RNAlib-2.2.0-RC3
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 __GNUC__
9 #define DEPRECATED(func) func __attribute__ ((deprecated))
10 #else
11 #define DEPRECATED(func) func
12 #endif
13 
31 extern int cut_point;
32 
36 extern int eos_debug;
37 
60  const char *structure);
61 
83  const char *structure);
84 
100 float vrna_eval_structure_simple( const char *string,
101  const char *structure);
102 
125  const char *structure,
126  FILE *file);
127 
147 float vrna_eval_structure_simple_verbose( const char *string,
148  const char *structure,
149  FILE *file);
150 
151 
171  const short *pt);
172 
187 int vrna_eval_structure_pt_simple(const char *string,
188  const short *pt);
189 
213  const short *pt,
214  FILE *file);
215 
239 int vrna_eval_structure_pt_simple_verbose(const char *string,
240  const short *pt,
241  FILE *file);
242 
252  int i,
253  const short *pt);
254 
269  const char *structure,
270  int m1,
271  int m2);
272 
288  short *pt,
289  int m1,
290  int m2);
291 
292 int vrna_eval_move_pt_simple( const char *string,
293  short *pt,
294  int m1,
295  int m2);
296 
315 DEPRECATED(float energy_of_structure(const char *string,
316  const char *structure,
317  int verbosity_level));
318 
334 DEPRECATED(float energy_of_struct_par( const char *string,
335  const char *structure,
336  vrna_param_t *parameters,
337  int verbosity_level));
338 
357 DEPRECATED(float energy_of_circ_structure( const char *string,
358  const char *structure,
359  int verbosity_level));
360 
376 DEPRECATED(float energy_of_circ_struct_par(const char *string,
377  const char *structure,
378  vrna_param_t *parameters,
379  int verbosity_level));
380 
381 
382 DEPRECATED(float energy_of_gquad_structure(const char *string,
383  const char *structure,
384  int verbosity_level));
385 
386 DEPRECATED(float energy_of_gquad_struct_par( const char *string,
387  const char *structure,
388  vrna_param_t *parameters,
389  int verbosity_level));
390 
391 
412 DEPRECATED(int energy_of_structure_pt( const char *string,
413  short *ptable,
414  short *s,
415  short *s1,
416  int verbosity_level));
417 
435 DEPRECATED(int energy_of_struct_pt_par(const char *string,
436  short *ptable,
437  short *s,
438  short *s1,
439  vrna_param_t *parameters,
440  int verbosity_level));
441 
442 
443 
460 DEPRECATED(float energy_of_move( const char *string,
461  const char *structure,
462  int m1,
463  int m2));
464 
465 
484 DEPRECATED(int energy_of_move_pt(short *pt,
485  short *s,
486  short *s1,
487  int m1,
488  int m2));
489 
503 DEPRECATED(int loop_energy(short *ptable,
504  short *s,
505  short *s1,
506  int i));
507 
522 DEPRECATED(float energy_of_struct(const char *string,
523  const char *structure));
524 
541 DEPRECATED(int energy_of_struct_pt( const char *string,
542  short *ptable,
543  short *s,
544  short *s1));
545 
560 DEPRECATED(float energy_of_circ_struct( const char *string,
561  const char *structure));
562 
567 #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 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)
int vrna_eval_loop_pt(vrna_fold_compound *vc, int i, const short *pt)
Calculate energy of a loop.
int cut_point
set to first pos of second seq for cofolding
int vrna_eval_move_pt(vrna_fold_compound *vc, short *pt, 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_structure_pt_verbose(vrna_fold_compound *vc, const short *pt, FILE *file)
Calculate the free energy of an already folded RNA.
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:698
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 vrna_eval_structure(vrna_fold_compound *vc, const char *structure)
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 vrna_eval_structure_verbose(vrna_fold_compound *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_circ_struct(const char *string, const char *structure)
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.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:41
int eos_debug
verbose info from energy_of_struct
float vrna_eval_move(vrna_fold_compound *vc, const char *structure, int m1, int m2)
Calculate energy of a move (closing or opening of a base pair)
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)
float vrna_eval_covar_structure(vrna_fold_compound *vc, const char *structure)
Calculate the pseudo energy derived by the covariance scores of a set of aligned sequences.
int loop_energy(short *ptable, short *s, short *s1, int i)
Calculate energy of a loop.
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)
int vrna_eval_structure_pt(vrna_fold_compound *vc, const short *pt)
Calculate the free energy of an already folded RNA.