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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
187 char *pbacktrack_circ(char *sequence);
188
204 void free_pf_arrays(void);
205
215 void update_pf_params(int length);
216
223 void update_pf_params_par(int length, pf_paramT *parameters);
224
241 FLT_OR_DBL *export_bppm(void);
242
243 /*
244 #################################################
245 # OTHER PARTITION FUNCTION RELATED DECLARATIONS #
246 #################################################
247 */
248
266 void assign_plist_from_pr( plist **pl,
267 FLT_OR_DBL *probs,
268 int length,
269 double cutoff);
270
271 /* this doesn't work if free_pf_arrays() is called before */
272 void assign_plist_gquad_from_pr(plist **pl,
273 int length,
274 double cut_off);
275
276 char *get_centroid_struct_gquad_pr(int length,
277 double *dist);
278
294 int get_pf_arrays(short **S_p,
295 short **S1_p,
296 char **ptype_p,
297 FLT_OR_DBL **qb_p,
298 FLT_OR_DBL **qm_p,
299 FLT_OR_DBL **q1k_p,
300 FLT_OR_DBL **qln_p);
301
305 double get_subseq_F(int i, int j);
306
323 char *get_centroid_struct_pl(int length,
324 double *dist,
325 plist *pl);
326
343 char *get_centroid_struct_pr(int length,
344 double *dist,
345 FLT_OR_DBL *pr);
346
359 double mean_bp_distance(int length);
360
378 double mean_bp_distance_pr(int length,
379 FLT_OR_DBL *pr);
380
384 void bppm_to_structure(char *structure,
385 FLT_OR_DBL *pr,
386 unsigned int length);
387
388 plist *stackProb(double cutoff);
389
393 char bppm_symbol(const float *x);
394
395
396 /*
397 #################################################
398 # DEPRECATED FUNCTIONS #
399 #################################################
400 */
401
407 DEPRECATED(void init_pf_fold(int length));
408
413 DEPRECATED(char *centroid(int length,
414 double *dist)); /* mean pair distance of ensemble */
415
421 DEPRECATED(double mean_bp_dist(int length));
422
426 DEPRECATED(double expLoopEnergy(int u1,
427 int u2,
428 int type,
429 int type2,
430 short si1,
431 short sj1,
432 short sp1,
433 short sq1));
434
438 DEPRECATED(double expHairpinEnergy( int u,
439 int type,
440 short si1,
441 short sj1,
442 const char *string));
443
444 #endif