RNAlib-2.2.5
|
Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches. More...
Go to the source code of this file.
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_DBL( | vrna_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... | |
Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches.