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. 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, 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. More... | |
| void | assign_plist_from_pr (plist **pl, double *probs, int length, double cutoff) |
| Create a plist from a probability matrix. More... | |
| 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. More... | |
| 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. More... | |
| char * | get_centroid_struct_pr (int length, double *dist, double *pr) |
| Get the centroid structure of the ensemble. More... | |
| 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, double *pr) |
| Get the mean base pair distance in the thermodynamic ensemble. More... | |
| 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() More... | |
| 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. 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
| 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!
| 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
