RNAlib-2.2.5
eval.h
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1 #ifndef VIENNA_RNA_PACKAGE_EVAL_H
2 #define VIENNA_RNA_PACKAGE_EVAL_H
3 
4 #include <stdio.h>
6 #include <ViennaRNA/params.h> /* for deprecated functions */
7 
8 #ifdef DEPRECATION_WARNINGS
9 # ifdef __GNUC__
10 # define DEPRECATED(func) func __attribute__ ((deprecated))
11 # else
12 # define DEPRECATED(func) func
13 # endif
14 #else
15 # define DEPRECATED(func) func
16 #endif
17 
18 /* make this interface backward compatible with RNAlib < 2.2.0 */
19 #define VRNA_BACKWARD_COMPAT
20 
37 extern int cut_point;
38 
42 extern int eos_debug;
43 
66  const char *structure);
67 
89  const char *structure);
90 
106 float vrna_eval_structure_simple( const char *string,
107  const char *structure);
108 
131  const char *structure,
132  FILE *file);
133 
153 float vrna_eval_structure_simple_verbose( const char *string,
154  const char *structure,
155  FILE *file);
156 
157 
177  const short *pt);
178 
193 int vrna_eval_structure_pt_simple(const char *string,
194  const short *pt);
195 
219  const short *pt,
220  FILE *file);
221 
245 int vrna_eval_structure_pt_simple_verbose(const char *string,
246  const short *pt,
247  FILE *file);
248 
258  int i,
259  const short *pt);
260 
275  const char *structure,
276  int m1,
277  int m2);
278 
294  short *pt,
295  int m1,
296  int m2);
297 
298 int vrna_eval_move_pt_simple( const char *string,
299  short *pt,
300  int m1,
301  int m2);
302 
303 #ifdef VRNA_BACKWARD_COMPAT
304 
323 DEPRECATED(float energy_of_structure(const char *string,
324  const char *structure,
325  int verbosity_level));
326 
342 DEPRECATED(float energy_of_struct_par( const char *string,
343  const char *structure,
344  vrna_param_t *parameters,
345  int verbosity_level));
346 
365 DEPRECATED(float energy_of_circ_structure( const char *string,
366  const char *structure,
367  int verbosity_level));
368 
384 DEPRECATED(float energy_of_circ_struct_par(const char *string,
385  const char *structure,
386  vrna_param_t *parameters,
387  int verbosity_level));
388 
389 
390 DEPRECATED(float energy_of_gquad_structure(const char *string,
391  const char *structure,
392  int verbosity_level));
393 
394 DEPRECATED(float energy_of_gquad_struct_par( const char *string,
395  const char *structure,
396  vrna_param_t *parameters,
397  int verbosity_level));
398 
399 
420 DEPRECATED(int energy_of_structure_pt( const char *string,
421  short *ptable,
422  short *s,
423  short *s1,
424  int verbosity_level));
425 
443 DEPRECATED(int energy_of_struct_pt_par(const char *string,
444  short *ptable,
445  short *s,
446  short *s1,
447  vrna_param_t *parameters,
448  int verbosity_level));
449 
450 
451 
468 DEPRECATED(float energy_of_move( const char *string,
469  const char *structure,
470  int m1,
471  int m2));
472 
473 
492 DEPRECATED(int energy_of_move_pt(short *pt,
493  short *s,
494  short *s1,
495  int m1,
496  int m2));
497 
511 DEPRECATED(int loop_energy(short *ptable,
512  short *s,
513  short *s1,
514  int i));
515 
530 DEPRECATED(float energy_of_struct(const char *string,
531  const char *structure));
532 
549 DEPRECATED(int energy_of_struct_pt( const char *string,
550  short *ptable,
551  short *s,
552  short *s1));
553 
568 DEPRECATED(float energy_of_circ_struct( const char *string,
569  const char *structure));
570 
571 #endif
572 
577 #endif
int energy_of_struct_pt_par(const char *string, short *ptable, short *s, short *s1, vrna_param_t *parameters, int verbosity_level)
Calculate the free energy of an already folded RNA.
float vrna_eval_structure(vrna_fold_compound_t *vc, const char *structure)
Calculate the free energy of an already folded RNA.
float energy_of_circ_struct_par(const char *string, const char *structure, vrna_param_t *parameters, int verbosity_level)
Calculate the free energy of an already folded circular RNA.
float energy_of_struct(const char *string, const char *structure)
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:397
int vrna_eval_structure_pt_verbose(vrna_fold_compound_t *vc, const short *pt, FILE *file)
Calculate the free energy of an already folded RNA.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:55
int cut_point
set to first pos of second seq for cofolding
float vrna_eval_move(vrna_fold_compound_t *vc, const char *structure, int m1, int m2)
Calculate energy of a move (closing or opening of a base pair)
float energy_of_circ_structure(const char *string, const char *structure, int verbosity_level)
Calculate the free energy of an already folded circular RNA.
float vrna_eval_structure_simple_verbose(const char *string, const char *structure, FILE *file)
Calculate the free energy of an already folded RNA and print contributions per loop.
int vrna_eval_move_pt(vrna_fold_compound_t *vc, short *pt, int m1, int m2)
Calculate energy of a move (closing or opening of a base pair)
float vrna_eval_covar_structure(vrna_fold_compound_t *vc, const char *structure)
Calculate the pseudo energy derived by the covariance scores of a set of aligned sequences.
int energy_of_structure_pt(const char *string, short *ptable, short *s, short *s1, int verbosity_level)
Calculate the free energy of an already folded RNA.
Various data structures and pre-processor macros.
float energy_of_structure(const char *string, const char *structure, int verbosity_level)
Calculate the free energy of an already folded RNA using global model detail settings.
Functions to deal with sets of energy parameters.
float vrna_eval_structure_simple(const char *string, const char *structure)
Calculate the free energy of an already folded RNA.
float energy_of_circ_struct(const char *string, const char *structure)
int vrna_eval_loop_pt(vrna_fold_compound_t *vc, int i, const short *pt)
Calculate energy of a loop.
int energy_of_move_pt(short *pt, short *s, short *s1, int m1, int m2)
Calculate energy of a move (closing or opening of a base pair)
int vrna_eval_structure_pt_simple_verbose(const char *string, const short *pt, FILE *file)
Calculate the free energy of an already folded RNA.
int vrna_eval_structure_pt_simple(const char *string, const short *pt)
Calculate the free energy of an already folded RNA.
float vrna_eval_structure_verbose(vrna_fold_compound_t *vc, const char *structure, FILE *file)
Calculate the free energy of an already folded RNA and print contributions on a per-loop base...
int eos_debug
verbose info from energy_of_struct
float energy_of_move(const char *string, const char *structure, int m1, int m2)
Calculate energy of a move (closing or opening of a base pair)
int loop_energy(short *ptable, short *s, short *s1, int i)
Calculate energy of a loop.
int vrna_eval_structure_pt(vrna_fold_compound_t *vc, const short *pt)
Calculate the free energy of an already folded RNA.
float energy_of_struct_par(const char *string, const char *structure, vrna_param_t *parameters, int verbosity_level)
Calculate the free energy of an already folded RNA.
int energy_of_struct_pt(const char *string, short *ptable, short *s, short *s1)