RNAlib-2.4.11

Methods to compute the neighbors of an RNA secondary structure. More...

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Data Structures

struct  vrna_move_s
 An atomic representation of the transition / move from one structure to its neighbor. More...
 

Macros

#define VRNA_MOVESET_INSERTION   4
 Option flag indicating insertion move. More...
 
#define VRNA_MOVESET_DELETION   8
 Option flag indicating deletion move. More...
 
#define VRNA_MOVESET_SHIFT   16
 Option flag indicating shift move. More...
 
#define VRNA_MOVESET_NO_LP   32
 Option flag indicating moves without lonely base pairs. More...
 
#define VRNA_MOVESET_DEFAULT   (VRNA_MOVESET_INSERTION | VRNA_MOVESET_DELETION)
 Option flag indicating default move set, i.e. insertions/deletion of a base pair. More...
 

Functions

void vrna_move_list_free (vrna_move_t *moves)
 
void vrna_move_apply (short *pt, const vrna_move_t *m)
 Apply a particular move / transition to a secondary structure, i.e. transform a structure. More...
 
void vrna_loopidx_update (int *loopidx, const short *pt, int length, const vrna_move_t *m)
 Alters the loopIndices array that was constructed with vrna_loopidx_from_ptable(). More...
 
vrna_move_tvrna_neighbors (vrna_fold_compound_t *vc, const short *pt, unsigned int options)
 Generate neighbors of a secondary structure. More...
 
vrna_move_tvrna_neighbors_successive (const vrna_fold_compound_t *vc, const vrna_move_t *curr_move, const short *prev_pt, const vrna_move_t *prev_neighbors, int size_prev_neighbors, int *size_neighbors, unsigned int options)
 Generate neighbors of a secondary structure (the fast way) More...
 

Detailed Description

Methods to compute the neighbors of an RNA secondary structure.