RNAlib-2.1.1
part_func.h
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1 #ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_H__
2 #define __VIENNA_RNA_PACKAGE_PART_FUNC_H__
3 
4 #include "data_structures.h"
5 
6 #ifdef __GNUC__
7 #define DEPRECATED(func) func __attribute__ ((deprecated))
8 #else
9 #define DEPRECATED(func) func
10 #endif
11 
12 
34 extern int st_back;
35 
36 /*
37 #################################################
38 # PARTITION FUNCTION COMPUTATION #
39 #################################################
40 */
41 
80 float pf_fold_par( const char *sequence,
81  char *structure,
82  pf_paramT *parameters,
83  int calculate_bppm,
84  int is_constrained,
85  int is_circular);
86 
126 float pf_fold(const char *sequence,
127  char *structure);
128 
154 float pf_circ_fold( const char *sequence,
155  char *structure);
156 
166 char *pbacktrack(char *sequence);
167 
179 char *pbacktrack_circ(char *sequence);
180 
196 void free_pf_arrays(void);
197 
207 void update_pf_params(int length);
208 
215 void update_pf_params_par(int length, pf_paramT *parameters);
216 
233 FLT_OR_DBL *export_bppm(void);
234 
235 /*
236 #################################################
237 # OTHER PARTITION FUNCTION RELATED DECLARATIONS #
238 #################################################
239 */
240 
258 void assign_plist_from_pr( plist **pl,
259  FLT_OR_DBL *probs,
260  int length,
261  double cutoff);
262 
263 /* this doesn't work if free_pf_arrays() is called before */
264 void assign_plist_gquad_from_pr(plist **pl,
265  int length,
266  double cut_off);
267 
268 char *get_centroid_struct_gquad_pr(int length,
269  double *dist);
270 
286 int get_pf_arrays(short **S_p,
287  short **S1_p,
288  char **ptype_p,
289  FLT_OR_DBL **qb_p,
290  FLT_OR_DBL **qm_p,
291  FLT_OR_DBL **q1k_p,
292  FLT_OR_DBL **qln_p);
293 
297 double get_subseq_F(int i, int j);
298 
315 char *get_centroid_struct_pl(int length,
316  double *dist,
317  plist *pl);
318 
335 char *get_centroid_struct_pr(int length,
336  double *dist,
337  FLT_OR_DBL *pr);
338 
351 double mean_bp_distance(int length);
352 
370 double mean_bp_distance_pr(int length,
371  FLT_OR_DBL *pr);
372 
376 void bppm_to_structure(char *structure,
377  FLT_OR_DBL *pr,
378  unsigned int length);
379 
380 plist *stackProb(double cutoff);
381 
385 char bppm_symbol(const float *x);
386 
387 
388 /*
389 #################################################
390 # DEPRECATED FUNCTIONS #
391 #################################################
392 */
393 
399 DEPRECATED(void init_pf_fold(int length));
400 
405 DEPRECATED(char *centroid(int length,
406  double *dist)); /* mean pair distance of ensemble */
407 
413 DEPRECATED(double mean_bp_dist(int length));
414 
418 DEPRECATED(double expLoopEnergy(int u1,
419  int u2,
420  int type,
421  int type2,
422  short si1,
423  short sj1,
424  short sp1,
425  short sq1));
426 
430 DEPRECATED(double expHairpinEnergy( int u,
431  int type,
432  short si1,
433  short sj1,
434  const char *string));
435 
436 #endif