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part_func.h
Go to the documentation of this file.
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