Hairpin Loops

Functions to evaluate the free energy contributions for hairpin loops. More...

Detailed Description

Functions to evaluate the free energy contributions for hairpin loops.

Collaboration diagram for Hairpin Loops:

Files
file	hairpin.h
	Energy evaluation of hairpin loops for MFE and partition function calculations.

Basic free energy interface
int	vrna_E_hp_loop (vrna_fold_compound_t *fc, int i, int j)
	Evaluate the free energy of a hairpin loop and consider hard constraints if they apply. More...
int	vrna_E_ext_hp_loop (vrna_fold_compound_t *fc, int i, int j)
	Evaluate the free energy of an exterior hairpin loop and consider possible hard constraints. More...
int	vrna_eval_ext_hp_loop (vrna_fold_compound_t *fc, int i, int j)
	Evaluate free energy of an exterior hairpin loop.
int	vrna_eval_hp_loop (vrna_fold_compound_t *fc, int i, int j)
	Evaluate free energy of a hairpin loop. More...
PRIVATE int	E_Hairpin (int size, int type, int si1, int sj1, const char *string, vrna_param_t *P)
	Compute the Energy of a hairpin-loop. More...

Boltzmann weight (partition function) interface
PRIVATE FLT_OR_DBL	exp_E_Hairpin (int u, int type, short si1, short sj1, const char *string, vrna_exp_param_t *P)
	Compute Boltzmann weight of a hairpin loop. More...
FLT_OR_DBL	vrna_exp_E_hp_loop (vrna_fold_compound_t *fc, int i, int j)
	High-Level function for hairpin loop energy evaluation (partition function variant) More...

Function Documentation

int vrna_E_hp_loop	(	vrna_fold_compound_t *	fc,
		int	i,
		int	j
	)

#include <ViennaRNA/loops/hairpin.h>

Evaluate the free energy of a hairpin loop and consider hard constraints if they apply.

This function evaluates the free energy of a hairpin loop

In case the base pair is not allowed due to a constraint conflict, this function returns INF.

Note

This function is polymorphic! The provided vrna_fold_compound_t may be of type VRNA_FC_TYPE_SINGLE or VRNA_FC_TYPE_COMPARATIVE

Parameters

fc	The vrna_fold_compound_t that stores all relevant model settings
i	The 5' nucleotide of the base pair (3' to evaluate the pair as exterior hairpin loop)
j	The 3' nucleotide of the base pair (5' to evaluate the pair as exterior hairpin loop)

Returns

The free energy of the hairpin loop in 10cal/mol

int vrna_E_ext_hp_loop	(	vrna_fold_compound_t *	fc,
		int	i,
		int	j
	)

#include <ViennaRNA/loops/hairpin.h>

Evaluate the free energy of an exterior hairpin loop and consider possible hard constraints.

Note

This function is polymorphic! The provided vrna_fold_compound_t may be of type VRNA_FC_TYPE_SINGLE or VRNA_FC_TYPE_COMPARATIVE

int vrna_eval_hp_loop	(	vrna_fold_compound_t *	fc,
		int	i,
		int	j
	)

#include <ViennaRNA/loops/hairpin.h>

Evaluate free energy of a hairpin loop.

Note

This function is polymorphic! The provided vrna_fold_compound_t may be of type VRNA_FC_TYPE_SINGLE or VRNA_FC_TYPE_COMPARATIVE

Parameters

fc	The vrna_fold_compound_t for the particular energy evaluation
i	5'-position of the base pair
j	3'-position of the base pair

Returns

Free energy of the hairpin loop closed by in deka-kal/mol

SWIG Wrapper Notes:

This function is attached as method eval_hp_loop() to objects of type fold_compound

PRIVATE int E_Hairpin	(	int	size,
		int	type,
		int	si1,
		int	sj1,
		const char *	string,
		vrna_param_t *	P
	)

#include <ViennaRNA/loops/hairpin.h>

Compute the Energy of a hairpin-loop.

To evaluate the free energy of a hairpin-loop, several parameters have to be known. A general hairpin-loop has this structure:

      a3 a4
    a2     a5
    a1     a6
      X - Y
      |   |
      5'  3'

where X-Y marks the closing pair [e.g. a (G,C) pair]. The length of this loop is 6 as there are six unpaired nucleotides (a1-a6) enclosed by (X,Y). The 5' mismatching nucleotide is a1 while the 3' mismatch is a6. The nucleotide sequence of this loop is "a1.a2.a3.a4.a5.a6"

Note

The parameter sequence should contain the sequence of the loop in capital letters of the nucleic acid alphabet if the loop size is below 7. This is useful for unusually stable tri-, tetra- and hexa-loops which are treated differently (based on experimental data) if they are tabulated.

See also

scale_parameters()

vrna_param_t

Warning

Not (really) thread safe! A threadsafe implementation will replace this function in a future release!
Energy evaluation may change due to updates in global variable "tetra_loop"

Parameters

size	The size of the loop (number of unpaired nucleotides)
type	The pair type of the base pair closing the hairpin
si1	The 5'-mismatching nucleotide
sj1	The 3'-mismatching nucleotide
string	The sequence of the loop (May be NULL, otherwise mst be at least long)
P	The datastructure containing scaled energy parameters

Returns

The Free energy of the Hairpin-loop in dcal/mol

PRIVATE FLT_OR_DBL exp_E_Hairpin	(	int	u,
		int	type,
		short	si1,
		short	sj1,
		const char *	string,
		vrna_exp_param_t *	P
	)

#include <ViennaRNA/loops/hairpin.h>

Compute Boltzmann weight of a hairpin loop.

multiply by scale[u+2]

See also

get_scaled_pf_parameters()

vrna_exp_param_t

E_Hairpin()

Warning

Not (really) thread safe! A threadsafe implementation will replace this function in a future release!
Energy evaluation may change due to updates in global variable "tetra_loop"

Parameters

u	The size of the loop (number of unpaired nucleotides)
type	The pair type of the base pair closing the hairpin
si1	The 5'-mismatching nucleotide
sj1	The 3'-mismatching nucleotide
string	The sequence of the loop (May be NULL, otherwise mst be at least long)
P	The datastructure containing scaled Boltzmann weights of the energy parameters

Returns

The Boltzmann weight of the Hairpin-loop

FLT_OR_DBL vrna_exp_E_hp_loop	(	vrna_fold_compound_t *	fc,
		int	i,
		int	j
	)

#include <ViennaRNA/loops/hairpin.h>

High-Level function for hairpin loop energy evaluation (partition function variant)

See also

vrna_E_hp_loop() for it's free energy counterpart

Note

This function is polymorphic! The provided vrna_fold_compound_t may be of type VRNA_FC_TYPE_SINGLE or VRNA_FC_TYPE_COMPARATIVE