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RNAlib-2.2.9
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Implementation of heuristics to explore optimal (re-)folding paths between two secondary structures. More...
Collaboration diagram for Direct refolding paths between two secondary structures:Data Structures | |
| struct | vrna_path_s |
| An element of a refolding path list. More... | |
Typedefs | |
| typedef struct vrna_path_s | vrna_path_t |
| Typename for the refolding path data structure vrna_path_s. | |
| typedef struct vrna_path_s | path_t |
| Old typename of vrna_path_s. More... | |
Functions | |
| int | vrna_path_findpath_saddle (vrna_fold_compound_t *vc, const char *struc1, const char *struc2, int max) |
| Find energy of a saddle point between 2 structures (search only direct path) More... | |
| vrna_path_t * | vrna_path_findpath (vrna_fold_compound_t *vc, const char *s1, const char *s2, int maxkeep) |
| Find refolding path between 2 structures (search only direct path) More... | |
| int | find_saddle (const char *seq, const char *struc1, const char *struc2, int max) |
| Find energy of a saddle point between 2 structures (search only direct path) More... | |
| void | free_path (vrna_path_t *path) |
| Free memory allocated by get_path() function. More... | |
| vrna_path_t * | get_path (const char *seq, const char *s1, const char *s2, int maxkeep) |
| Find refolding path between 2 structures (search only direct path) More... | |
Implementation of heuristics to explore optimal (re-)folding paths between two secondary structures.
| struct vrna_path_s |
An element of a refolding path list.
Data Fields | |
| double | en |
| Free energy of current structure. | |
| char * | s |
| Secondary structure in dot-bracket notation. | |
| typedef struct vrna_path_s path_t |
| int vrna_path_findpath_saddle | ( | vrna_fold_compound_t * | vc, |
| const char * | struc1, | ||
| const char * | struc2, | ||
| int | max | ||
| ) |
#include <ViennaRNA/findpath.h>
Find energy of a saddle point between 2 structures (search only direct path)
This function uses an inplementation of the findpath algorithm [5] for near-optimal direct refolding path prediction.
Model details, and energy parameters are used as provided via the parameter 'vc'. The vrna_fold_compound_t does not require memory for any DP matrices, but requires all most basic init values as one would get from a call like this:
| vc | The vrna_fold_compound_t with precomputed sequence encoding and model details |
| struc1 | The start structure in dot-brakcet notation |
| struc2 | The target structure in dot-bracket notation |
| max | A number specifying how many strutures are being kept at each step during the search |
| vrna_path_t* vrna_path_findpath | ( | vrna_fold_compound_t * | vc, |
| const char * | s1, | ||
| const char * | s2, | ||
| int | maxkeep | ||
| ) |
#include <ViennaRNA/findpath.h>
Find refolding path between 2 structures (search only direct path)
This function uses an inplementation of the findpath algorithm [5] for near-optimal direct refolding path prediction.
Model details, and energy parameters are used as provided via the parameter 'vc'. The vrna_fold_compound_t does not require memory for any DP matrices, but requires all most basic init values as one would get from a call like this:
| vc | The vrna_fold_compound_t with precomputed sequence encoding and model details |
| s1 | The start structure in dot-brakcet notation |
| s2 | The target structure in dot-bracket notation |
| maxkeep | A number specifying how many strutures are being kept at each step during the search |
| int find_saddle | ( | const char * | seq, |
| const char * | struc1, | ||
| const char * | struc2, | ||
| int | max | ||
| ) |
#include <ViennaRNA/findpath.h>
Find energy of a saddle point between 2 structures (search only direct path)
| seq | RNA sequence |
| struc1 | A pointer to the character array where the first secondary structure in dot-bracket notation will be written to |
| struc2 | A pointer to the character array where the second secondary structure in dot-bracket notation will be written to |
| max | integer how many strutures are being kept during the search |
| void free_path | ( | vrna_path_t * | path | ) |
#include <ViennaRNA/findpath.h>
Free memory allocated by get_path() function.
| path | pointer to memory to be freed |
| vrna_path_t* get_path | ( | const char * | seq, |
| const char * | s1, | ||
| const char * | s2, | ||
| int | maxkeep | ||
| ) |
#include <ViennaRNA/findpath.h>
Find refolding path between 2 structures (search only direct path)
| seq | RNA sequence |
| s1 | A pointer to the character array where the first secondary structure in dot-bracket notation will be written to |
| s2 | A pointer to the character array where the second secondary structure in dot-bracket notation will be written to |
| maxkeep | integer how many strutures are being kept during the search |