RNAlib-2.2.0RC0
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 
7 #ifdef __GNUC__
8 #define DEPRECATED(func) func __attribute__ ((deprecated))
9 #else
10 #define DEPRECATED(func) func
11 #endif
12 
31 extern int cut_point;
32 
37 extern int eos_debug;
38 
66 float vrna_eval_structure(const char *string,
67  const char *structure,
68  paramT *P);
69 
91 float vrna_eval_structure_verbose(const char *string,
92  const char *structure,
93  paramT *P,
94  FILE *file);
95 
113 int vrna_eval_structure_pt( const char *string,
114  const short *pt,
115  paramT *P);
116 
138 int vrna_eval_structure_pt_verbose( const char *string,
139  const short *pt,
140  paramT *P,
141  FILE *file);
142 
143 int vrna_eval_structure_pt_fast(const char *string,
144  const short *pt,
145  const short *s,
146  const short *s1,
147  paramT *parameters);
148 
159 int vrna_eval_loop_pt(const short *pt,
160  const short *s,
161  const short *s1,
162  int i,
163  paramT *P);
164 
183 float vrna_eval_move( const char *string,
184  const char *structure,
185  int m1,
186  int m2,
187  paramT *P);
188 
209 int vrna_eval_move_pt(short *pt,
210  const short *s,
211  const short *s1,
212  int m1,
213  int m2,
214  paramT *P);
215 
235 DEPRECATED(float energy_of_structure(const char *string,
236  const char *structure,
237  int verbosity_level));
238 
255 DEPRECATED(float energy_of_struct_par( const char *string,
256  const char *structure,
257  paramT *parameters,
258  int verbosity_level));
259 
280 DEPRECATED(float energy_of_circ_structure( const char *string,
281  const char *structure,
282  int verbosity_level));
283 
301 DEPRECATED(float energy_of_circ_struct_par(const char *string,
302  const char *structure,
303  paramT *parameters,
304  int verbosity_level));
305 
306 
307 DEPRECATED(float energy_of_gquad_structure(const char *string,
308  const char *structure,
309  int verbosity_level));
310 
311 DEPRECATED(float energy_of_gquad_struct_par( const char *string,
312  const char *structure,
313  paramT *parameters,
314  int verbosity_level));
315 
316 
339 DEPRECATED(int energy_of_structure_pt( const char *string,
340  short *ptable,
341  short *s,
342  short *s1,
343  int verbosity_level));
344 
364 DEPRECATED(int energy_of_struct_pt_par(const char *string,
365  short *ptable,
366  short *s,
367  short *s1,
368  paramT *parameters,
369  int verbosity_level));
370 
371 
372 
389 DEPRECATED(float energy_of_move( const char *string,
390  const char *structure,
391  int m1,
392  int m2));
393 
394 
413 DEPRECATED(int energy_of_move_pt(short *pt,
414  short *s,
415  short *s1,
416  int m1,
417  int m2));
418 
432 DEPRECATED(int loop_energy(short *ptable,
433  short *s,
434  short *s1,
435  int i));
436 
451 DEPRECATED(float energy_of_struct(const char *string,
452  const char *structure));
453 
470 DEPRECATED(int energy_of_struct_pt( const char *string,
471  short *ptable,
472  short *s,
473  short *s1));
474 
489 DEPRECATED(float energy_of_circ_struct( const char *string,
490  const char *structure));
491 
492 #endif
int vrna_eval_structure_pt(const char *string, const short *pt, paramT *P)
Calculate the free energy of an already folded RNA.
int vrna_eval_structure_pt_verbose(const char *string, const short *pt, paramT *P, FILE *file)
Calculate the free energy of an already folded RNA.
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
float vrna_eval_move(const char *string, const char *structure, int m1, int m2, paramT *P)
Calculate energy of a move (closing or opening of a base pair)
float energy_of_struct_par(const char *string, const char *structure, paramT *parameters, int verbosity_level)
Calculate the free energy of an already folded RNA.
float vrna_eval_structure(const char *string, const char *structure, paramT *P)
Calculate the free energy of an already folded RNA.
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: data_structures.h:180
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 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.
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
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.
int vrna_eval_move_pt(short *pt, const short *s, const short *s1, int m1, int m2, paramT *P)
Calculate energy of a move (closing or opening of a base pair)
float energy_of_struct(const char *string, const char *structure)
int eos_debug
verbose info from energy_of_struct
int energy_of_struct_pt_par(const char *string, short *ptable, short *s, short *s1, paramT *parameters, int verbosity_level)
Calculate the free energy of an already folded RNA.
int vrna_eval_loop_pt(const short *pt, const short *s, const short *s1, int i, paramT *P)
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)
float vrna_eval_structure_verbose(const char *string, const char *structure, paramT *P, 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, paramT *parameters, int verbosity_level)
Calculate the free energy of an already folded circular 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)