RNAlib-2.3.1
eval.h
Go to the documentation of this file.
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 
123  const char *structure,
124  FILE *file);
125 
152  const char *structure,
153  int verbosity_level,
154  FILE *file);
155 
170 float vrna_eval_structure_simple_verbose( const char *string,
171  const char *structure,
172  FILE *file);
173 
174 
198 float vrna_eval_structure_simple_v( const char *string,
199  const char *structure,
200  int verbosity_level,
201  FILE *file);
202 
203 
223  const short *pt);
224 
239 int vrna_eval_structure_pt_simple(const char *string,
240  const short *pt);
241 
256  const short *pt,
257  FILE *file);
258 
285  const short *pt,
286  int verbosity_level,
287  FILE *file);
288 
302 int vrna_eval_structure_pt_simple_verbose(const char *string,
303  const short *pt,
304  FILE *file);
305 
330 int vrna_eval_structure_pt_simple_v(const char *string,
331  const short *pt,
332  int verbosity_level,
333  FILE *file);
334 
344  int i,
345  const short *pt);
346 
361  const char *structure,
362  int m1,
363  int m2);
364 
380  short *pt,
381  int m1,
382  int m2);
383 
384 int vrna_eval_move_pt_simple( const char *string,
385  short *pt,
386  int m1,
387  int m2);
388 
389 #ifdef VRNA_BACKWARD_COMPAT
390 
409 DEPRECATED(float energy_of_structure(const char *string,
410  const char *structure,
411  int verbosity_level));
412 
428 DEPRECATED(float energy_of_struct_par( const char *string,
429  const char *structure,
430  vrna_param_t *parameters,
431  int verbosity_level));
432 
451 DEPRECATED(float energy_of_circ_structure( const char *string,
452  const char *structure,
453  int verbosity_level));
454 
470 DEPRECATED(float energy_of_circ_struct_par(const char *string,
471  const char *structure,
472  vrna_param_t *parameters,
473  int verbosity_level));
474 
475 
476 DEPRECATED(float energy_of_gquad_structure(const char *string,
477  const char *structure,
478  int verbosity_level));
479 
480 DEPRECATED(float energy_of_gquad_struct_par( const char *string,
481  const char *structure,
482  vrna_param_t *parameters,
483  int verbosity_level));
484 
485 
506 DEPRECATED(int energy_of_structure_pt( const char *string,
507  short *ptable,
508  short *s,
509  short *s1,
510  int verbosity_level));
511 
529 DEPRECATED(int energy_of_struct_pt_par(const char *string,
530  short *ptable,
531  short *s,
532  short *s1,
533  vrna_param_t *parameters,
534  int verbosity_level));
535 
536 
537 
554 DEPRECATED(float energy_of_move( const char *string,
555  const char *structure,
556  int m1,
557  int m2));
558 
559 
578 DEPRECATED(int energy_of_move_pt(short *pt,
579  short *s,
580  short *s1,
581  int m1,
582  int m2));
583 
597 DEPRECATED(int loop_energy(short *ptable,
598  short *s,
599  short *s1,
600  int i));
601 
616 DEPRECATED(float energy_of_struct(const char *string,
617  const char *structure));
618 
635 DEPRECATED(int energy_of_struct_pt( const char *string,
636  short *ptable,
637  short *s,
638  short *s1));
639 
654 DEPRECATED(float energy_of_circ_struct( const char *string,
655  const char *structure));
656 
657 #endif
658 
663 #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 vrna_eval_structure_simple_v(const char *string, const char *structure, int verbosity_level, FILE *file)
Calculate the free energy of an already folded RNA and print contributions per loop.
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:454
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_v(const char *string, const short *pt, int verbosity_level, FILE *file)
Calculate the free energy of an already folded RNA.
int vrna_eval_structure_pt_v(vrna_fold_compound_t *vc, const short *pt, int verbosity_level, 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)
float vrna_eval_structure_v(vrna_fold_compound_t *vc, const char *structure, int verbosity_level, FILE *file)
Calculate the free energy of an already folded RNA and print contributions on a per-loop base...