RNAlib-2.1.4
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 
41 extern int st_back;
42 
43 /*
44 #################################################
45 # PARTITION FUNCTION COMPUTATION #
46 #################################################
47 */
48 
87 float pf_fold_par( const char *sequence,
88  char *structure,
89  pf_paramT *parameters,
90  int calculate_bppm,
91  int is_constrained,
92  int is_circular);
93 
133 float pf_fold(const char *sequence,
134  char *structure);
135 
161 float pf_circ_fold( const char *sequence,
162  char *structure);
163 
173 char *pbacktrack(char *sequence);
174 
186 char *pbacktrack_circ(char *sequence);
187 
203 void free_pf_arrays(void);
204 
214 void update_pf_params(int length);
215 
222 void update_pf_params_par(int length, pf_paramT *parameters);
223 
240 FLT_OR_DBL *export_bppm(void);
241 
242 /*
243 #################################################
244 # OTHER PARTITION FUNCTION RELATED DECLARATIONS #
245 #################################################
246 */
247 
265 void assign_plist_from_pr( plist **pl,
266  FLT_OR_DBL *probs,
267  int length,
268  double cutoff);
269 
270 /* this doesn't work if free_pf_arrays() is called before */
271 void assign_plist_gquad_from_pr(plist **pl,
272  int length,
273  double cut_off);
274 
275 char *get_centroid_struct_gquad_pr(int length,
276  double *dist);
277 
293 int get_pf_arrays(short **S_p,
294  short **S1_p,
295  char **ptype_p,
296  FLT_OR_DBL **qb_p,
297  FLT_OR_DBL **qm_p,
298  FLT_OR_DBL **q1k_p,
299  FLT_OR_DBL **qln_p);
300 
304 double get_subseq_F(int i, int j);
305 
322 char *get_centroid_struct_pl(int length,
323  double *dist,
324  plist *pl);
325 
342 char *get_centroid_struct_pr(int length,
343  double *dist,
344  FLT_OR_DBL *pr);
345 
358 double mean_bp_distance(int length);
359 
377 double mean_bp_distance_pr(int length,
378  FLT_OR_DBL *pr);
379 
383 void bppm_to_structure(char *structure,
384  FLT_OR_DBL *pr,
385  unsigned int length);
386 
387 plist *stackProb(double cutoff);
388 
392 char bppm_symbol(const float *x);
393 
394 
395 /*
396 #################################################
397 # DEPRECATED FUNCTIONS #
398 #################################################
399 */
400 
406 DEPRECATED(void init_pf_fold(int length));
407 
412 DEPRECATED(char *centroid(int length,
413  double *dist)); /* mean pair distance of ensemble */
414 
420 DEPRECATED(double mean_bp_dist(int length));
421 
425 DEPRECATED(double expLoopEnergy(int u1,
426  int u2,
427  int type,
428  int type2,
429  short si1,
430  short sj1,
431  short sp1,
432  short sq1));
433 
437 DEPRECATED(double expHairpinEnergy( int u,
438  int type,
439  short si1,
440  short sj1,
441  const char *string));
442 
443 #endif