Detailed Description

Collaboration diagram for Deprecated Interface for Global MFE Prediction:

Files
file	alifold.h
	Functions for comparative structure prediction using RNA sequence alignments.

file	cofold.h
	MFE implementations for RNA-RNA interaction.

file	fold.h
	MFE calculations for single RNA sequences.

Functions
float	cofold (const char sequence, char structure)
	Compute the minimum free energy of two interacting RNA molecules. More...

float	cofold_par (const char string, char structure, vrna_param_t *parameters, int is_constrained)
	Compute the minimum free energy of two interacting RNA molecules. More...

void	free_co_arrays (void)
	Free memory occupied by cofold() More...

void	update_cofold_params (void)
	Recalculate parameters. More...

void	update_cofold_params_par (vrna_param_t *parameters)
	Recalculate parameters. More...

void	export_cofold_arrays_gq (int f5_p, int c_p, int fML_p, int fM1_p, int fc_p, int ggg_p, int indx_p, char ptype_p)
	Export the arrays of partition function cofold (with gquadruplex support) More...

void	export_cofold_arrays (int f5_p, int c_p, int fML_p, int fM1_p, int fc_p, int indx_p, char **ptype_p)
	Export the arrays of partition function cofold. More...

void	get_monomere_mfes (float e1, float e2)
	get_monomer_free_energies More...

void	initialize_cofold (int length)

float	fold_par (const char sequence, char structure, vrna_param_t *parameters, int is_constrained, int is_circular)
	Compute minimum free energy and an appropriate secondary structure of an RNA sequence. More...

float	fold (const char sequence, char structure)
	Compute minimum free energy and an appropriate secondary structure of an RNA sequence. More...

float	circfold (const char sequence, char structure)
	Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence. More...

void	free_arrays (void)
	Free arrays for mfe folding. More...

void	update_fold_params (void)
	Recalculate energy parameters. More...

void	update_fold_params_par (vrna_param_t *parameters)
	Recalculate energy parameters. More...

void	export_fold_arrays (int f5_p, int c_p, int fML_p, int fM1_p, int indx_p, char ptype_p)

void	export_fold_arrays_par (int f5_p, int c_p, int fML_p, int fM1_p, int indx_p, char ptype_p, vrna_param_t **P_p)

void	export_circfold_arrays (int Fc_p, int FcH_p, int FcI_p, int FcM_p, int fM2_p, int f5_p, int c_p, int fML_p, int fM1_p, int indx_p, char **ptype_p)

void	export_circfold_arrays_par (int Fc_p, int FcH_p, int FcI_p, int FcM_p, int fM2_p, int f5_p, int c_p, int fML_p, int fM1_p, int indx_p, char ptype_p, vrna_param_t P_p)

int	LoopEnergy (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1)

int	HairpinE (int size, int type, int si1, int sj1, const char *string)

void	initialize_fold (int length)

float	alifold (const char *strings, char structure)
	Compute MFE and according consensus structure of an alignment of sequences. More...

float	circalifold (const char *strings, char structure)
	Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear. More...

void	free_alifold_arrays (void)
	Free the memory occupied by MFE alifold functions. More...

Function Documentation

float alifold	(	const char **	strings,
		char *	structure
	)

#include <ViennaRNA/alifold.h>

Compute MFE and according consensus structure of an alignment of sequences.

This function predicts the consensus structure for the aligned 'sequences' and returns the minimum free energy; the mfe structure in bracket notation is returned in 'structure'.

Sufficient space must be allocated for 'structure' before calling alifold().

Deprecated:: Usage of this function is discouraged! Use vrna_alifold(), or vrna_mfe() instead!

See also: vrna_alifold(), vrna_mfe()

Parameters

strings	A pointer to a NULL terminated array of character arrays
structure	A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE)

Returns: The free energy score in kcal/mol

float cofold	(	const char *	sequence,
		char *	structure
	)

#include <ViennaRNA/cofold.h>

Compute the minimum free energy of two interacting RNA molecules.

The code is analog to the fold() function. If cut_point ==-1 results should be the same as with fold().

Deprecated:: use vrna_mfe_dimer() instead

Parameters

sequence	The two sequences concatenated
structure	Will hold the barcket dot structure of the dimer molecule

Returns: minimum free energy of the structure

float cofold_par	(	const char *	string,
		char *	structure,
		vrna_param_t *	parameters,
		int	is_constrained
	)

#include <ViennaRNA/cofold.h>

Compute the minimum free energy of two interacting RNA molecules.

Deprecated:: use vrna_mfe_dimer() instead

void free_co_arrays ( void )

#include <ViennaRNA/cofold.h>

Free memory occupied by cofold()

Deprecated:: This function will only free memory allocated by a prior call of cofold() or cofold_par(). See vrna_mfe_dimer() for how to use the new API

Note: folding matrices now reside in the fold compound, and should be free'd there

See also: vrna_fc_destroy(), vrna_mfe_dimer()

void update_cofold_params ( void )

#include <ViennaRNA/cofold.h>

Recalculate parameters.

