RNAlib-2.2.9
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 
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 
124  const char *structure,
125  FILE *file);
126 
153  const char *structure,
154  int verbosity_level,
155  FILE *file);
156 
171 float vrna_eval_structure_simple_verbose( const char *string,
172  const char *structure,
173  FILE *file);
174 
175 
199 float vrna_eval_structure_simple_v( const char *string,
200  const char *structure,
201  int verbosity_level,
202  FILE *file);
203 
204 
224  const short *pt);
225 
240 int vrna_eval_structure_pt_simple(const char *string,
241  const short *pt);
242 
257  const short *pt,
258  FILE *file);
259 
286  const short *pt,
287  int verbosity_level,
288  FILE *file);
289 
303 int vrna_eval_structure_pt_simple_verbose(const char *string,
304  const short *pt,
305  FILE *file);
306 
331 int vrna_eval_structure_pt_simple_v(const char *string,
332  const short *pt,
333  int verbosity_level,
334  FILE *file);
335 
345  int i,
346  const short *pt);
347 
362  const char *structure,
363  int m1,
364  int m2);
365 
381  short *pt,
382  int m1,
383  int m2);
384 
385 int vrna_eval_move_pt_simple( const char *string,
386  short *pt,
387  int m1,
388  int m2);
389 
390 #ifdef VRNA_BACKWARD_COMPAT
391 
410 DEPRECATED(float energy_of_structure(const char *string,
411  const char *structure,
412  int verbosity_level));
413 
429 DEPRECATED(float energy_of_struct_par( const char *string,
430  const char *structure,
431  vrna_param_t *parameters,
432  int verbosity_level));
433 
452 DEPRECATED(float energy_of_circ_structure( const char *string,
453  const char *structure,
454  int verbosity_level));
455 
471 DEPRECATED(float energy_of_circ_struct_par(const char *string,
472  const char *structure,
473  vrna_param_t *parameters,
474  int verbosity_level));
475 
476 
477 DEPRECATED(float energy_of_gquad_structure(const char *string,
478  const char *structure,
479  int verbosity_level));
480 
481 DEPRECATED(float energy_of_gquad_struct_par( const char *string,
482  const char *structure,
483  vrna_param_t *parameters,
484  int verbosity_level));
485 
486 
507 DEPRECATED(int energy_of_structure_pt( const char *string,
508  short *ptable,
509  short *s,
510  short *s1,
511  int verbosity_level));
512 
530 DEPRECATED(int energy_of_struct_pt_par(const char *string,
531  short *ptable,
532  short *s,
533  short *s1,
534  vrna_param_t *parameters,
535  int verbosity_level));
536 
537 
538 
555 DEPRECATED(float energy_of_move( const char *string,
556  const char *structure,
557  int m1,
558  int m2));
559 
560 
579 DEPRECATED(int energy_of_move_pt(short *pt,
580  short *s,
581  short *s1,
582  int m1,
583  int m2));
584 
598 DEPRECATED(int loop_energy(short *ptable,
599  short *s,
600  short *s1,
601  int i));
602 
617 DEPRECATED(float energy_of_struct(const char *string,
618  const char *structure));
619 
636 DEPRECATED(int energy_of_struct_pt( const char *string,
637  short *ptable,
638  short *s,
639  short *s1));
640 
655 DEPRECATED(float energy_of_circ_struct( const char *string,
656  const char *structure));
657 
658 #endif
659 
664 #endif
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 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...
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.
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.
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 cut_point
set to first pos of second seq for cofolding
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:424
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.
int loop_energy(short *ptable, short *s, short *s1, int i)
Calculate energy of a loop.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
int eos_debug
verbose info from energy_of_struct
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.
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...
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.
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_struct(const char *string, const char *structure)
float vrna_eval_structure(vrna_fold_compound_t *vc, const char *structure)
Calculate the free energy of an already folded RNA.
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.
int vrna_eval_structure_pt_simple(const char *string, const short *pt)
Calculate the free energy of an already folded RNA.
int vrna_eval_loop_pt(vrna_fold_compound_t *vc, int i, const short *pt)
Calculate energy of a loop.
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)
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)
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.
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.
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)
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.
float energy_of_circ_structure(const char *string, const char *structure, int verbosity_level)
Calculate the free energy of an already folded circular RNA.
int vrna_eval_structure_pt(vrna_fold_compound_t *vc, const short *pt)
Calculate the free energy of an already folded RNA.
int vrna_eval_structure_pt_simple_verbose(const char *string, const short *pt, FILE *file)
Calculate the free energy of an already folded RNA.
float energy_of_circ_struct(const char *string, const char *structure)
int energy_of_struct_pt(const char *string, short *ptable, short *s, short *s1)