soft.h File Reference

Functions and data structures for secondary structure soft constraints. More...

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Data Structures
struct	vrna_sc_bp_storage_t
	A base pair constraint. More...
struct	vrna_sc_s
	The soft constraints data structure. More...

Typedefs
typedef struct vrna_sc_s	vrna_sc_t
	Typename for the soft constraints data structure vrna_sc_s.
typedef int(	vrna_callback_sc_energy) (int i, int j, int k, int l, unsigned char d, void *data)
	Callback to retrieve pseudo energy contribution for soft constraint feature. More...
typedef FLT_OR_DBL(	vrna_callback_sc_exp_energy) (int i, int j, int k, int l, unsigned char d, void *data)
	Callback to retrieve pseudo energy contribution as Boltzmann Factors for soft constraint feature. More...
typedef vrna_basepair_t *(	vrna_callback_sc_backtrack) (int i, int j, int k, int l, unsigned char d, void *data)
	Callback to retrieve auxiliary base pairs for soft constraint feature. More...

Enumerations

Functions
void	vrna_sc_init (vrna_fold_compound_t *vc)
	Initialize an empty soft constraints data structure within a vrna_fold_compound_t. More...
void	vrna_sc_set_bp (vrna_fold_compound_t *vc, const FLT_OR_DBL **constraints, unsigned int options)
	Set soft constraints for paired nucleotides. More...
void	vrna_sc_add_bp (vrna_fold_compound_t *vc, int i, int j, FLT_OR_DBL energy, unsigned int options)
	Add soft constraints for paired nucleotides. More...
void	vrna_sc_set_up (vrna_fold_compound_t *vc, const FLT_OR_DBL *constraints, unsigned int options)
	Set soft constraints for unpaired nucleotides. More...
void	vrna_sc_add_up (vrna_fold_compound_t *vc, int i, FLT_OR_DBL energy, unsigned int options)
	Add soft constraints for unpaired nucleotides. More...
void	vrna_sc_remove (vrna_fold_compound_t *vc)
	Remove soft constraints from vrna_fold_compound_t. More...
void	vrna_sc_free (vrna_sc_t *sc)
	Free memory occupied by a vrna_sc_t data structure. More...
void	vrna_sc_add_data (vrna_fold_compound_t *vc, void *data, vrna_callback_free_auxdata *free_data)
	Add an auxiliary data structure for the generic soft constraints callback function. More...
void	vrna_sc_add_f (vrna_fold_compound_t *vc, vrna_callback_sc_energy *f)
	Bind a function pointer for generic soft constraint feature (MFE version) More...
void	vrna_sc_add_bt (vrna_fold_compound_t *vc, vrna_callback_sc_backtrack *f)
	Bind a backtracking function pointer for generic soft constraint feature. More...
void	vrna_sc_add_exp_f (vrna_fold_compound_t *vc, vrna_callback_sc_exp_energy *exp_f)
	Bind a function pointer for generic soft constraint feature (PF version) More...

Detailed Description

Functions and data structures for secondary structure soft constraints.

Enumeration Type Documentation

enum vrna_sc_type_e

The type of a soft constraint.

Enumerator
VRNA_SC_DEFAULT	Default Soft Constraints.
VRNA_SC_WINDOW	Soft Constraints suitable for local structure prediction using window approach. See also vrna_mfe_window(), vrna_mfe_window_zscore(), pfl_fold()