RNAlib-2.4.0
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/neighbor.h"
7 #include <ViennaRNA/params.h> /* for deprecated functions */
8 
9 #ifdef VRNA_WARN_DEPRECATED
10 # ifdef __GNUC__
11 # define DEPRECATED(func) func __attribute__ ((deprecated))
12 # else
13 # define DEPRECATED(func) func
14 # endif
15 #else
16 # define DEPRECATED(func) func
17 #endif
18 
19 /* make this interface backward compatible with RNAlib < 2.2.0 */
20 #define VRNA_BACKWARD_COMPAT
21 
38 extern int cut_point;
39 
43 extern int eos_debug;
44 
67  const char *structure);
68 
69 
91  const char *structure);
92 
93 
109 float vrna_eval_structure_simple(const char *string,
110  const char *structure);
111 
112 
127  const char *structure,
128  FILE *file);
129 
130 
157  const char *structure,
158  int verbosity_level,
159  FILE *file);
160 
161 
176 float vrna_eval_structure_simple_verbose(const char *string,
177  const char *structure,
178  FILE *file);
179 
180 
204 float vrna_eval_structure_simple_v(const char *string,
205  const char *structure,
206  int verbosity_level,
207  FILE *file);
208 
209 
229  const short *pt);
230 
231 
246 int vrna_eval_structure_pt_simple(const char *string,
247  const short *pt);
248 
249 
264  const short *pt,
265  FILE *file);
266 
267 
294  const short *pt,
295  int verbosity_level,
296  FILE *file);
297 
298 
312 int vrna_eval_structure_pt_simple_verbose(const char *string,
313  const short *pt,
314  FILE *file);
315 
316 
341 int vrna_eval_structure_pt_simple_v(const char *string,
342  const short *pt,
343  int verbosity_level,
344  FILE *file);
345 
346 
356  int i,
357  const short *pt);
358 
359 
374  const char *structure,
375  int m1,
376  int m2);
377 
378 
394  short *pt,
395  int m1,
396  int m2);
397 
398 
399 int vrna_eval_move_pt_simple(const char *string,
400  short *pt,
401  int m1,
402  int m2);
403 
404 
405 int
406 vrna_eval_move_shift_pt(vrna_fold_compound_t *vc,
407  vrna_move_t *m,
408  short *structure);
409 
410 
411 #ifdef VRNA_BACKWARD_COMPAT
412 
431 DEPRECATED(float energy_of_structure(const char *string,
432  const char *structure,
433  int verbosity_level));
434 
450 DEPRECATED(float energy_of_struct_par(const char *string,
451  const char *structure,
452  vrna_param_t *parameters,
453  int verbosity_level));
454 
473 DEPRECATED(float energy_of_circ_structure(const char *string,
474  const char *structure,
475  int verbosity_level));
476 
492 DEPRECATED(float energy_of_circ_struct_par(const char *string,
493  const char *structure,
494  vrna_param_t *parameters,
495  int verbosity_level));
496 
497 
498 DEPRECATED(float energy_of_gquad_structure(const char *string,
499  const char *structure,
500  int verbosity_level));
501 
502 DEPRECATED(float energy_of_gquad_struct_par(const char *string,
503  const char *structure,
504  vrna_param_t *parameters,
505  int verbosity_level));
506 
507 
528 DEPRECATED(int energy_of_structure_pt(const char *string,
529  short *ptable,
530  short *s,
531  short *s1,
532  int verbosity_level));
533 
551 DEPRECATED(int energy_of_struct_pt_par(const char *string,
552  short *ptable,
553  short *s,
554  short *s1,
555  vrna_param_t *parameters,
556  int verbosity_level));
557 
558 
575 DEPRECATED(float energy_of_move(const char *string,
576  const char *structure,
577  int m1,
578  int m2));
579 
580 
599 DEPRECATED(int energy_of_move_pt(short *pt,
600  short *s,
601  short *s1,
602  int m1,
603  int m2));
604 
618 DEPRECATED(int loop_energy(short *ptable,
619  short *s,
620  short *s1,
621  int i));
622 
637 DEPRECATED(float energy_of_struct(const char *string,
638  const char *structure));
639 
656 DEPRECATED(int energy_of_struct_pt(const char *string,
657  short *ptable,
658  short *s,
659  short *s1));
660 
675 DEPRECATED(float energy_of_circ_struct(const char *string,
676  const char *structure));
677 
678 #endif
679 
684 #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:463
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:57
int cut_point
set to first pos of second seq for cofolding
Methods to compute the neighbors of an RNA secondary structure.
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...
An atomic representation of the transition / move from one structure to its neighbor.
Definition: neighbor.h:151