1 #ifndef VIENNA_RNA_PACKAGE_EVAL_H
2 #define VIENNA_RNA_PACKAGE_EVAL_H
8 #ifdef DEPRECATION_WARNINGS
10 # define DEPRECATED(func) func __attribute__ ((deprecated))
12 # define DEPRECATED(func) func
15 # define DEPRECATED(func) func
19 #define VRNA_BACKWARD_COMPAT
66 const char *structure);
89 const char *structure);
107 const char *structure);
131 const char *structure,
154 const char *structure,
275 const char *structure,
298 int vrna_eval_move_pt_simple(
const char *
string,
303 #ifdef VRNA_BACKWARD_COMPAT
324 const char *structure,
325 int verbosity_level));
343 const char *structure,
345 int verbosity_level));
366 const char *structure,
367 int verbosity_level));
385 const char *structure,
387 int verbosity_level));
390 DEPRECATED(
float energy_of_gquad_structure(
const char *
string,
391 const char *structure,
392 int verbosity_level));
394 DEPRECATED(
float energy_of_gquad_struct_par(
const char *
string,
395 const char *structure,
397 int verbosity_level));
424 int verbosity_level));
448 int verbosity_level));
469 const char *structure,
531 const char *structure));
569 const char *structure));
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 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:397
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:55
int cut_point
set to first pos of second seq for cofolding
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(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)