Deprecated:: See vrna_params_subst() for an alternative using the new API

void update_cofold_params_par ( vrna_param_t * parameters )

#include <ViennaRNA/cofold.h>

Recalculate parameters.

Deprecated:: See vrna_params_subst() for an alternative using the new API

void export_cofold_arrays_gq	(	int **	f5_p,
		int **	c_p,
		int **	fML_p,
		int **	fM1_p,
		int **	fc_p,
		int **	ggg_p,
		int **	indx_p,
		char **	ptype_p
	)

#include <ViennaRNA/cofold.h>

Export the arrays of partition function cofold (with gquadruplex support)

Export the cofold arrays for use e.g. in the concentration Computations or suboptimal secondary structure backtracking

Deprecated:: folding matrices now reside within the fold compound. Thus, this function will only work in conjunction with a prior call to cofold() or cofold_par()

See also: vrna_mfe_dimer() for the new API

Parameters

f5_p	A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]
c_p	A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j
fML_p	A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem
fM1_p	A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem
fc_p	A pointer to the 'fc' array, i.e. array ...
ggg_p	A pointer to the 'ggg' array, i.e. array containing best free energy of a gquadruplex delimited by [i,j]
indx_p	A pointer to the indexing array used for accessing the energy matrices
ptype_p	A pointer to the ptype array containing the base pair types for each possibility (i,j)

void export_cofold_arrays	(	int **	f5_p,
		int **	c_p,
		int **	fML_p,
		int **	fM1_p,
		int **	fc_p,
		int **	indx_p,
		char **	ptype_p
	)

#include <ViennaRNA/cofold.h>

Export the arrays of partition function cofold.

Export the cofold arrays for use e.g. in the concentration Computations or suboptimal secondary structure backtracking

Deprecated:: folding matrices now reside within the vrna_fold_compound_t. Thus, this function will only work in conjunction with a prior call to the deprecated functions cofold() or cofold_par()

See also: vrna_mfe_dimer() for the new API

Parameters

f5_p	A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]
c_p	A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j
fML_p	A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem
fM1_p	A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem
fc_p	A pointer to the 'fc' array, i.e. array ...
indx_p	A pointer to the indexing array used for accessing the energy matrices
ptype_p	A pointer to the ptype array containing the base pair types for each possibility (i,j)

void get_monomere_mfes	(	float *	e1,
		float *	e2
	)

#include <ViennaRNA/cofold.h>

get_monomer_free_energies

Export monomer free energies out of cofold arrays

Deprecated:: {This function is obsolete and will be removed soon!}

Parameters

e1	A pointer to a variable where the energy of molecule A will be written to
e2	A pointer to a variable where the energy of molecule B will be written to

void initialize_cofold ( int length )

#include <ViennaRNA/cofold.h>

allocate arrays for folding

Deprecated:: {This function is obsolete and will be removed soon!}

float fold_par	(	const char *	sequence,
		char *	structure,
		vrna_param_t *	parameters,
		int	is_constrained,
		int	is_circular
	)

#include <ViennaRNA/fold.h>

Compute minimum free energy and an appropriate secondary structure of an RNA sequence.

The first parameter given, the RNA sequence, must be uppercase and should only contain an alphabet $\Sigma$ that is understood by the RNAlib
(e.g. $\Sigma = \{A,U,C,G\}$ )
The second parameter, structure, must always point to an allocated block of memory with a size of at least $\mathrm{strlen}(\mathrm{sequence})+1$

If the third parameter is NULL, global model detail settings are assumed for the folding recursions. Otherwise, the provided parameters are used.

The fourth parameter indicates whether a secondary structure constraint in enhanced dot-bracket notation is passed through the structure parameter or not. If so, the characters " | x < > " are recognized to mark bases that are paired, unpaired, paired upstream, or downstream, respectively. Matching brackets " ( ) " denote base pairs, dots "." are used for unconstrained bases.

To indicate that the RNA sequence is circular and thus has to be post-processed, set the last parameter to non-zero

After a successful call of fold_par(), a backtracked secondary structure (in dot-bracket notation) that exhibits the minimum of free energy will be written to the memory structure is pointing to. The function returns the minimum of free energy for any fold of the sequence given.

Note: OpenMP: Passing NULL to the 'parameters' argument involves access to several global model detail variables and thus is not to be considered threadsafe

Deprecated:: use vrna_mfe() instead!

See also: vrna_mfe(), fold(), circfold(), vrna_md_t, set_energy_model(), get_scaled_parameters()

Parameters

sequence	RNA sequence
structure	A pointer to the character array where the secondary structure in dot-bracket notation will be written to
parameters	A data structure containing the pre-scaled energy contributions and the model details. (NULL may be passed, see OpenMP notes above)
is_constrained	Switch to indicate that a structure constraint is passed via the structure argument (0==off)
is_circular	Switch to (de-)activate post-processing steps in case RNA sequence is circular (0==off)

Returns: the minimum free energy (MFE) in kcal/mol

float fold	(	const char *	sequence,
		char *	structure
	)

#include <ViennaRNA/fold.h>

Compute minimum free energy and an appropriate secondary structure of an RNA sequence.

