Partition function implementations. More...

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Data Structures
struct	vrna_dimer_pf_s
	Data structure returned by vrna_pf_dimer() More...

Typedefs
typedef struct vrna_dimer_pf_s	vrna_dimer_pf_t
	Typename for the data structure that stores the dimer partition functions, vrna_dimer_pf_s, as returned by vrna_pf_dimer()

typedef struct vrna_dimer_pf_s	cofoldF
	Backward compatibility typedef for vrna_dimer_pf_s.

Functions
int	vrna_pf_float_precision (void)
	Find out whether partition function computations are using single precision floating points. More...

float	pf_fold_par (const char sequence, char structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained, int is_circular)
	Compute the partition function for a given RNA sequence. More...

float	pf_fold (const char sequence, char structure)
	Compute the partition function of an RNA sequence. More...

float	pf_circ_fold (const char sequence, char structure)
	Compute the partition function of a circular RNA sequence. More...

char *	pbacktrack (char *sequence)
	Sample a secondary structure from the Boltzmann ensemble according its probability. More...

char *	pbacktrack5 (char *sequence, int length)
	Sample a sub-structure from the Boltzmann ensemble according its probability.

char *	pbacktrack_circ (char *sequence)
	Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability. More...

void	free_pf_arrays (void)
	Free arrays for the partition function recursions. More...

void	update_pf_params (int length)
	Recalculate energy parameters. More...

void	update_pf_params_par (int length, vrna_exp_param_t *parameters)
	Recalculate energy parameters. More...

FLT_OR_DBL *	export_bppm (void)
	Get a pointer to the base pair probability array. More...

int	get_pf_arrays (short S_p, short S1_p, char ptype_p, FLT_OR_DBL qb_p, FLT_OR_DBL qm_p, FLT_OR_DBL q1k_p, FLT_OR_DBL **qln_p)
	Get the pointers to (almost) all relavant computation arrays used in partition function computation. More...

double	get_subseq_F (int i, int j)
	Get the free energy of a subsequence from the q[] array.

double	mean_bp_distance (int length)
	Get the mean base pair distance of the last partition function computation. More...

double	mean_bp_distance_pr (int length, FLT_OR_DBL *pr)
	Get the mean base pair distance in the thermodynamic ensemble. More...

vrna_ep_t *	stackProb (double cutoff)
	Get the probability of stacks. More...

void	init_pf_fold (int length)
	Allocate space for pf_fold() More...

char *	centroid (int length, double *dist)

char *	get_centroid_struct_gquad_pr (int length, double *dist)

double	mean_bp_dist (int length)

double	expLoopEnergy (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)

double	expHairpinEnergy (int u, int type, short si1, short sj1, const char *string)

Basic global partition function interface
float	vrna_pf (vrna_fold_compound_t vc, char structure)
	Compute the partition function for a given RNA sequence, or sequence alignment. More...

vrna_dimer_pf_t	vrna_pf_dimer (vrna_fold_compound_t vc, char structure)
	Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers. More...

Simplified global partition function computation using sequence(s) or multiple sequence alignment(s)
float	vrna_pf_fold (const char sequence, char structure, vrna_ep_t **pl)
	Compute Partition function (and base pair probabilities) for an RNA sequence using a comparative method. More...

float	vrna_pf_circfold (const char sequence, char structure, vrna_ep_t **pl)
	Compute Partition function (and base pair probabilities) for a circular RNA sequences using a comparative method. More...

float	vrna_pf_alifold (const char *sequences, char structure, vrna_ep_t **pl)
	Compute Partition function (and base pair probabilities) for an RNA sequence alignment using a comparative method. More...

float	vrna_pf_circalifold (const char *sequences, char structure, vrna_ep_t **pl)
	Compute Partition function (and base pair probabilities) for an alignment of circular RNA sequences using a comparative method. More...

vrna_dimer_pf_t	vrna_pf_co_fold (const char seq, char structure, vrna_ep_t **pl)
	Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers. More...

Variables
int	st_back
	Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking. More...

Detailed Description

Partition function implementations.

, This file includes (almost) all function declarations within the RNAlib that are related to Partion function computations

Function Documentation

char* centroid	(	int	length,
		double *	dist
	)

Deprecated:: This function is deprecated and should not be used anymore as it is not threadsafe!

See also: get_centroid_struct_pl(), get_centroid_struct_pr()

char* get_centroid_struct_gquad_pr	(	int	length,
		double *	dist
	)

Deprecated:: This function is deprecated and should not be used anymore as it is not threadsafe!

See also: vrna_centroid(), vrna_centroid_from_probs(), vrna_centroid_from_plist()

double mean_bp_dist ( int length )

get the mean pair distance of ensemble

Deprecated:: This function is not threadsafe and should not be used anymore. Use mean_bp_distance() instead!

double expLoopEnergy	(	int	u1,
		int	u2,
		int	type,
		int	type2,
		short	si1,
		short	sj1,
		short	sp1,
		short	sq1
	)

Deprecated:: Use exp_E_IntLoop() from loop_energies.h instead

double expHairpinEnergy	(	int	u,
		int	type,
		short	si1,
		short	sj1,
		const char *	string
	)

Deprecated:: Use exp_E_Hairpin() from loop_energies.h instead

Data Structures

Typedefs

Functions

Variables

Detailed Description

Function Documentation