| | Sample a secondary structure from the Boltzmann ensemble according its probability
+
+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.
|
+| 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.
+
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
-
+
Function Documentation
+
| void init_pf_fold |
( |
- int |
- length | ) |
+ int |
+ length |
+ ) |
|
-
+
+
-
+
| char* centroid |
( |
- int |
- length, |
+ int |
+ length, |
|
|
- double * |
- dist |
+ double * |
+ dist | |
|
) |
- | |
+ | | |
-
+
+
-
+
| double mean_bp_dist |
( |
- int |
- length | ) |
+ 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 |
+ u1, |
|
|
- int |
- u2, |
+ int |
+ u2, |
|
|
- int |
- type, |
+ int |
+ type, |
|
|
- int |
- type2, |
+ int |
+ type2, |
|
|
- short |
- si1, |
+ short |
+ si1, |
|
|
- short |
- sj1, |
+ short |
+ sj1, |
|
|
- short |
- sp1, |
+ short |
+ sp1, |
|
|
- short |
- sq1 |
+ short |
+ sq1 | |
|
) |
- | |
+ | | |
-
+
+
-
+
| double expHairpinEnergy |
( |
- int |
- u, |
+ int |
+ u, |
|
|
- int |
- type, |
+ int |
+ type, |
|
|
- short |
- si1, |
+ short |
+ si1, |
|
|
- short |
- sj1, |
+ short |
+ sj1, |
|
|
- const char * |
- string |
+ const char * |
+ string | |
|
) |
- | |
+ | | |
-
+
+
-
-
-
-
+
Generated on 11 Apr 2017 for RNAlib-2.1.2 by
+
+ 1.6.1
|
1.8.1.1
- 
Include dependency graph for part_func.h:
+