RNAlib-2.1.1
fold.h
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1 #ifndef __VIENNA_RNA_PACKAGE_FOLD_H__
2 #define __VIENNA_RNA_PACKAGE_FOLD_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 
61 extern int logML;
62 
64 extern int uniq_ML;
65 
67 extern int cut_point;
68 
73 extern int eos_debug;
74 
75 
119 float fold_par( const char *sequence,
120  char *structure,
121  paramT *parameters,
122  int is_constrained,
123  int is_circular);
124 
143 float fold( const char *sequence,
144  char *structure);
145 
164 float circfold( const char *sequence,
165  char *structure);
166 
167 
195 float energy_of_structure(const char *string,
196  const char *structure,
197  int verbosity_level);
198 
214 float energy_of_struct_par( const char *string,
215  const char *structure,
216  paramT *parameters,
217  int verbosity_level);
218 
237 float energy_of_circ_structure( const char *string,
238  const char *structure,
239  int verbosity_level);
240 
256 float energy_of_circ_struct_par(const char *string,
257  const char *structure,
258  paramT *parameters,
259  int verbosity_level);
260 
261 
262 float energy_of_gquad_structure(const char *string,
263  const char *structure,
264  int verbosity_level);
265 
286 int energy_of_structure_pt( const char *string,
287  short *ptable,
288  short *s,
289  short *s1,
290  int verbosity_level);
291 
309 int energy_of_struct_pt_par(const char *string,
310  short *ptable,
311  short *s,
312  short *s1,
313  paramT *parameters,
314  int verbosity_level);
315 
322 void free_arrays(void);
323 
324 
330 void parenthesis_structure(char *structure,
331  bondT *bp,
332  int length);
333 
340 void parenthesis_zuker( char *structure,
341  bondT *bp,
342  int length);
343 
344 void letter_structure(char *structure,
345  bondT *bp,
346  int length);
347 
348 
354 void update_fold_params(void);
355 
361 void update_fold_params_par(paramT *parameters);
362 
368 char *backtrack_fold_from_pair(char *sequence,
369  int i,
370  int j);
371 
385 float energy_of_move( const char *string,
386  const char *structure,
387  int m1,
388  int m2);
389 
390 
406 int energy_of_move_pt(short *pt,
407  short *s,
408  short *s1,
409  int m1,
410  int m2);
411 
421 int loop_energy(short *ptable,
422  short *s,
423  short *s1,
424  int i);
425 
431 void export_fold_arrays(int **f5_p,
432  int **c_p,
433  int **fML_p,
434  int **fM1_p,
435  int **indx_p,
436  char **ptype_p);
437 
443 void export_fold_arrays_par(int **f5_p,
444  int **c_p,
445  int **fML_p,
446  int **fM1_p,
447  int **indx_p,
448  char **ptype_p,
449  paramT **P_p);
450 
456 void export_circfold_arrays(int *Fc_p,
457  int *FcH_p,
458  int *FcI_p,
459  int *FcM_p,
460  int **fM2_p,
461  int **f5_p,
462  int **c_p,
463  int **fML_p,
464  int **fM1_p,
465  int **indx_p,
466  char **ptype_p);
467 
473 void export_circfold_arrays_par(int *Fc_p,
474  int *FcH_p,
475  int *FcI_p,
476  int *FcM_p,
477  int **fM2_p,
478  int **f5_p,
479  int **c_p,
480  int **fML_p,
481  int **fM1_p,
482  int **indx_p,
483  char **ptype_p,
484  paramT **P_p);
485 
486 
504 void assign_plist_from_db(plist **pl,
505  const char *struc,
506  float pr);
507 
508 /* finally moved the loop energy function declarations to this header... */
509 /* BUT: The functions only exist for backward compatibility reasons! */
510 /* You better include "loop_energies.h" and call the functions: */
511 /* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get */
512 /* a pointer to the energy parameter datastructure as additional argument */
513 
518 DEPRECATED(int LoopEnergy(int n1,
519  int n2,
520  int type,
521  int type_2,
522  int si1,
523  int sj1,
524  int sp1,
525  int sq1));
526 
531 DEPRECATED(int HairpinE(int size,
532  int type,
533  int si1,
534  int sj1,
535  const char *string));
536 
542 DEPRECATED(void initialize_fold(int length));
543 
558 DEPRECATED(float energy_of_struct(const char *string,
559  const char *structure));
560 
577 DEPRECATED(int energy_of_struct_pt( const char *string,
578  short *ptable,
579  short *s,
580  short *s1));
581 
596 DEPRECATED(float energy_of_circ_struct( const char *string,
597  const char *structure));
598 
599 #endif