RNAlib-2.2.7
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 
38 extern int cut_point;
39 
43 extern int eos_debug;
44 
67  const char *structure);
68 
90  const char *structure);
91 
107 float vrna_eval_structure_simple( const char *string,
108  const char *structure);
109 
132  const char *structure,
133  FILE *file);
134 
154 float vrna_eval_structure_simple_verbose( const char *string,
155  const char *structure,
156  FILE *file);
157 
158 
178  const short *pt);
179 
194 int vrna_eval_structure_pt_simple(const char *string,
195  const short *pt);
196 
220  const short *pt,
221  FILE *file);
222 
246 int vrna_eval_structure_pt_simple_verbose(const char *string,
247  const short *pt,
248  FILE *file);
249 
259  int i,
260  const short *pt);
261 
276  const char *structure,
277  int m1,
278  int m2);
279 
295  short *pt,
296  int m1,
297  int m2);
298 
299 int vrna_eval_move_pt_simple( const char *string,
300  short *pt,
301  int m1,
302  int m2);
303 
304 #ifdef VRNA_BACKWARD_COMPAT
305 
324 DEPRECATED(float energy_of_structure(const char *string,
325  const char *structure,
326  int verbosity_level));
327 
343 DEPRECATED(float energy_of_struct_par( const char *string,
344  const char *structure,
345  vrna_param_t *parameters,
346  int verbosity_level));
347 
366 DEPRECATED(float energy_of_circ_structure( const char *string,
367  const char *structure,
368  int verbosity_level));
369 
385 DEPRECATED(float energy_of_circ_struct_par(const char *string,
386  const char *structure,
387  vrna_param_t *parameters,
388  int verbosity_level));
389 
390 
391 DEPRECATED(float energy_of_gquad_structure(const char *string,
392  const char *structure,
393  int verbosity_level));
394 
395 DEPRECATED(float energy_of_gquad_struct_par( const char *string,
396  const char *structure,
397  vrna_param_t *parameters,
398  int verbosity_level));
399 
400 
421 DEPRECATED(int energy_of_structure_pt( const char *string,
422  short *ptable,
423  short *s,
424  short *s1,
425  int verbosity_level));
426 
444 DEPRECATED(int energy_of_struct_pt_par(const char *string,
445  short *ptable,
446  short *s,
447  short *s1,
448  vrna_param_t *parameters,
449  int verbosity_level));
450 
451 
452 
469 DEPRECATED(float energy_of_move( const char *string,
470  const char *structure,
471  int m1,
472  int m2));
473 
474 
493 DEPRECATED(int energy_of_move_pt(short *pt,
494  short *s,
495  short *s1,
496  int m1,
497  int m2));
498 
512 DEPRECATED(int loop_energy(short *ptable,
513  short *s,
514  short *s1,
515  int i));
516 
531 DEPRECATED(float energy_of_struct(const char *string,
532  const char *structure));
533 
550 DEPRECATED(int energy_of_struct_pt( const char *string,
551  short *ptable,
552  short *s,
553  short *s1));
554 
569 DEPRECATED(float energy_of_circ_struct( const char *string,
570  const char *structure));
571 
572 #endif
573 
578 #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:390
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:50
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.
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.
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)