2	the index of the second sequence interacting with i1

Returns: the loop closure penalty for the left side of the interaction

Implements IntaRNA::InteractionEnergy.

◆ getE_endRight()

E_type IntaRNA::InteractionEnergyVrna::getE_endRight	(	const size_t	j1,
		const size_t	j2
	)		const

inlinevirtual

Provides the penalty for closing an interaction with the given base pair on the "right side" (j1 = 3' end of seq1 of the interaction)

Parameters

j1	the index of the first sequence interacting with j2
j2	the index of the second sequence interacting with j1

Returns: the loop closure penalty for the right side of the interaction

Implements IntaRNA::InteractionEnergy.

◆ getE_init()

E_type IntaRNA::InteractionEnergyVrna::getE_init ( ) const

inlinevirtual

Provides the duplex initiation energy.

Returns: the energy for duplex initiation

Implements IntaRNA::InteractionEnergy.

◆ getE_interLeft()

E_type IntaRNA::InteractionEnergyVrna::getE_interLeft	(	const size_t	i1,
		const size_t	j1,
		const size_t	i2,
		const size_t	j2
	)		const

inlinevirtual

Computes the energy estimate for the interaction loop region closed by the intermolecular base pairs (i1,i2) and (j1,j2) where the regions [i1,j1] and [i2,j2] are considered unpaired. The energy estimate is derived via the Vienna RNA package loop energies or is E_INF if the internal loop size exceeds the allowed maximum (see constructor).

Parameters

i1	the index of the first sequence (<j1) interacting with i2
j1	the index of the first sequence (>i1) interacting with j2
i2	the index of the second sequence (<j2) interacting with i1
j2	the index of the second sequence (>i2) interacting with j1

Returns: energy in kcal/mol for the loop closed by (i1,i2) or E_INF if the allowed loop size is exceeded or no valid internal loop boundaries

Implements IntaRNA::InteractionEnergy.

◆ getE_multiClosing()

E_type IntaRNA::InteractionEnergyVrna::getE_multiClosing ( ) const

inlinevirtual

Provides the energy contribution/penalty for closing an intermolecular multiloop on the left of a multi-site gap.

Returns: the energy contribution/penalty of the intermolecular helix within an intramolecular multiloop

Implements IntaRNA::InteractionEnergy.

◆ getE_multiHelix()

E_type IntaRNA::InteractionEnergyVrna::getE_multiHelix	(	const size_t	j1,
		const size_t	j2
	)		const

inlinevirtual

Provides the energy contribution/penalty of the helix repesented by the interaction right of a multi-site gap starting with base pair (j1,j2)

Parameters

j1	the end of the gap in seq1, ie the first base paired in the interaction site to the right of the gap
j2	the end of the gap in seq2, ie the first base paired in the interaction site to the right of the gap

Returns: the energy contribution/penalty of the intermolecular helix within an intramolecular multiloop

Implements IntaRNA::InteractionEnergy.

◆ getE_multiUnpaired()

E_type IntaRNA::InteractionEnergyVrna::getE_multiUnpaired ( const size_t numUnpaired ) const

inlinevirtual

Provides the energy contribution for a given number of unpaired nucleotides under the assumption that the region is part of an (intermolecular) multiloop.

Parameters

numUnpaired the number of unpaired bases

Returns: the energy contribution of the given number of unpaired bases within an intramolecular multiloop

Implements IntaRNA::InteractionEnergy.

◆ getEall1()

E_type IntaRNA::InteractionEnergyVrna::getEall1 ( ) const

inlinevirtual

Provides the overall ensemble energy for sequence 1 given its accessibility constraints

Returns: Eall(constraint-conform intra-molecular structures for seq1)

Implements IntaRNA::InteractionEnergy.

◆ getEall2()

E_type IntaRNA::InteractionEnergyVrna::getEall2 ( ) const

inlinevirtual

Provides the overall ensemble energy for sequence 2 given its accessibility constraints

Returns: Eall(constraint-conform intra-molecular structures for seq2)

Implements IntaRNA::InteractionEnergy.

