#include <InteractionEnergyIdxOffset.h>

Inheritance diagram for IntaRNA::InteractionEnergyIdxOffset:

Collaboration diagram for IntaRNA::InteractionEnergyIdxOffset:

[legend]

Public Member Functions
	InteractionEnergyIdxOffset (const InteractionEnergy &energyOriginal, const size_t offset1=0, const size_t offset2=0)

virtual	~InteractionEnergyIdxOffset () override

size_t	getOffset1 () const

void	setOffset1 (size_t offset1)

size_t	getOffset2 () const

void	setOffset2 (size_t offset2)

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 override

virtual E_type	getE (const Z_type Z) const override

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

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

virtual size_t	size1 () const override

virtual size_t	size2 () const override

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

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

virtual bool	isAccessible1 (const size_t i) const override

virtual bool	isAccessible2 (const size_t i) const override

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 override

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

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

virtual E_type	getE_multiUnpaired (const size_t numUnpaired) const override

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

virtual E_type	getE_multiClosing () const override

virtual E_type	getE_init () const override

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

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

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

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

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

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

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

virtual Z_type	getRT () const override

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

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

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

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

virtual E_type	getEall1 () const override

virtual E_type	getEall2 () const override

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 EnergyContributions	getE_contributions (const Interaction &interaction) 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 E_type	getEnergyAdd () const

bool	isInternalLoopGUallowed () const

Protected Attributes
const InteractionEnergy &	energyOriginal

size_t	offset1

size_t	offset2

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

Wrapper for a given InteractionEnergy object where indices are shifted by a given positive offset (shifted towards infinity). This is useful for local interaction computations.

Author: Martin Mann

Constructor & Destructor Documentation

◆ InteractionEnergyIdxOffset()

IntaRNA::InteractionEnergyIdxOffset::InteractionEnergyIdxOffset	(	const InteractionEnergy &	energyOriginal,
		const size_t	offset1 = `0`,
		const size_t	offset2 = `0`
	)

inline

construction

Parameters

energyOriginal	wrapped energy object used for computations
offset1	the index offset for sequence 1
offset2	the index offset for sequence 2

◆ ~InteractionEnergyIdxOffset()

IntaRNA::InteractionEnergyIdxOffset::~InteractionEnergyIdxOffset ( )

inlineoverridevirtual

Member Function Documentation

◆ areComplementary()

bool IntaRNA::InteractionEnergyIdxOffset::areComplementary	(	const size_t	i1,
		const size_t	i2
	)		const

inlineoverridevirtual

Checks whether or not two positions (shifted by offset) can form a base pair

Parameters

i1	index in first sequence
i2	index in second sequence

Returns: true if seq1(i1) can form a base pair with seq2(i2)

Reimplemented from IntaRNA::InteractionEnergy.

◆ getBasePair()

Interaction::BasePair IntaRNA::InteractionEnergyIdxOffset::getBasePair	(	const size_t	i1,
		const size_t	i2
	)		const

inlineoverridevirtual

Provides the base pair encoding for the given indices after shifting by the used offset

Parameters

i1	the index in the first sequence
i2	the index in the (reversed) second sequence

Returns: the according base pair (i1+offset1,reverseIdx(i2+offset2))

Reimplemented from IntaRNA::InteractionEnergy.

◆ getE() [1/2]

E_type IntaRNA::InteractionEnergyIdxOffset::getE	(	const size_t	i1,
		const size_t	j1,
		const size_t	i2,
		const size_t	j2,
		const E_type	hybridE
	)		const

inlineoverridevirtual

Provides the overall energy for an interaction from [i1,j1] in the first sequence and [i2,j2] in the second sequence given the hybridization energy contribution.

Parameters

i1	the index of the first sequence interacting with i2
j1	the index of the first sequence interacting with j2 with i1<=j1
i2	the index of the second sequence interacting with i1
j2	the index of the second sequence interacting with j1 with i2<=j2
hybridE	the hybridization energy for the interaction

Returns

E = hybridE

ED1(i1,j1) + ED2(i2,j2)
Edangle(i1,i2) + Edangle(j1,j2)
Eend(i1,i2) + Eend(j1,j2)

Reimplemented from IntaRNA::InteractionEnergy.

◆ getE() [2/2]

E_type IntaRNA::InteractionEnergyIdxOffset::getE ( const Z_type Z ) const

inlineoverridevirtual

Provides the ensemble energy for a given partition function Z.

Parameters

Z	the ensemble's partition function to convert

Returns: E = -RT * log( Z )

Reimplemented from IntaRNA::InteractionEnergy.

◆ getE_danglingLeft()

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

inlineoverridevirtual

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).

Note, the indices are shifted by an offset for computation.

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::InteractionEnergyIdxOffset::getE_danglingRight	(	const size_t	j1,
		const size_t	j2
	)		const

inlineoverridevirtual

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).

Note, the indices are shifted by an offset for computation.

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::InteractionEnergyIdxOffset::getE_endLeft	(	const size_t	i1,
		const size_t	i2
	)		const

inlineoverridevirtual

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

Note, the indices are shifted by an offset for computation.

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::InteractionEnergyIdxOffset::getE_endRight	(	const size_t	j1,
		const size_t	j2
	)		const

inlineoverridevirtual

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

Note, the indices are shifted by an offset for computation.

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::InteractionEnergyIdxOffset::getE_init ( ) const

inlineoverridevirtual

Provides the duplex initiation energy.

Returns: the energy for duplex initiation

Implements IntaRNA::InteractionEnergy.

◆ getE_interLeft()

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

inlineoverridevirtual

Computes the energy estimate for the 'left side' interaction loop region closed by the intermolecular base pairs (i1,i2) and enclosing (j1,j2) where the regions [i1,j1] and [i2,j2] are considered unpaired or E_INF is the internal loop size exceeds the allowed maximum (see constructor).

Note, the indices are shifted by an offset for computation.

Note, the right interaction base pair (j1,j2) is not included in the returned energy value.

Parameters

i1	the index of the first sequence interacting with i2
j1	the index of the first sequence interacting with j2 with i1<=j1
i2	the index of the second sequence interacting with i1
j2	the index of the second sequence interacting with j1 with i2<=j2

Returns: the energy for the loop or E_INF if the allowed loop size is exceeded or no valid internal loop boundaries

Implements IntaRNA::InteractionEnergy.

◆ getE_multi()

E_type IntaRNA::InteractionEnergyIdxOffset::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

inlineoverridevirtual

Provides the energy contribution of an interaction site gap, i.e. the provided regions are without intermolecular base pairs but are considered to be involved in intramolecular base pairs only. The multi-site gap is scored according to a multiloop in a single structure prediction model. The ends of the two regions are supposed to form an intermolecular base pair each, i.e. (i1,i2) and (j1,j2) have to be complementary.

Parameters

i1	the start of the structured region of seq1
j1	the end of the structured region of seq1
i2	the start of the structured region of seq2
j2	the end of the structured region of seq2
ES_mode	defines for which sequence intramolecular structure contributions are to be considered

Returns: the energy contribution of a multi-site interaction gap

Reimplemented from IntaRNA::InteractionEnergy.

◆ getE_multiClosing()

E_type IntaRNA::InteractionEnergyIdxOffset::getE_multiClosing ( ) const

inlineoverridevirtual

Provides the energy contribution/penalty for closing an intermolecular interaction 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::InteractionEnergyIdxOffset::getE_multiHelix	(	const size_t	j1,
		const size_t	j2
	)		const

inlineoverridevirtual

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::InteractionEnergyIdxOffset::getE_multiUnpaired ( const size_t numUnpaired ) const

inlineoverridevirtual

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::InteractionEnergyIdxOffset::getEall1 ( ) const

inlineoverridevirtual

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::InteractionEnergyIdxOffset::getEall2 ( ) const

inlineoverridevirtual

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

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

Implements IntaRNA::InteractionEnergy.

◆ getED1()

E_type IntaRNA::InteractionEnergyIdxOffset::getED1	(	const size_t	i1,
		const size_t	j1
	)		const

inlineoverridevirtual

Provides the ED penalty for making a region with sequence 1 accessible

Note, the indices are shifted by an offset for computation.

Parameters

i1	the start of the accessible region
j1	the end of the accessible region

Returns: the ED value for [i1,j1]

Reimplemented from IntaRNA::InteractionEnergy.

