RNAlib-2.2.0-RC2
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Partition function of single RNA sequences. More...
Go to the source code of this file.
Functions | |
float | vrna_pf_fold (vrna_fold_compound *vc, char *structure) |
Compute the partition function ![]() | |
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 ![]() | |
float | pf_fold (const char *sequence, char *structure) |
Compute the partition function ![]() | |
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 * | vrna_pbacktrack5 (vrna_fold_compound *vc, int length) |
Sample a secondary structure of a subsequence from the Boltzmann ensemble according its probability . More... | |
char * | vrna_pbacktrack (vrna_fold_compound *vc) |
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... | |
void | vrna_update_pf_params (vrna_fold_compound *vc, vrna_exp_param_t *params) |
Update the energy parameters for subsequent partition function computations. More... | |
void | vrna_rescale_pf_params (vrna_fold_compound *vc, double *mfe) |
Rescale Boltzmann factors for partition function computations. 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... | |
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 *vc) |
Get the mean base pair distance in the thermodynamic ensemble. 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... | |
Partition function of single RNA sequences.
This file includes (almost) all function declarations within the RNAlib that are related to Partion function folding...
void init_pf_fold | ( | int | length | ) |
Allocate space for pf_fold()
char* centroid | ( | int | length, |
double * | dist | ||
) |
char* get_centroid_struct_gquad_pr | ( | int | length, |
double * | dist | ||
) |
double mean_bp_dist | ( | int | length | ) |
get the mean pair distance of ensemble
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 | ||
) |