◆ getES1()

E_type IntaRNA::InteractionEnergyVrna::getES1	(	const size_t	i1,
		const size_t	j1
	)		const

inlinevirtual

Provides the ensemble energy (ES) of all intramolecular substructures that can be formed within a given region of sequence 1 under the assumption that the region is part of an (intermolecular) multiloop, i.e. at least one base pair is formed by each substructure.

If no structure can be formed within the region, E_INF is returned.

Parameters

i1	the start of the structured region of seq1
j1	the end of the structured region of seq1

Returns: the ES value for [i1,j1] or E_INF if no intramolecular structure can be formed

Implements IntaRNA::InteractionEnergy.

◆ getES2()

E_type IntaRNA::InteractionEnergyVrna::getES2	(	const size_t	i2,
		const size_t	j2
	)		const

inlinevirtual

Provides the ensemble energy (ES) of all intramolecular substructures that can be formed within a given region of sequence 2 under the assumption that the region is part of an (intermolecular) multiloop, i.e. at least one base pair is formed by each substructure.

If no structure can be formed within the region, E_INF is returned.

Parameters

i2	the start of the structured region of seq2
j2	the end of the structured region of seq2

Returns: the ES value for [i2,j2] or E_INF if no intramolecular structure can be formed

Implements IntaRNA::InteractionEnergy.

◆ getRT()

Z_type IntaRNA::InteractionEnergyVrna::getRT ( ) const

inlinevirtual

Provides the overall partition function for sequence 2 given its accessibility constraints

Returns: Z(constraint-conform intra-molecular structures for seq2)

Implements IntaRNA::InteractionEnergy.

◆ isGC()

bool IntaRNA::InteractionEnergyVrna::isGC	(	const size_t	i1,
		const size_t	i2
	)		const

inlineprotected

Checks whether or not a given base pair is a GC base pair

Parameters

i1	the index in the first sequence
i2	the index in the second sequence

Returns: true if (seq1(i1),seq2(i2)) is (G,C) or (C,G)

Member Data Documentation

◆ bpCG

const int IntaRNA::InteractionEnergyVrna::bpCG

protected

base pair code for (C,G)

◆ bpGC

const int IntaRNA::InteractionEnergyVrna::bpGC

protected

base pair code for (G,C)

◆ Eall1

E_type IntaRNA::InteractionEnergyVrna::Eall1

mutableprotected

ensemble energy of intra-molecular structures of seq1

◆ Eall2

E_type IntaRNA::InteractionEnergyVrna::Eall2

mutableprotected

ensemble energy of intra-molecular structures of seq2

◆ esValues1

EsMatrix* IntaRNA::InteractionEnergyVrna::esValues1

protected

the ES values for seq1 if computed (otherwise NULL)

◆ esValues2

EsMatrix* IntaRNA::InteractionEnergyVrna::esValues2

protected

the ES values for seq2 if computed (otherwise NULL)

◆ foldModel

vrna_md_t IntaRNA::InteractionEnergyVrna::foldModel

protected

Vienna RNA package : folding model to be used for the energy computation.

◆ foldParams

vrna_param_t* IntaRNA::InteractionEnergyVrna::foldParams

protected

Vienna RNA package : folding parameters to be used for the energy computation

◆ RT

Z_type IntaRNA::InteractionEnergyVrna::RT

protected

the RT constant to be used for Boltzmann weight computations

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

src/IntaRNA/InteractionEnergyVrna.h

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ EsMatrix

Constructor & Destructor Documentation

◆ InteractionEnergyVrna()

◆ ~InteractionEnergyVrna()

Member Function Documentation

◆ computeES()

◆ computeIntraEall()

◆ getE_danglingLeft()

◆ getE_danglingRight()

◆ getE_endLeft()

◆ getE_endRight()

◆ getE_init()

◆ getE_interLeft()

◆ getE_multiClosing()

◆ getE_multiHelix()

◆ getE_multiUnpaired()

◆ getEall1()

◆ getEall2()

◆ getES1()

◆ getES2()

◆ getRT()

◆ isGC()

Member Data Documentation

◆ bpCG

◆ bpGC

◆ Eall1

◆ Eall2

◆ esValues1

◆ esValues2

◆ foldModel

◆ foldParams

◆ RT