RNAlib-2.2.5

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

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Data Structures

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

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_ML_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   (VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP | VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_ML_LOOP)
 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 looptype, void *data)
 Callback to retrieve binding free energy of a ligand bound to an unpaired sequence segment.
 
typedef FLT_OR_DBLvrna_callback_ud_exp_energy) (vrna_fold_compound_t *vc, int i, int j, unsigned int looptype, void *data)
 Callback to retrieve Boltzmann factor of the binding free energy of a ligand bound to an unpaired sequence segment.
 
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.
 
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)
 

Functions

void vrna_ud_add_motif (vrna_fold_compound_t *vc, const char *motif, double motif_en, unsigned int loop_type)
 Add a ligand binding motif. More...
 
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)
 Attach an auxiliary data structure. More...
 
void vrna_ud_set_prod_rule (vrna_fold_compound_t *vc, vrna_callback_ud_production *rule)
 Attach production rule for free energies. More...
 
void vrna_ud_set_exp_prod_rule (vrna_fold_compound_t *vc, vrna_callback_ud_exp_production *rule)
 Attach production rule for partition function. More...
 
void vrna_ud_set_energy (vrna_fold_compound_t *vc, vrna_callback_ud_energy *e)
 Attach evaluation function for free energies. More...
 
void vrna_ud_set_exp_energy (vrna_fold_compound_t *vc, vrna_callback_ud_exp_energy *exp_e)
 Attach evaluation function for Boltzmann factors. More...
 

Detailed Description

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