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 67 const char *structure);
90 const char *structure);
108 const char *structure);
124 const char *structure,
153 const char *structure,
172 const char *structure,
200 const char *structure,
362 const char *structure,
385 int vrna_eval_move_pt_simple(
const char *
string,
390 #ifdef VRNA_BACKWARD_COMPAT 411 const char *structure,
412 int verbosity_level));
430 const char *structure,
432 int verbosity_level));
453 const char *structure,
454 int verbosity_level));
472 const char *structure,
474 int verbosity_level));
477 DEPRECATED(
float energy_of_gquad_structure(
const char *
string,
478 const char *structure,
479 int verbosity_level));
481 DEPRECATED(
float energy_of_gquad_struct_par(
const char *
string,
482 const char *structure,
484 int verbosity_level));
511 int verbosity_level));
535 int verbosity_level));
556 const char *structure,
618 const char *structure));
656 const char *structure));
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 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...
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.
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.
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
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:424
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.
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: params.h:50
int eos_debug
verbose info from energy_of_struct
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.
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...
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.
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 energy_of_struct(const char *string, const char *structure)
float vrna_eval_structure(vrna_fold_compound_t *vc, const char *structure)
Calculate the free energy of an already folded 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.
int vrna_eval_structure_pt_simple(const char *string, const short *pt)
Calculate the free energy of an already folded RNA.
int vrna_eval_loop_pt(vrna_fold_compound_t *vc, int i, const short *pt)
Calculate energy of a loop.
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)
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)
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.
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.
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_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.
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 vrna_eval_structure_pt(vrna_fold_compound_t *vc, const short *pt)
Calculate the free energy of an already folded RNA.
int vrna_eval_structure_pt_simple_verbose(const char *string, const short *pt, FILE *file)
Calculate the free energy of an already folded 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)