1 #ifndef __VIENNA_RNA_PACKAGE_EVAL_H__
2 #define __VIENNA_RNA_PACKAGE_EVAL_H__
8 #define DEPRECATED(func) func __attribute__ ((deprecated))
10 #define DEPRECATED(func) func
67 const char *structure,
92 const char *structure,
143 int vrna_eval_structure_pt_fast(
const char *
string,
184 const char *structure,
236 const char *structure,
237 int verbosity_level));
256 const char *structure,
258 int verbosity_level));
281 const char *structure,
282 int verbosity_level));
302 const char *structure,
304 int verbosity_level));
307 DEPRECATED(
float energy_of_gquad_structure(
const char *
string,
308 const char *structure,
309 int verbosity_level));
311 DEPRECATED(
float energy_of_gquad_struct_par(
const char *
string,
312 const char *structure,
314 int verbosity_level));
343 int verbosity_level));
369 int verbosity_level));
390 const char *structure,
452 const char *structure));
490 const char *structure));
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)