RNAlib-2.5.0alpha2
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Partition function implementations. More...
Go to the source code of this file.
Data Structures | |
struct | vrna_dimer_pf_s |
Data structure returned by vrna_pf_dimer() More... | |
struct | vrna_multimer_pf_s |
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 ![]() | |
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 * | 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 ![]() | |
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... | |
FLT_OR_DBL | vrna_pf_multimer (vrna_fold_compound_t *vc, char *structure) |
FLT_OR_DBL * | vrna_pf_substrands (vrna_fold_compound_t *fc, size_t complex_size) |
FLT_OR_DBL | vrna_pf_add (FLT_OR_DBL dG1, FLT_OR_DBL dG2, double kT) |
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 ![]() | |
float | vrna_pf_circfold (const char *sequence, char *structure, vrna_ep_t **pl) |
Compute Partition function ![]() | |
float | vrna_pf_alifold (const char **sequences, char *structure, vrna_ep_t **pl) |
Compute Partition function ![]() | |
float | vrna_pf_circalifold (const char **sequences, char *structure, vrna_ep_t **pl) |
Compute Partition function ![]() | |
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... | |
Partition function implementations.
, This file includes (almost) all function declarations within the RNAlib that are related to Partion function computations