1#ifndef VIENNA_RNA_PACKAGE_NEIGHBOR_H
2#define VIENNA_RNA_PACKAGE_NEIGHBOR_H
4#ifdef VRNA_WARN_DEPRECATED
5# if defined(DEPRECATED)
9# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
10# elif defined(__GNUC__)
11# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
13# define DEPRECATED(func, msg) func
16# define DEPRECATED(func, msg) func
148 "Use vrna_move_update_f instead!");
157#define VRNA_NEIGHBOR_CHANGE 1
165#define VRNA_NEIGHBOR_INVALID 2
173#define VRNA_NEIGHBOR_NEW 3
212 unsigned int options);
239 const short *prev_pt,
241 int size_prev_neighbors,
243 unsigned int options);
273 unsigned int options);
297 unsigned int options);
The Basic Fold Compound API.
The most basic data structure required by many functions throughout the RNAlib.
Definition fold_compound.h:168
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().
vrna_move_t * vrna_move_neighbor_diff(vrna_fold_compound_t *fc, short *ptable, vrna_move_t move, vrna_move_t **invalid_moves, unsigned int options)
Apply a move to a secondary structure and indicate which neighbors have changed consequentially.
int vrna_move_neighbor_diff_cb(vrna_fold_compound_t *fc, short *ptable, vrna_move_t move, vrna_move_update_f cb, void *data, unsigned int options)
Apply a move to a secondary structure and indicate which neighbors have changed consequentially.
vrna_move_t * vrna_neighbors(vrna_fold_compound_t *fc, const short *pt, unsigned int options)
Generate neighbors of a secondary structure.
vrna_move_t * vrna_neighbors_successive(const vrna_fold_compound_t *fc, 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)
void(* vrna_move_update_f)(vrna_fold_compound_t *fc, vrna_move_t neighbor, unsigned int state, void *data)
Prototype of the neighborhood update callback.
Definition neighbor.h:139
An atomic representation of the transition / move from one structure to its neighbor.
Definition move.h:78
Methods to operate with structural neighbors of RNA secondary structures.