Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches.
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#define | VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP 1U |
| Flag to indicate ligand bound to unpiared stretch in the exterior loop.
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#define | VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP 2U |
| Flag to indicate ligand bound to unpaired stretch in a hairpin loop.
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#define | VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP 4U |
| Flag to indicate ligand bound to unpiared stretch in an interior loop.
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#define | VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP 8U |
| Flag to indicate ligand bound to unpiared stretch in a multibranch loop.
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#define | VRNA_UNSTRUCTURED_DOMAIN_MOTIF 16U |
| Flag to indicate ligand binding without additional unbound nucleotides (motif-only)
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#define | VRNA_UNSTRUCTURED_DOMAIN_ALL_LOOPS |
| Flag to indicate ligand bound to unpiared stretch in any loop (convenience macro)
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typedef struct vrna_unstructured_domain_s | vrna_ud_t |
| Typename for the ligand binding extension data structure vrna_unstructured_domain_s.
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typedef int(* | vrna_ud_f) (vrna_fold_compound_t *fc, 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.
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typedef FLT_OR_DBL(* | vrna_ud_exp_f) (vrna_fold_compound_t *fc, 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.
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typedef void(* | vrna_ud_production_f) (vrna_fold_compound_t *fc, void *data) |
| Callback for pre-processing the production rule of the ligand binding to unpaired stretches feature.
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typedef void(* | vrna_ud_exp_production_f) (vrna_fold_compound_t *fc, void *data) |
| Callback for pre-processing the production rule of the ligand binding to unpaired stretches feature (partition function variant)
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typedef void(* | vrna_ud_add_probs_f) (vrna_fold_compound_t *fc, 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.
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typedef FLT_OR_DBL(* | vrna_ud_get_probs_f) (vrna_fold_compound_t *fc, 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.
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vrna_ud_motif_t * | vrna_ud_motifs_centroid (vrna_fold_compound_t *fc, const char *structure) |
| Detect unstructured domains in centroid structure.
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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.
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vrna_ud_motif_t * | vrna_ud_motifs_MFE (vrna_fold_compound_t *fc, const char *structure) |
| Detect unstructured domains in MFE structure.
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void | vrna_ud_add_motif (vrna_fold_compound_t *fc, const char *motif, double motif_en, const char *motif_name, unsigned int loop_type) |
| Add an unstructured domain motif, e.g. for ligand binding.
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int * | vrna_ud_get_motif_size_at (vrna_fold_compound_t *fc, int i, unsigned int loop_type) |
| Get a list of unique motif sizes that start at a certain position within the sequence.
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void | vrna_ud_remove (vrna_fold_compound_t *fc) |
| Remove ligand binding to unpaired stretches.
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void | vrna_ud_set_data (vrna_fold_compound_t *fc, void *data, vrna_auxdata_free_f free_cb) |
| Attach an auxiliary data structure.
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void | vrna_ud_set_prod_rule_cb (vrna_fold_compound_t *fc, vrna_ud_production_f pre_cb, vrna_ud_f e_cb) |
| Attach production rule callbacks for free energies computations.
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void | vrna_ud_set_exp_prod_rule_cb (vrna_fold_compound_t *fc, vrna_ud_exp_production_f pre_cb, vrna_ud_exp_f exp_e_cb) |
| Attach production rule for partition function.
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void | vrna_ud_set_prob_cb (vrna_fold_compound_t *fc, vrna_ud_add_probs_f setter, vrna_ud_get_probs_f getter) |
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Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches.