#include <InteractionEnergy.h>

Inheritance diagram for IntaRNA::InteractionEnergy:

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Collaboration diagram for IntaRNA::InteractionEnergy:

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Classes
struct	EnergyContributions

Public Types
enum	ES_multi_mode { ES_multi_1only , ES_multi_2only , ES_multi_both }

Public Member Functions
	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 E_type	getES1 (const size_t i1, const size_t j1) const =0

virtual E_type	getES2 (const size_t i2, const size_t j2) const =0

virtual E_type	getE_multiUnpaired (const size_t numUnpaired) const =0

virtual E_type	getE_multiHelix (const size_t j1, const size_t j2) const =0

virtual E_type	getE_multiClosing () const =0

virtual E_type	getE_init () const =0

virtual E_type	getE_interLeft (const size_t i1, const size_t j1, const size_t i2, const size_t j2) const =0

virtual E_type	getE_danglingLeft (const size_t i1, const size_t i2) const =0

virtual E_type	getE_danglingRight (const size_t j1, const size_t j2) const =0

virtual E_type	getE_endLeft (const size_t i1, const size_t i2) const =0

virtual E_type	getE_endRight (const size_t j1, const size_t j2) const =0

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	getRT () const =0

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

virtual E_type	getEall1 () const =0

virtual E_type	getEall2 () const =0

Static Protected Member Functions
static bool	isAllowedLoopRegion (const RnaSequence &seq, const size_t i, const size_t j, const size_t maxInternalLoopSize)

Protected Attributes
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

Detailed Description

Abstract utility class that covers necessary energy related functionalities for the interaction energy computation given two RNAs.

Author: Martin Mann 2014

Member Enumeration Documentation

◆ ES_multi_mode

enum IntaRNA::InteractionEnergy::ES_multi_mode

defines where intramolecular structure contributions are to be considered e.g. in getE_multi().

Enumerator
ES_multi_1only	incorporate ES for seq1 only
ES_multi_2only	incorporate ES for seq2 only
ES_multi_both	incorporate ES for both sequences

Constructor & Destructor Documentation

◆ InteractionEnergy()

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
	)

inline

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

Parameters

accS1	accessibility of the first sequence
accS2	accessibility of the second sequence (reversed to 3'-5' index reading)
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+maxInternalLoopSize1)
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+maxInternalLoopSize2)
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
energyWithDangle	whether or not danling end energy contributions are taken into account for the overall energy computation
internalLoopGU	whether or not GU base pairs are allowed within internal loops

◆ ~InteractionEnergy()

IntaRNA::InteractionEnergy::~InteractionEnergy ( )

inlinevirtual

destruction

Member Function Documentation

◆ areComplementary()

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

inlinevirtual

Checks whether or not two positions 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) and both positions are accessible

Reimplemented in IntaRNA::InteractionEnergyIdxOffset.

◆ getAccessibility1()

const Accessibility & IntaRNA::InteractionEnergy::getAccessibility1 ( ) const

inlinevirtual

Access to the accessibility object of the first sequence (including sequence access)

Returns: the accessibility object for the first sequence

◆ getAccessibility2()

const ReverseAccessibility & IntaRNA::InteractionEnergy::getAccessibility2 ( ) const

inlinevirtual

Access to the accessibility object of the second sequence (including sequence access)

Returns: the reverse accessibility object for the second sequence

◆ getBasePair()

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

inlinevirtual

Provides the base pair encoding for the given indices.

Parameters

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

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

Reimplemented in IntaRNA::InteractionEnergyIdxOffset.

◆ getBoltzmannWeight() [1/2]

Z_type IntaRNA::InteractionEnergy::getBoltzmannWeight ( const E_type energy ) const

inlinevirtual

Provides the Boltzmann weight for a given energy.

Parameters

energy the energy (internal representation) the Boltzmann weight is to be computed for

Returns: the Boltzmann weight, i.e. exp( - energy / RT );

◆ getBoltzmannWeight() [2/2]

Z_type IntaRNA::InteractionEnergy::getBoltzmannWeight ( const Z_type energy ) const

inlinevirtual

Provides the Boltzmann weight for a given energy.

