Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches. More...

Include dependency graph for unstructured_domains.h:

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Data Structures
struct	vrna_unstructured_domain_s
	Data structure to store all functionality for ligand binding. More...

struct	vrna_unstructured_domain_motif_s

Macros
#define	VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP 1U
	Flag to indicate ligand bound to unpiared stretch in the exterior loop.

#define	VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP 2U
	Flag to indicate ligand bound to unpaired stretch in a hairpin loop.

#define	VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP 4U
	Flag to indicate ligand bound to unpiared stretch in an interior loop.

#define	VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP 8U
	Flag to indicate ligand bound to unpiared stretch in a multibranch loop.

#define	VRNA_UNSTRUCTURED_DOMAIN_MOTIF 16U
	Flag to indicate ligand binding without additional unbound nucleotides (motif-only)

#define	VRNA_UNSTRUCTURED_DOMAIN_ALL_LOOPS
	Flag to indicate ligand bound to unpiared stretch in any loop (convenience macro)

Typedefs
typedef struct vrna_unstructured_domain_s	vrna_ud_t
	Typename for the ligand binding extension data structure vrna_unstructured_domain_s.

typedef int(	vrna_callback_ud_energy) (vrna_fold_compound_t vc, int i, int j, unsigned int loop_type, void data)
	Callback to retrieve binding free energy of a ligand bound to an unpaired sequence segment. More...

typedef FLT_OR_DBL(	vrna_callback_ud_exp_energy) (vrna_fold_compound_t vc, int i, int j, unsigned int loop_type, void data)
	Callback to retrieve Boltzmann factor of the binding free energy of a ligand bound to an unpaired sequence segment. More...

typedef void(	vrna_callback_ud_production) (vrna_fold_compound_t vc, void data)
	Callback for pre-processing the production rule of the ligand binding to unpaired stretches feature. More...

typedef void(	vrna_callback_ud_exp_production) (vrna_fold_compound_t vc, void data)
	Callback for pre-processing the production rule of the ligand binding to unpaired stretches feature (partition function variant) More...

typedef void(	vrna_callback_ud_probs_add) (vrna_fold_compound_t vc, int i, int j, unsigned int loop_type, FLT_OR_DBL exp_energy, void data)
	Callback to store/add equilibrium probability for a ligand bound to an unpaired sequence segment. More...

typedef FLT_OR_DBL(	vrna_callback_ud_probs_get) (vrna_fold_compound_t vc, int i, int j, unsigned int loop_type, int motif, void data)
	Callback to retrieve equilibrium probability for a ligand bound to an unpaired sequence segment. More...

Functions
vrna_ud_motif_t *	vrna_ud_motifs_centroid (vrna_fold_compound_t fc, const char structure)
	Detect unstructured domains in centroid structure. More...

vrna_ud_motif_t *	vrna_ud_motifs_MEA (vrna_fold_compound_t fc, const char structure, vrna_ep_t *probability_list)
	Detect unstructured domains in MEA structure. More...

vrna_ud_motif_t *	vrna_ud_motifs_MFE (vrna_fold_compound_t fc, const char structure)
	Detect unstructured domains in MFE structure. More...

void	vrna_ud_add_motif (vrna_fold_compound_t vc, const char motif, double motif_en, const char *motif_name, unsigned int loop_type)
	Add an unstructured domain motif, e.g. for ligand binding. More...

int *	vrna_ud_get_motif_size_at (vrna_fold_compound_t *vc, int i, unsigned int loop_type)
	Get a list of unique motif sizes that start at a certain position within the sequence.

void	vrna_ud_remove (vrna_fold_compound_t *vc)
	Remove ligand binding to unpaired stretches. More...

void	vrna_ud_set_data (vrna_fold_compound_t vc, void data, vrna_callback_free_auxdata *free_cb)
	Attach an auxiliary data structure. More...

void	vrna_ud_set_prod_rule_cb (vrna_fold_compound_t vc, vrna_callback_ud_production pre_cb, vrna_callback_ud_energy *e_cb)
	Attach production rule callbacks for free energies computations. More...

void	vrna_ud_set_exp_prod_rule_cb (vrna_fold_compound_t vc, vrna_callback_ud_exp_production pre_cb, vrna_callback_ud_exp_energy *exp_e_cb)
	Attach production rule for partition function. More...

void	vrna_ud_set_prob_cb (vrna_fold_compound_t vc, vrna_callback_ud_probs_add setter, vrna_callback_ud_probs_get *getter)

Detailed Description

Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches.

Function Documentation

void vrna_ud_set_prob_cb	(	vrna_fold_compound_t *	vc,
		vrna_callback_ud_probs_add *	setter,
		vrna_callback_ud_probs_get *	getter
	)

SWIG Wrapper Notes:: This function is attached as method ud_set_prob_cb() to objects of type fold_compound

Data Structures

Macros

Typedefs

Functions

Detailed Description

Function Documentation