This function essentially does the same thing as fold_par(). However, it takes its model details, i.e. temperature, dangles, tetra_loop, noGU, no_closingGU, fold_constrained, noLonelyPairs from the current global settings within the library

Deprecated:: use vrna_fold(), or vrna_mfe() instead!

See also: fold_par(), circfold()

Parameters

sequence	RNA sequence
structure	A pointer to the character array where the secondary structure in dot-bracket notation will be written to

Returns: the minimum free energy (MFE) in kcal/mol

float circfold	(	const char *	sequence,
		char *	structure
	)

#include <ViennaRNA/fold.h>

Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence.

This function essentially does the same thing as fold_par(). However, it takes its model details, i.e. temperature, dangles, tetra_loop, noGU, no_closingGU, fold_constrained, noLonelyPairs from the current global settings within the library

Deprecated:: Use vrna_circfold(), or vrna_mfe() instead!

See also: fold_par(), circfold()

Parameters

sequence	RNA sequence
structure	A pointer to the character array where the secondary structure in dot-bracket notation will be written to

Returns: the minimum free energy (MFE) in kcal/mol

void free_arrays ( void )

#include <ViennaRNA/fold.h>

Free arrays for mfe folding.

Deprecated:: See vrna_fold(), vrna_circfold(), or vrna_mfe() and vrna_fold_compound_t for the usage of the new API!

void update_fold_params ( void )

#include <ViennaRNA/fold.h>

Recalculate energy parameters.

Deprecated:: For non-default model settings use the new API with vrna_params_subst() and vrna_mfe() instead!

void update_fold_params_par ( vrna_param_t * parameters )

#include <ViennaRNA/fold.h>

Recalculate energy parameters.

Deprecated:: For non-default model settings use the new API with vrna_params_subst() and vrna_mfe() instead!

void export_fold_arrays	(	int **	f5_p,
		int **	c_p,
		int **	fML_p,
		int **	fM1_p,
		int **	indx_p,
		char **	ptype_p
	)

#include <ViennaRNA/fold.h>

Deprecated:: See vrna_mfe() and vrna_fold_compound_t for the usage of the new API!

void export_fold_arrays_par	(	int **	f5_p,
		int **	c_p,
		int **	fML_p,
		int **	fM1_p,
		int **	indx_p,
		char **	ptype_p,
		vrna_param_t **	P_p
	)

#include <ViennaRNA/fold.h>

Deprecated:: See vrna_mfe() and vrna_fold_compound_t for the usage of the new API!

void export_circfold_arrays	(	int *	Fc_p,
		int *	FcH_p,
		int *	FcI_p,
		int *	FcM_p,
		int **	fM2_p,
		int **	f5_p,
		int **	c_p,
		int **	fML_p,
		int **	fM1_p,
		int **	indx_p,
		char **	ptype_p
	)

#include <ViennaRNA/fold.h>

Deprecated:: See vrna_mfe() and vrna_fold_compound_t for the usage of the new API!

void export_circfold_arrays_par	(	int *	Fc_p,
		int *	FcH_p,
		int *	FcI_p,
		int *	FcM_p,
		int **	fM2_p,
		int **	f5_p,
		int **	c_p,
		int **	fML_p,
		int **	fM1_p,
		int **	indx_p,
		char **	ptype_p,
		vrna_param_t **	P_p
	)

#include <ViennaRNA/fold.h>

Deprecated:: See vrna_mfe() and vrna_fold_compound_t for the usage of the new API!

int LoopEnergy	(	int	n1,
		int	n2,
		int	type,
		int	type_2,
		int	si1,
		int	sj1,
		int	sp1,
		int	sq1
	)

#include <ViennaRNA/fold.h>

Deprecated:: {This function is deprecated and will be removed soon. Use E_IntLoop() instead!}

int HairpinE	(	int	size,
		int	type,
		int	si1,
		int	sj1,
		const char *	string
	)

#include <ViennaRNA/fold.h>

Deprecated:: {This function is deprecated and will be removed soon. Use E_Hairpin() instead!}

void initialize_fold ( int length )

#include <ViennaRNA/fold.h>

Allocate arrays for folding

Deprecated:: See vrna_mfe() and vrna_fold_compound_t for the usage of the new API!

float circalifold	(	const char **	strings,
		char *	structure
	)

#include <ViennaRNA/alifold.h>

Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear.

Deprecated:: Usage of this function is discouraged! Use vrna_alicircfold(), and vrna_mfe() instead!

See also: vrna_alicircfold(), vrna_alifold(), vrna_mfe()

Parameters

strings	A pointer to a NULL terminated array of character arrays
structure	A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE)

Returns: The free energy score in kcal/mol

void free_alifold_arrays ( void )

#include <ViennaRNA/alifold.h>

Free the memory occupied by MFE alifold functions.

Deprecated:: Usage of this function is discouraged! It only affects memory being free'd that was allocated by an old API function before. Release of memory occupied by the newly introduced vrna_fold_compound_t is handled by vrna_fold_compound_free()

See also: vrna_fold_compound_free()

Detailed Description

Files

Functions

Function Documentation