1#ifndef __VIENNA_RNA_PACKAGE_FOLD_H__
2#define __VIENNA_RNA_PACKAGE_FOLD_H__
7#define DEPRECATED(func) func __attribute__ ((deprecated))
9#define DEPRECATED(func) func
143float fold(
const char *sequence,
196 const char *structure,
197 int verbosity_level);
215 const char *structure,
217 int verbosity_level);
238 const char *structure,
239 int verbosity_level);
257 const char *structure,
259 int verbosity_level);
262float energy_of_gquad_structure(
const char *
string,
263 const char *structure,
264 int verbosity_level);
266float energy_of_gquad_struct_par(
const char *
string,
267 const char *structure,
269 int verbosity_level);
295 int verbosity_level);
319 int verbosity_level);
349void letter_structure(
char *structure,
366void update_fold_params_par(
paramT *parameters);
373char *backtrack_fold_from_pair(
char *sequence,
391 const char *structure,
436void export_fold_arrays(
int **f5_p,
448void export_fold_arrays_par(
int **f5_p,
461void export_circfold_arrays(
int *Fc_p,
478void export_circfold_arrays_par(
int *Fc_p,
540 const char *
string));
564 const char *structure));
602 const char *structure));
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
int LoopEnergy(int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1)
int energy_of_struct_pt(const char *string, short *ptable, short *s, short *s1)
void parenthesis_zuker(char *structure, bondT *bp, int length)
Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calcul...
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 loop_energy(short *ptable, short *s, short *s1, int i)
Calculate energy of a 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)
float energy_of_circ_struct(const char *string, const char *structure)
int uniq_ML
do ML decomposition uniquely (for subopt)
int logML
if nonzero use logarithmic ML energy in energy_of_struct
void parenthesis_structure(char *structure, bondT *bp, int length)
Create a dot-backet/parenthesis structure from backtracking stack.
int HairpinE(int size, int type, int si1, int sj1, const char *string)
int cut_point
set to first pos of second seq for cofolding
float energy_of_struct(const char *string, const char *structure)
void initialize_fold(int length)
void assign_plist_from_db(plist **pl, const char *struc, float pr)
Create a plist from a dot-bracket string.
double * pr
A pointer to the base pair probability matrix.
int eos_debug
verbose info from energy_of_struct
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.
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.
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.
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.
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 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.
void free_arrays(void)
Free arrays for mfe folding.
void update_fold_params(void)
Recalculate energy parameters.
float circfold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence.
float fold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
float fold_par(const char *sequence, char *structure, paramT *parameters, int is_constrained, int is_circular)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
Base pair.
Definition data_structures.h:84
The datastructure that contains temperature scaled energy parameters.
Definition data_structures.h:122
this datastructure is used as input parameter in functions of PS_dot.h and others
Definition data_structures.h:48