Parameters

energy the energy (in kcal/mol) the Boltzmann weight is to be computed for

Returns: the Boltzmann weight, i.e. exp( - energy / RT );

◆ getE() [1/2]

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

inlinevirtual

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 in IntaRNA::InteractionEnergyIdxOffset.

◆ getE() [2/2]

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

inlinevirtual

Provides the ensemble energy (in internal energy representation) for a given partition function Z.

Parameters

Z	the ensemble's partition function to convert

Returns: E = -RT * log( Z ) in internal energy representation

Reimplemented in IntaRNA::InteractionEnergyIdxOffset.

◆ getE_contributions()

virtual EnergyContributions IntaRNA::InteractionEnergy::getE_contributions ( const Interaction & interaction ) const

virtual

Provides details about the energy contributions for the given interaction

Parameters

interaction the interaction of interest

Returns: the individual energy contributions

◆ getE_danglingLeft()

virtual E_type IntaRNA::InteractionEnergy::getE_danglingLeft	(	const size_t	i1,
		const size_t	i2
	)		const

pure virtual

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

Implemented in IntaRNA::InteractionEnergyBasePair, IntaRNA::InteractionEnergyIdxOffset, and IntaRNA::InteractionEnergyVrna.

◆ getE_danglingRight()

virtual E_type IntaRNA::InteractionEnergy::getE_danglingRight	(	const size_t	j1,
		const size_t	j2
	)		const

pure virtual

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

Implemented in IntaRNA::InteractionEnergyBasePair, IntaRNA::InteractionEnergyIdxOffset, and IntaRNA::InteractionEnergyVrna.

◆ getE_endLeft()

virtual E_type IntaRNA::InteractionEnergy::getE_endLeft	(	const size_t	i1,
		const size_t	i2
	)		const

pure virtual

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

Implemented in IntaRNA::InteractionEnergyBasePair, IntaRNA::InteractionEnergyIdxOffset, and IntaRNA::InteractionEnergyVrna.

◆ getE_endRight()

virtual E_type IntaRNA::InteractionEnergy::getE_endRight	(	const size_t	j1,
		const size_t	j2
	)		const

pure virtual

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

Implemented in IntaRNA::InteractionEnergyBasePair, IntaRNA::InteractionEnergyIdxOffset, and IntaRNA::InteractionEnergyVrna.

◆ getE_init()

virtual E_type IntaRNA::InteractionEnergy::getE_init ( ) const

pure virtual

Provides the duplex initiation energy.

Returns: the energy for duplex initiation

Implemented in IntaRNA::InteractionEnergyBasePair, IntaRNA::InteractionEnergyIdxOffset, and IntaRNA::InteractionEnergyVrna.

◆ getE_interLeft()

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

pure virtual

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 if the internal loop size exceeds the allowed maximum (see constructor).

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

Implemented in IntaRNA::InteractionEnergyBasePair, IntaRNA::InteractionEnergyIdxOffset, and IntaRNA::InteractionEnergyVrna.

◆ getE_multi()

E_type IntaRNA::InteractionEnergy::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

inlinevirtual

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 in IntaRNA::InteractionEnergyIdxOffset.

◆ getE_multiClosing()

virtual E_type IntaRNA::InteractionEnergy::getE_multiClosing ( ) const

pure virtual

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

Implemented in IntaRNA::InteractionEnergyBasePair, IntaRNA::InteractionEnergyIdxOffset, and IntaRNA::InteractionEnergyVrna.

◆ getE_multiHelix()

virtual E_type IntaRNA::InteractionEnergy::getE_multiHelix	(	const size_t	j1,
		const size_t	j2
	)		const

pure virtual

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

Implemented in IntaRNA::InteractionEnergyBasePair, IntaRNA::InteractionEnergyIdxOffset, and IntaRNA::InteractionEnergyVrna.

◆ getE_multiUnpaired()

virtual E_type IntaRNA::InteractionEnergy::getE_multiUnpaired ( const size_t numUnpaired ) const

pure virtual

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

Implemented in IntaRNA::InteractionEnergyBasePair, IntaRNA::InteractionEnergyIdxOffset, and IntaRNA::InteractionEnergyVrna.

