eval.h
Go to the documentation of this file.
#ifndef VIENNA_RNA_PACKAGE_EVAL_H
#define VIENNA_RNA_PACKAGE_EVAL_H
#include <stdio.h>
#include <ViennaRNA/data_structures.h>
#include <ViennaRNA/params.h> /* for deprecated functions */
#ifdef DEPRECATION_WARNINGS
# ifdef __GNUC__
# define DEPRECATED(func) func __attribute__ ((deprecated))
# else
# define DEPRECATED(func) func
# endif
#else
# define DEPRECATED(func) func
#endif
/* make this interface backward compatible with RNAlib < 2.2.0 */
#define VRNA_BACKWARD_COMPAT
extern int cut_point;
extern int eos_debug;
float vrna_eval_structure(vrna_fold_compound_t *vc,
const char *structure);
float vrna_eval_covar_structure(vrna_fold_compound_t *vc,
const char *structure);
float vrna_eval_structure_simple( const char *string,
const char *structure);
float vrna_eval_structure_verbose(vrna_fold_compound_t *vc,
const char *structure,
FILE *file);
float vrna_eval_structure_v(vrna_fold_compound_t *vc,
const char *structure,
int verbosity_level,
FILE *file);
float vrna_eval_structure_simple_verbose( const char *string,
const char *structure,
FILE *file);
float vrna_eval_structure_simple_v( const char *string,
const char *structure,
int verbosity_level,
FILE *file);
int vrna_eval_structure_pt( vrna_fold_compound_t *vc,
const short *pt);
int vrna_eval_structure_pt_simple(const char *string,
const short *pt);
int vrna_eval_structure_pt_verbose( vrna_fold_compound_t *vc,
const short *pt,
FILE *file);
int vrna_eval_structure_pt_v( vrna_fold_compound_t *vc,
const short *pt,
int verbosity_level,
FILE *file);
int vrna_eval_structure_pt_simple_verbose(const char *string,
const short *pt,
FILE *file);
int vrna_eval_structure_pt_simple_v(const char *string,
const short *pt,
int verbosity_level,
FILE *file);
int vrna_eval_loop_pt(vrna_fold_compound_t *vc,
int i,
const short *pt);
float vrna_eval_move( vrna_fold_compound_t *vc,
const char *structure,
int m1,
int m2);
int vrna_eval_move_pt(vrna_fold_compound_t *vc,
short *pt,
int m1,
int m2);
int vrna_eval_move_pt_simple( const char *string,
short *pt,
int m1,
int m2);
#ifdef VRNA_BACKWARD_COMPAT
DEPRECATED(float energy_of_structure(const char *string,
const char *structure,
int verbosity_level));
DEPRECATED(float energy_of_struct_par( const char *string,
const char *structure,
vrna_param_t *parameters,
int verbosity_level));
DEPRECATED(float energy_of_circ_structure( const char *string,
const char *structure,
int verbosity_level));
DEPRECATED(float energy_of_circ_struct_par(const char *string,
const char *structure,
vrna_param_t *parameters,
int verbosity_level));
DEPRECATED(float energy_of_gquad_structure(const char *string,
const char *structure,
int verbosity_level));
DEPRECATED(float energy_of_gquad_struct_par( const char *string,
const char *structure,
vrna_param_t *parameters,
int verbosity_level));
DEPRECATED(int energy_of_structure_pt( const char *string,
short *ptable,
short *s,
short *s1,
int verbosity_level));
DEPRECATED(int energy_of_struct_pt_par(const char *string,
short *ptable,
short *s,
short *s1,
vrna_param_t *parameters,
int verbosity_level));
DEPRECATED(float energy_of_move( const char *string,
const char *structure,
int m1,
int m2));
DEPRECATED(int energy_of_move_pt(short *pt,
short *s,
short *s1,
int m1,
int m2));
DEPRECATED(int loop_energy(short *ptable,
short *s,
short *s1,
int i));
DEPRECATED(float energy_of_struct(const char *string,
const char *structure));
DEPRECATED(int energy_of_struct_pt( const char *string,
short *ptable,
short *s,
short *s1));
DEPRECATED(float energy_of_circ_struct( const char *string,
const char *structure));
#endif
#endif
energy_of_circ_struct_par
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.
vrna_eval_structure_verbose
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...
energy_of_struct_par
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.
vrna_eval_structure_simple_verbose
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.
energy_of_move
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)
cut_point
int cut_point
set to first pos of second seq for cofolding
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:390
vrna_eval_structure_simple_v
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.
loop_energy
int loop_energy(short *ptable, short *s, short *s1, int i)
Calculate energy of a loop.
vrna_param_s
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
eos_debug
int eos_debug
verbose info from energy_of_struct
vrna_eval_structure_pt_simple_v
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.
vrna_eval_structure_v
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...
vrna_eval_structure_pt_v
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.
energy_of_structure
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.
data_structures.h
vrna_eval_structure_simple
float vrna_eval_structure_simple(const char *string, const char *structure)
Calculate the free energy of an already folded RNA.
energy_of_struct
float energy_of_struct(const char *string, const char *structure)
vrna_eval_structure
float vrna_eval_structure(vrna_fold_compound_t *vc, const char *structure)
Calculate the free energy of an already folded RNA.
params.h
energy_of_structure_pt
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.
vrna_eval_structure_pt_simple
int vrna_eval_structure_pt_simple(const char *string, const short *pt)
Calculate the free energy of an already folded RNA.
vrna_eval_loop_pt
int vrna_eval_loop_pt(vrna_fold_compound_t *vc, int i, const short *pt)
Calculate energy of a loop.
vrna_eval_move
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)
vrna_eval_move_pt
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)
vrna_eval_structure_pt_verbose
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.
energy_of_struct_pt_par
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.
energy_of_move_pt
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)
vrna_eval_covar_structure
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.
energy_of_circ_structure
float energy_of_circ_structure(const char *string, const char *structure, int verbosity_level)
Calculate the free energy of an already folded circular RNA.
vrna_eval_structure_pt
int vrna_eval_structure_pt(vrna_fold_compound_t *vc, const short *pt)
Calculate the free energy of an already folded RNA.
vrna_eval_structure_pt_simple_verbose
int vrna_eval_structure_pt_simple_verbose(const char *string, const short *pt, FILE *file)
Calculate the free energy of an already folded RNA.
energy_of_circ_struct
float energy_of_circ_struct(const char *string, const char *structure)
energy_of_struct_pt
int energy_of_struct_pt(const char *string, short *ptable, short *s, short *s1)