1 #ifndef VIENNA_RNA_PACKAGE_EVAL_H 2 #define VIENNA_RNA_PACKAGE_EVAL_H 9 #ifdef VRNA_WARN_DEPRECATED 11 # define DEPRECATED(func) func __attribute__ ((deprecated)) 13 # define DEPRECATED(func) func 16 # define DEPRECATED(func) func 20 #define VRNA_BACKWARD_COMPAT 67 const char *structure);
91 const char *structure);
110 const char *structure);
127 const char *structure,
157 const char *structure,
177 const char *structure,
205 const char *structure,
374 const char *structure,
399 int vrna_eval_move_pt_simple(
const char *
string,
411 #ifdef VRNA_BACKWARD_COMPAT 432 const char *structure,
433 int verbosity_level));
451 const char *structure,
453 int verbosity_level));
474 const char *structure,
475 int verbosity_level));
493 const char *structure,
495 int verbosity_level));
498 DEPRECATED(
float energy_of_gquad_structure(
const char *
string,
499 const char *structure,
500 int verbosity_level));
502 DEPRECATED(
float energy_of_gquad_struct_par(
const char *
string,
503 const char *structure,
505 int verbosity_level));
532 int verbosity_level));
556 int verbosity_level));
576 const char *structure,
638 const char *structure));
676 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 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.
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: fold_compound.h:130
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:57
int cut_point
set to first pos of second seq for cofolding
Methods to compute the neighbors of an RNA secondary structure.
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_v(const char *string, const short *pt, int verbosity_level, FILE *file)
Calculate the free energy of an already folded RNA.
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.
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)
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...
An atomic representation of the transition / move from one structure to its neighbor.
Definition: neighbor.h:156