◆ getEall1()

virtual E_type IntaRNA::InteractionEnergy::getEall1 ( ) const

pure virtual

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

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

Implemented in IntaRNA::InteractionEnergyBasePair, IntaRNA::InteractionEnergyIdxOffset, and IntaRNA::InteractionEnergyVrna.

◆ getEall2()

virtual E_type IntaRNA::InteractionEnergy::getEall2 ( ) const

pure virtual

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

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

Implemented in IntaRNA::InteractionEnergyBasePair, IntaRNA::InteractionEnergyIdxOffset, and IntaRNA::InteractionEnergyVrna.

◆ getED1()

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

inlinevirtual

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

Parameters

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

Returns: the ED value for [i1,j1]

Reimplemented in IntaRNA::InteractionEnergyIdxOffset.

◆ getED2()

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

inlinevirtual

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

Parameters

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

Returns: the ED value for [i2,j2]

Reimplemented in IntaRNA::InteractionEnergyIdxOffset.

◆ getEnergyAdd()

E_type IntaRNA::InteractionEnergy::getEnergyAdd ( ) const

inlinevirtual

Provides the energy shift used

Returns: the energy contribution always added to compute the overall energy

◆ getES1()

virtual E_type IntaRNA::InteractionEnergy::getES1	(	const size_t	i1,
		const size_t	j1
	)		const

pure virtual

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

Implemented in IntaRNA::InteractionEnergyBasePair, IntaRNA::InteractionEnergyIdxOffset, and IntaRNA::InteractionEnergyVrna.

◆ getES2()

virtual E_type IntaRNA::InteractionEnergy::getES2	(	const size_t	i2,
		const size_t	j2
	)		const

pure virtual

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

Implemented in IntaRNA::InteractionEnergyBasePair, IntaRNA::InteractionEnergyIdxOffset, and IntaRNA::InteractionEnergyVrna.

◆ getIndex1()

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

inlinevirtual

Provides the index within the first sequence of the given base pair.

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

Reimplemented in IntaRNA::InteractionEnergyIdxOffset.

◆ getIndex2()

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

inlinevirtual

Provides the index within the second sequence of the given base pair.

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

Reimplemented in IntaRNA::InteractionEnergyIdxOffset.

◆ getMaxInternalLoopSize1()

const size_t IntaRNA::InteractionEnergy::getMaxInternalLoopSize1 ( ) const

inline

Access to the maximal size of an unpaired stretch within seq1 within an interaction.

Returns: the maximal internal loop size of an interaction for seq1

◆ getMaxInternalLoopSize2()

const size_t IntaRNA::InteractionEnergy::getMaxInternalLoopSize2 ( ) const

inline

Access to the maximal size of an unpaired stretch within seq2 within an interaction.

Returns: the maximal internal loop size of an interaction for seq2

◆ getPr_danglingLeft()

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

inlinevirtual

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].

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 in IntaRNA::InteractionEnergyIdxOffset.

◆ getPr_danglingRight()

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

inlinevirtual

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].

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 in IntaRNA::InteractionEnergyIdxOffset.

◆ getRT()

virtual Z_type IntaRNA::InteractionEnergy::getRT ( ) const

pure virtual

Access to the normalized temperature for Boltzmann weight computation

Implemented in IntaRNA::InteractionEnergyBasePair, IntaRNA::InteractionEnergyIdxOffset, and IntaRNA::InteractionEnergyVrna.

◆ isAccessible1()

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

inlinevirtual

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

Parameters

i	the position of interest in sequence 1

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

Reimplemented in IntaRNA::InteractionEnergyIdxOffset.

◆ isAccessible2()

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

inlinevirtual

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

Parameters

i	the position of interest in sequence 2

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

Reimplemented in IntaRNA::InteractionEnergyIdxOffset.

◆ isAllowedLoopRegion()

bool IntaRNA::InteractionEnergy::isAllowedLoopRegion	(	const RnaSequence &	seq,
		const size_t	i,
		const size_t	j,
		const size_t	maxInternalLoopSize
	)

inlinestaticprotected

Checks whether or not the given indices are valid index region within the sequence for an intermolecular loop and do not violate the maximal internal loop size.

