1#ifndef VIENNA_RNA_PACKAGE_UNSTRUCTURED_DOMAIN_H
2#define VIENNA_RNA_PACKAGE_UNSTRUCTURED_DOMAIN_H
4#ifdef VRNA_WARN_DEPRECATED
5# if defined(DEPRECATED)
9# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
10# elif defined(__GNUC__)
11# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
13# define DEPRECATED(func, msg) func
16# define DEPRECATED(func, msg) func
113 unsigned int loop_type,
119 unsigned int loop_type,
121 "Use vrna_ud_f instead!");
144 unsigned int loop_type,
150 unsigned int loop_type,
152 "Use vrna_ud_exp_f instead!");
169 "Use vrna_ud_production_f instead!");
186 "Use vrna_ud_exp_production_f instead!");
201 unsigned int loop_type,
208 unsigned int loop_type,
211 "Use vrna_ud_add_probs_f instead!");
225 unsigned int loop_type,
232 unsigned int loop_type,
235 "Use vrna_ud_get_probs_f instead!");
242#define VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP 1U
248#define VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP 2U
254#define VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP 4U
260#define VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP 8U
266#define VRNA_UNSTRUCTURED_DOMAIN_MOTIF 16U
272#define VRNA_UNSTRUCTURED_DOMAIN_ALL_LOOPS (VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP | \
273 VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP | \
274 VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP | \
275 VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP)
345 const char *structure);
371 const char *structure,
396 const char *structure);
427 const char *motif_name,
428 unsigned int loop_type);
437 unsigned int loop_type);
443 unsigned int loop_type);
448 const char *structure);
Various data structures and pre-processor macros.
The Basic Fold Compound API.
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition basic.h:43
vrna_ud_exp_production_f exp_prod_cb
Callback to ligand binding production rule, i.e. create/fill DP partition function matrices.
Definition unstructured_domains.h:307
vrna_ud_production_f prod_cb
Callback to ligand binding production rule, i.e. create/fill DP free energy matrices.
Definition unstructured_domains.h:303
unsigned int * uniq_motif_size
An array storing a unique list of motif lengths.
Definition unstructured_domains.h:288
vrna_auxdata_free_f free_data
Callback to free auxiliary data structure.
Definition unstructured_domains.h:311
vrna_ud_get_probs_f probs_get
Callback to retrieve outside partition function.
Definition unstructured_domains.h:313
vrna_ud_f energy_cb
Callback to evaluate free energy of ligand binding to a particular unpaired stretch.
Definition unstructured_domains.h:308
unsigned int * motif_type
Type of motif, i.e. loop type the ligand binds to.
Definition unstructured_domains.h:295
int motif_count
Total number of distinguished motifs.
Definition unstructured_domains.h:290
unsigned int * motif_size
Motif lengths.
Definition unstructured_domains.h:293
void * data
Auxiliary data structure passed to energy evaluation callbacks.
Definition unstructured_domains.h:310
double * motif_en
Ligand binding free energy contribution.
Definition unstructured_domains.h:294
char ** motif_name
Motif identifier/name.
Definition unstructured_domains.h:292
vrna_ud_exp_f exp_energy_cb
Callback to evaluate Boltzmann factor of ligand binding to a particular unpaired stretch.
Definition unstructured_domains.h:309
int uniq_motif_count
The unique number of motifs of different lengths.
Definition unstructured_domains.h:287
vrna_ud_add_probs_f probs_add
Callback to store/add outside partition function.
Definition unstructured_domains.h:312
char ** motif
Motif sequences.
Definition unstructured_domains.h:291
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 seq...
Definition unstructured_domains.h:141
void vrna_ud_remove(vrna_fold_compound_t *fc)
Remove ligand binding to unpaired stretches.
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.
vrna_ud_motif_t * vrna_ud_motifs_MFE(vrna_fold_compound_t *fc, const char *structure)
Detect unstructured domains in MFE structure.
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.
Definition unstructured_domains.h:222
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 (...
Definition unstructured_domains.h:181
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.
Definition unstructured_domains.h:198
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.
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.
Definition unstructured_domains.h:164
vrna_ud_motif_t * vrna_ud_motifs_centroid(vrna_fold_compound_t *fc, const char *structure)
Detect unstructured domains in centroid structure.
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.
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.
Definition unstructured_domains.h:110
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.
void vrna_ud_set_data(vrna_fold_compound_t *fc, void *data, vrna_auxdata_free_f free_cb)
Attach an auxiliary data structure.
Data structure to store all functionality for ligand binding.
Definition unstructured_domains.h:281
void(* vrna_auxdata_free_f)(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition fold_compound.h:58
The most basic data structure required by many functions throughout the RNAlib.
Definition fold_compound.h:168
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition structures.h:486
Definition unstructured_domains.h:317
void vrna_ud_set_prob_cb(vrna_fold_compound_t *fc, vrna_ud_add_probs_f setter, vrna_ud_get_probs_f getter)
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.
Various utility- and helper-functions for secondary structure parsing, converting,...