|
RNAlib-2.2.9
|
Collaboration diagram for Suboptimal structures within an energy band arround the MFE:Typedefs | |
| typedef void( | vrna_subopt_callback) (const char *stucture, float energy, void *data) |
| Callback for vrna_subopt_cb() | |
Functions | |
| vrna_subopt_solution_t * | vrna_subopt (vrna_fold_compound_t *vc, int delta, int sorted, FILE *fp) |
| Returns list of subopt structures or writes to fp. More... | |
| void | vrna_subopt_cb (vrna_fold_compound_t *vc, int delta, vrna_subopt_callback *cb, void *data) |
| Generate suboptimal structures within an energy band arround the MFE. More... | |
| SOLUTION * | subopt (char *seq, char *structure, int delta, FILE *fp) |
| Returns list of subopt structures or writes to fp. More... | |
| SOLUTION * | subopt_par (char *seq, char *structure, vrna_param_t *parameters, int delta, int is_constrained, int is_circular, FILE *fp) |
| Returns list of subopt structures or writes to fp. | |
| SOLUTION * | subopt_circ (char *seq, char *sequence, int delta, FILE *fp) |
| Returns list of circular subopt structures or writes to fp. More... | |
Variables | |
| double | print_energy |
| printing threshold for use with logML | |
| int | subopt_sorted |
| Sort output by energy. | |
| vrna_subopt_solution_t* vrna_subopt | ( | vrna_fold_compound_t * | vc, |
| int | delta, | ||
| int | sorted, | ||
| FILE * | fp | ||
| ) |
#include <ViennaRNA/subopt.h>
Returns list of subopt structures or writes to fp.
This function produces all suboptimal secondary structures within 'delta' * 0.01 kcal/mol of the optimum, see [18]. The results are either directly written to a 'fp' (if 'fp' is not NULL), or (fp==NULL) returned in a vrna_subopt_solution_t * list terminated by an entry were the 'structure' member is NULL.
| vc | |
| delta | |
| sorted | Sort results by energy in ascending order |
| fp |
| void vrna_subopt_cb | ( | vrna_fold_compound_t * | vc, |
| int | delta, | ||
| vrna_subopt_callback * | cb, | ||
| void * | data | ||
| ) |
#include <ViennaRNA/subopt.h>
Generate suboptimal structures within an energy band arround the MFE.
This is the most generic implementation of the suboptimal structure generator according to Wuchty et al. 1999 [18]. Identical to vrna_subopt(), it computes all secondary structures within an energy band delta arround the MFE. However, this function does not print the resulting structures and their corresponding free energies to a file pointer, or returns them as a list. Instead, it calls a user-provided callback function which it passes the structure in dot-bracket format, the corresponding free energy in kcal/mol, and a user-provided data structure each time a structure was backtracked successfully. This function indicates the final output, i.e. the end of the backtracking procedure by passing NULL instead of an actual dot-bracket string to the callback.
| vc | fold compount with the sequence data |
| delta | Energy band arround the MFE in 10cal/mol, i.e. deka-calories |
| cb | Pointer to a callback function that handles the backtracked structure and its free energy in kcal/mol |
| data | Pointer to some data structure that is passed along to the callback |
| SOLUTION* subopt | ( | char * | seq, |
| char * | structure, | ||
| int | delta, | ||
| FILE * | fp | ||
| ) |
#include <ViennaRNA/subopt.h>
Returns list of subopt structures or writes to fp.
This function produces all suboptimal secondary structures within 'delta' * 0.01 kcal/mol of the optimum. The results are either directly written to a 'fp' (if 'fp' is not NULL), or (fp==NULL) returned in a SOLUTION * list terminated by an entry were the 'structure' pointer is NULL.
| seq | |
| structure | |
| delta | |
| fp |
| SOLUTION* subopt_circ | ( | char * | seq, |
| char * | sequence, | ||
| int | delta, | ||
| FILE * | fp | ||
| ) |
#include <ViennaRNA/subopt.h>
Returns list of circular subopt structures or writes to fp.
This function is similar to subopt() but calculates secondary structures assuming the RNA sequence to be circular instead of linear
| seq | |
| sequence | |
| delta | |
| fp |