part_func.h File Reference
RNA Secondary Structure Prediction » Computing Partition Functions and Pair Probabilities

Partition function of single RNA sequences. More...

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## Functions

float | vrna_pf (vrna_fold_compound_t *vc, char *structure)
| Compute the partition function for a given RNA sequence, or sequence alignment. More...
float | vrna_pf_fold (const char *seq, char *structure, vrna_plist_t **pl)
| Compute Partition function (and base pair probabilities) for an RNA sequence using a comparative method. More...
float | vrna_pf_circfold (const char *seq, char *structure, vrna_plist_t **pl)
| Compute Partition function (and base pair probabilities) for a circular RNA sequences using a comparative method. More...
int | vrna_pf_float_precision (void)
| Find out whether partition function computations are using single precision floating points. More...
double | vrna_mean_bp_distance_pr (int length, FLT_OR_DBL *pr)
| Get the mean base pair distance in the thermodynamic ensemble from a probability matrix. More...
double | vrna_mean_bp_distance (vrna_fold_compound_t *vc)
| Get the mean base pair distance in the thermodynamic ensemble. More...
vrna_plist_t * | vrna_stack_prob (vrna_fold_compound_t *vc, double cutoff)
| Compute stacking probabilities. 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 * | 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 arrayAccessing the base pair probabilities for a pair (i,j) is achieved by. 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_plist_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)

## 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 of single RNA sequences.

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

## Function Documentation

int vrna_pf_float_precision | ( | void |  | ) |

Find out whether partition function computations are using single precision floating points.

See also
  FLT_OR_DBL

Returns
  1 if single precision is used, 0 otherwise

vrna_plist_t* stackProb | ( | double | cutoff | ) |

Get the probability of stacks.

Deprecated:
  Use vrna_stack_prob() instead!

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()

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