◆ getED2()

E_type IntaRNA::InteractionEnergyIdxOffset::getED2	(	const size_t	i2,
		const size_t	j2
	)		const

inlineoverridevirtual

Provides the ED penalty for making a region with (the reversed) sequence 2 accessible

Note, the indices are shifted by an offset for computation.

Parameters

i2	the start of the accessible region
j2	the end of the accessible region

Returns: the ED value for [i2,j2]

Reimplemented from IntaRNA::InteractionEnergy.

◆ getES1()

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

inlineoverridevirtual

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::InteractionEnergyIdxOffset::getES2	(	const size_t	i2,
		const size_t	j2
	)		const

inlineoverridevirtual

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.

◆ getIndex1()

size_t IntaRNA::InteractionEnergyIdxOffset::getIndex1 ( const Interaction::BasePair & bp ) const

inlineoverridevirtual

Provides the index within the first sequence of the given base pair shifted by the offset.

Returns: the shifted index of the first sequence within the base pair encoding

Reimplemented from IntaRNA::InteractionEnergy.

◆ getIndex2()

size_t IntaRNA::InteractionEnergyIdxOffset::getIndex2 ( const Interaction::BasePair & bp ) const

inlineoverridevirtual

Provides the (reversed) index within the second sequence of the given base pair shifted by the offset.

Returns: the shifted index of the second sequence within the base pair encoding

Reimplemented from IntaRNA::InteractionEnergy.

◆ getOffset1()

size_t IntaRNA::InteractionEnergyIdxOffset::getOffset1 ( ) const

inline

Access to the currently used index offset for sequence 1

Returns: the index offset for sequence 1 used

◆ getOffset2()

size_t IntaRNA::InteractionEnergyIdxOffset::getOffset2 ( ) const

inline

Access to the currently used index offset for sequence 2

Returns: the index offset for sequence 2 used

◆ getPr_danglingLeft()

Z_type IntaRNA::InteractionEnergyIdxOffset::getPr_danglingLeft	(	const size_t	i1,
		const size_t	j1,
		const size_t	i2,
		const size_t	j2
	)		const

inlineoverridevirtual

Computes the probability of the dangling ends for the left side (i1-1 and i2-1) of the interaction closed by the intermolecular base pair (i1,i2) for an interaction of [i1,j1] with [i2,j2].

Note, the indices are shifted by an offset for computation.

Parameters

i1	the index of the first sequence interacting with i2
j1	the index of the first sequence interacting with j2 with i1<=j1
i2	the index of the second sequence interacting with i1
j2	the index of the second sequence interacting with j1 with i2<=j2

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

Reimplemented from IntaRNA::InteractionEnergy.

◆ getPr_danglingRight()

Z_type IntaRNA::InteractionEnergyIdxOffset::getPr_danglingRight	(	const size_t	i1,
		const size_t	j1,
		const size_t	i2,
		const size_t	j2
	)		const

inlineoverridevirtual

Computes the probability of the dangling ends for the right side (j1+1 and j2+1) of the interaction closed by the intermolecular base pair (j1,j2) for an interaction of [i1,j1] with [i2,j2].

Note, the indices are shifted by an offset for computation.

Parameters

i1	the index of the first sequence interacting with i2
j1	the index of the first sequence interacting with j2 with i1<=j1
i2	the index of the second sequence interacting with i1
j2	the index of the second sequence interacting with j1 with i2<=j2

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

Reimplemented from IntaRNA::InteractionEnergy.

◆ getRT()

Z_type IntaRNA::InteractionEnergyIdxOffset::getRT ( ) const

inlineoverridevirtual

Access to the normalized temperature for Boltzmann weight computation

Implements IntaRNA::InteractionEnergy.

◆ isAccessible1()

bool IntaRNA::InteractionEnergyIdxOffset::isAccessible1 ( const size_t i ) const

inlineoverridevirtual

Whether or not position i is accessible for interaction in sequence 1

Note, the index is shifted by an offset for computation.

Parameters

i	the position of interest in sequence 1

Returns: true if the position can partake in an interaction; false otherwise

Reimplemented from IntaRNA::InteractionEnergy.

◆ isAccessible2()

bool IntaRNA::InteractionEnergyIdxOffset::isAccessible2 ( const size_t i ) const

inlineoverridevirtual

Whether or not position i is accessible for interaction in sequence 2

Note, the index is shifted by an offset for computation.

