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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>
5 #include <ViennaRNA/data_structures.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
66 float vrna_eval_structure(vrna_fold_compound_t *vc,
67 const char *structure);
68
89 float vrna_eval_covar_structure(vrna_fold_compound_t *vc,
90 const char *structure);
91
107 float vrna_eval_structure_simple( const char *string,
108 const char *structure);
109
123 float vrna_eval_structure_verbose(vrna_fold_compound_t *vc,
124 const char *structure,
125 FILE *file);
126
152 float vrna_eval_structure_v(vrna_fold_compound_t *vc,
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
223 int vrna_eval_structure_pt( vrna_fold_compound_t *vc,
224 const short *pt);
225
240 int vrna_eval_structure_pt_simple(const char *string,
241 const short *pt);
242
256 int vrna_eval_structure_pt_verbose( vrna_fold_compound_t *vc,
257 const short *pt,
258 FILE *file);
259
285 int vrna_eval_structure_pt_v( vrna_fold_compound_t *vc,
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
344 int vrna_eval_loop_pt(vrna_fold_compound_t *vc,
345 int i,
346 const short *pt);
347
361 float vrna_eval_move( vrna_fold_compound_t *vc,
362 const char *structure,
363 int m1,
364 int m2);
365
380 int vrna_eval_move_pt(vrna_fold_compound_t *vc,
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
energy_of_circ_struct_par
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.
vrna_eval_structure_verbose
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...
energy_of_struct_par
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.
vrna_eval_structure_simple_verbose
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.
energy_of_move
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)
cut_point
int cut_point
set to first pos of second seq for cofolding
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:424
vrna_eval_structure_simple_v
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.
loop_energy
int loop_energy(short *ptable, short *s, short *s1, int i)
Calculate energy of a loop.
vrna_param_s
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
eos_debug
int eos_debug
verbose info from energy_of_struct
vrna_eval_structure_pt_simple_v
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.
vrna_eval_structure_v
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...
vrna_eval_structure_pt_v
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.
energy_of_structure
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.
data_structures.h
vrna_eval_structure_simple
float vrna_eval_structure_simple(const char *string, const char *structure)
Calculate the free energy of an already folded RNA.
energy_of_struct
float energy_of_struct(const char *string, const char *structure)
vrna_eval_structure
float vrna_eval_structure(vrna_fold_compound_t *vc, const char *structure)
Calculate the free energy of an already folded RNA.
params.h
energy_of_structure_pt
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.
vrna_eval_structure_pt_simple
int vrna_eval_structure_pt_simple(const char *string, const short *pt)
Calculate the free energy of an already folded RNA.
vrna_eval_loop_pt
int vrna_eval_loop_pt(vrna_fold_compound_t *vc, int i, const short *pt)
Calculate energy of a loop.
vrna_eval_move
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)
vrna_eval_move_pt
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)
vrna_eval_structure_pt_verbose
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.
energy_of_struct_pt_par
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.
energy_of_move_pt
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)
vrna_eval_covar_structure
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.
energy_of_circ_structure
float energy_of_circ_structure(const char *string, const char *structure, int verbosity_level)
Calculate the free energy of an already folded circular RNA.
vrna_eval_structure_pt
int vrna_eval_structure_pt(vrna_fold_compound_t *vc, const short *pt)
Calculate the free energy of an already folded RNA.
vrna_eval_structure_pt_simple_verbose
int vrna_eval_structure_pt_simple_verbose(const char *string, const short *pt, FILE *file)
Calculate the free energy of an already folded RNA.
energy_of_circ_struct
float energy_of_circ_struct(const char *string, const char *structure)
energy_of_struct_pt
int energy_of_struct_pt(const char *string, short *ptable, short *s, short *s1)