RNAlib-2.4.0
neighbor.h
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1 #ifndef VIENNA_RNA_PACKAGE_NEIGHBOR_H
2 #define VIENNA_RNA_PACKAGE_NEIGHBOR_H
3 
111 typedef struct vrna_move_s vrna_move_t;
112 
114 
119 #define VRNA_MOVESET_INSERTION 4
120 
125 #define VRNA_MOVESET_DELETION 8
126 
131 #define VRNA_MOVESET_SHIFT 16
132 
137 #define VRNA_MOVESET_DEFAULT (VRNA_MOVESET_INSERTION | VRNA_MOVESET_DELETION)
138 
139 
151 struct vrna_move_s {
152  int pos_5;
153  int pos_3;
154 };
155 
162 void
163 vrna_move_apply(short *pt,
164  const vrna_move_t *m);
165 
166 
167 void
168 vrna_move_apply_to_db(char *structure,
169  const short *pt,
170  const vrna_move_t *m);
171 
172 
184 void
185 vrna_loopidx_update(int *loopidx,
186  const short *pt,
187  int length,
188  const vrna_move_t *m);
189 
190 
206 vrna_move_t *
208  const short *pt,
209  unsigned int options);
210 
211 
233 vrna_move_t *
235  const vrna_move_t *curr_move,
236  const short *prev_pt,
237  const vrna_move_t *prev_neighbors,
238  int size_prev_neighbors,
239  int *size_neighbors,
240  unsigned int options);
241 
242 
246 #endif /* VIENNA_RNA_PACKAGE_NEIGHBOR_H */
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().
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:463
int pos_5
Definition: neighbor.h:152
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.
Various data structures and pre-processor macros.
vrna_move_t * vrna_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)
vrna_move_t * vrna_neighbors(vrna_fold_compound_t *vc, const short *pt, unsigned int options)
Generate neighbors of a secondary structure.
An atomic representation of the transition / move from one structure to its neighbor.
Definition: neighbor.h:151
int pos_3
Definition: neighbor.h:153