Parameters

i	the position of interest in sequence 2

Returns: true if the position can partake in an interaction; false otherwise

Reimplemented from IntaRNA::InteractionEnergy.

◆ isGU()

bool IntaRNA::InteractionEnergyIdxOffset::isGU	(	const size_t	i1,
		const size_t	i2
	)		const

inlineoverridevirtual

Checks whether or not two positions can form a GU base pair

Parameters

i1	index in first sequence
i2	index in second sequence

Returns: true if seq1(i1) can form a GU base pair with seq2(i2)

Reimplemented from IntaRNA::InteractionEnergy.

◆ isValidInternalLoop()

bool IntaRNA::InteractionEnergyIdxOffset::isValidInternalLoop	(	const size_t	i1,
		const size_t	j1,
		const size_t	i2,
		const size_t	j2
	)		const

inlineoverridevirtual

Checks whether or not the given indices mark valid internal loop boundaries, i.e.

(i1,i2) and (j1,j2) are complementary
i1..j1 and i2..j2 are allowed loop regions
no boundary overlap ( (j1-i1==0 && j2-i2==0) || (j1-i1>0 && j2-i2>0) )
if !internalLoopGU : both ends are no GU base pairs

Parameters

i1	the index of the first sequence interacting with i2
j1	the index of the first sequence interacting with j2 with i1<=j1
i2	the index of the second sequence interacting with i1
j2	the index of the second sequence interacting with j1 with i2<=j2

Returns: true if the boundaries are sound for internal loop calculation; false otherwise

Reimplemented from IntaRNA::InteractionEnergy.

◆ setOffset1()

void IntaRNA::InteractionEnergyIdxOffset::setOffset1 ( size_t offset1 )

inline

Sets the index offset to be used for sequence 1

Parameters

offset1 the index offset for sequence 1 to be used

◆ setOffset2()

void IntaRNA::InteractionEnergyIdxOffset::setOffset2 ( size_t offset2 )

inline

Sets the index offset to be used for sequence 2

Parameters

offset2 the index offset for sequence 2 to be used

◆ size1()

size_t IntaRNA::InteractionEnergyIdxOffset::size1 ( ) const

inlineoverridevirtual

Length of sequence 1 excluding the index offset

Returns: length of sequence 1 excluding index offset

Reimplemented from IntaRNA::InteractionEnergy.

◆ size2()

size_t IntaRNA::InteractionEnergyIdxOffset::size2 ( ) const

inlineoverridevirtual

Length of sequence 2 excluding index offset

Returns: length of sequence 2 excluding index offset

Reimplemented from IntaRNA::InteractionEnergy.

Member Data Documentation

◆ energyOriginal

const InteractionEnergy& IntaRNA::InteractionEnergyIdxOffset::energyOriginal

protected

the wrapped energy computation handler

◆ offset1

size_t IntaRNA::InteractionEnergyIdxOffset::offset1

protected

the index offset in sequence 1

◆ offset2

size_t IntaRNA::InteractionEnergyIdxOffset::offset2

protected

the index offset in sequence 2

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

src/IntaRNA/InteractionEnergyIdxOffset.h

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ InteractionEnergyIdxOffset()

◆ ~InteractionEnergyIdxOffset()

Member Function Documentation

◆ areComplementary()

◆ getBasePair()

◆ getE() [1/2]

◆ getE() [2/2]

◆ getE_danglingLeft()

◆ getE_danglingRight()

◆ getE_endLeft()

◆ getE_endRight()

◆ getE_init()

◆ getE_interLeft()

◆ getE_multi()

◆ getE_multiClosing()

◆ getE_multiHelix()

◆ getE_multiUnpaired()

◆ getEall1()

◆ getEall2()

◆ getED1()

◆ getED2()

◆ getES1()

◆ getES2()

◆ getIndex1()

◆ getIndex2()

◆ getOffset1()

◆ getOffset2()

◆ getPr_danglingLeft()

◆ getPr_danglingRight()

◆ getRT()

◆ isAccessible1()

◆ isAccessible2()

◆ isGU()

◆ isValidInternalLoop()

◆ setOffset1()

◆ setOffset2()

◆ size1()

◆ size2()

Member Data Documentation

◆ energyOriginal

◆ offset1

◆ offset2