Parameters

seq	the sequence the indices correspond to
i	begin index of the region in the sequence
j	end index of the region in the sequence
maxInternalLoopSize	the maximally allowed distance of i and j, ie. (j-i+1) <= maxInternalLoopSize

Returns: true if the indices are fulfilling 0 <= i <= j < seq.length, both sequence positions denote non-ambiguous nucleotides (!= N) and (j-i+1) <= maxInternalLoopSize; false otherwise

◆ isGU()

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

inlinevirtual

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 in IntaRNA::InteractionEnergyIdxOffset.

◆ isInternalLoopGUallowed()

bool IntaRNA::InteractionEnergy::isInternalLoopGUallowed ( ) const

inline

Whether or not GU base pairs are allowed within internal loops.

Parameters

true	if GU base pairs are allowed; false otherwise

◆ isValidInternalLoop()

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

inlinevirtual

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 in IntaRNA::InteractionEnergyIdxOffset.

◆ size1()

size_t IntaRNA::InteractionEnergy::size1 ( ) const

inlinevirtual

Length of sequence 1

Returns: length of sequence 1

Reimplemented in IntaRNA::InteractionEnergyIdxOffset.

◆ size2()

size_t IntaRNA::InteractionEnergy::size2 ( ) const

inlinevirtual

Length of sequence 2

Returns: length of sequence 2

Reimplemented in IntaRNA::InteractionEnergyIdxOffset.

Member Data Documentation

◆ accS1

const Accessibility& IntaRNA::InteractionEnergy::accS1

protected

accessibility values for sequence S1

◆ accS2

const ReverseAccessibility& IntaRNA::InteractionEnergy::accS2

protected

accessibility values for sequence S2 (reversed index order)

◆ energyAdd

const E_type IntaRNA::InteractionEnergy::energyAdd

protected

user defined shift of the energy spectrum

◆ energyWithDangles

const bool IntaRNA::InteractionEnergy::energyWithDangles

protected

whether or not dangling end energy contributions are to be added

◆ internalLoopGU

const bool IntaRNA::InteractionEnergy::internalLoopGU

protected

whether or not GU base pairs allowed in internal loops

◆ maxInternalLoopSize1

const size_t IntaRNA::InteractionEnergy::maxInternalLoopSize1

protected

maximally allowed unpaired range between two base pairs in sequence S1 forming an intermolecular internal loop

◆ maxInternalLoopSize2

const size_t IntaRNA::InteractionEnergy::maxInternalLoopSize2

protected

maximally allowed unpaired range between two base pairs in sequence S2 forming an intermolecular internal loop

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

src/IntaRNA/InteractionEnergy.h

Classes

Public Types

Public Member Functions

Static Protected Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

◆ ES_multi_mode

Constructor & Destructor Documentation

◆ InteractionEnergy()

◆ ~InteractionEnergy()

Member Function Documentation

◆ areComplementary()

◆ getAccessibility1()

◆ getAccessibility2()

◆ getBasePair()

◆ getBoltzmannWeight() [1/2]

◆ getBoltzmannWeight() [2/2]

◆ getE() [1/2]

◆ getE() [2/2]

◆ getE_contributions()

◆ getE_danglingLeft()

◆ getE_danglingRight()

◆ getE_endLeft()

◆ getE_endRight()

◆ getE_init()

◆ getE_interLeft()

◆ getE_multi()

◆ getE_multiClosing()

◆ getE_multiHelix()

◆ getE_multiUnpaired()

◆ getEall1()

◆ getEall2()

◆ getED1()

◆ getED2()

◆ getEnergyAdd()

◆ getES1()

◆ getES2()

◆ getIndex1()

◆ getIndex2()

◆ getMaxInternalLoopSize1()

◆ getMaxInternalLoopSize2()

◆ getPr_danglingLeft()

◆ getPr_danglingRight()

◆ getRT()

◆ isAccessible1()

◆ isAccessible2()

◆ isAllowedLoopRegion()

◆ isGU()

◆ isInternalLoopGUallowed()

◆ isValidInternalLoop()

◆ size1()

◆ size2()

Member Data Documentation

◆ accS1

◆ accS2

◆ energyAdd

◆ energyWithDangles

◆ internalLoopGU

◆ maxInternalLoopSize1

◆ maxInternalLoopSize2