/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part_func.h File Reference

Partition function of single RNA sequences. More...

Include dependency graph for part_func.h:

Go to the source code of this file.

Functions
float	pf_fold_par (const char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular)
	Compute the partition function for a given RNA sequence.
float	pf_fold (const char *sequence, char *structure)
	Compute the partition function of an RNA sequence.
float	pf_circ_fold (const char *sequence, char *structure)
	Compute the partition function of a circular RNA sequence.
char *	pbacktrack (char *sequence)
	Sample a secondary 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.
void	free_pf_arrays (void)
	Free arrays for the partition function recursions.
void	update_pf_params (int length)
	Recalculate energy parameters.
void	update_pf_params_par (int length, pf_paramT *parameters)
	Recalculate energy parameters.
double *	export_bppm (void)
	Get a pointer to the base pair probability arrayAccessing the base pair probabilities for a pair (i,j) is achieved by.
void	assign_plist_from_pr (plist **pl, double *probs, int length, double cutoff)
	Create a plist from a probability matrix.
int	get_pf_arrays (short **S_p, short **S1_p, char **ptype_p, double **qb_p, double **qm_p, double **q1k_p, double **qln_p)
	Get the pointers to (almost) all relavant computation arrays used in partition function computation.
double	get_subseq_F (int i, int j)
	Get the free energy of a subsequence from the q[] array.
char *	get_centroid_struct_pl (int length, double *dist, plist *pl)
	Get the centroid structure of the ensemble.
char *	get_centroid_struct_pr (int length, double *dist, double *pr)
	Get the centroid structure of the ensemble.
double	mean_bp_distance (int length)
	Get the mean base pair distance of the last partition function computation.
double	mean_bp_distance_pr (int length, double *pr)
	Get the mean base pair distance in the thermodynamic ensemble.
void	bppm_to_structure (char *structure, double *pr, unsigned int length)
	Create a dot-bracket like structure string from base pair probability matrix.
char	bppm_symbol (const float *x)
	Get a pseudo dot bracket notation for a given probability information.
void	init_pf_fold (int length)
	Allocate space for pf_fold().
char *	centroid (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)
Variables
int	st_back
	Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking.

---

Detailed Description

Partition function of single RNA sequences.

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

---

Function Documentation

void init_pf_fold

(

int

length

)

Allocate space for pf_fold().

Deprecated:

This function is obsolete and will be removed soon!

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()

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