RNAlib-2.5.1
unstructured_domains.h
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1#ifndef VIENNA_RNA_PACKAGE_UNSTRUCTURED_DOMAIN_H
2#define VIENNA_RNA_PACKAGE_UNSTRUCTURED_DOMAIN_H
3
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96 int i,
97 int j,
98 unsigned int loop_type,
99 void *data);
100
120 int i,
121 int j,
122 unsigned int loop_type,
123 void *data);
124
136 void *data);
137
149 void *data);
150
151
162 int i,
163 int j,
164 unsigned int loop_type,
165 FLT_OR_DBL exp_energy,
166 void *data);
167
178 int i,
179 int j,
180 unsigned int loop_type,
181 int motif,
182 void *data);
183
184
189#define VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP 1U
190
195#define VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP 2U
196
201#define VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP 4U
202
207#define VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP 8U
208
213#define VRNA_UNSTRUCTURED_DOMAIN_MOTIF 16U
214
219#define VRNA_UNSTRUCTURED_DOMAIN_ALL_LOOPS (VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP | \
220 VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP | \
221 VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP | \
222 VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP)
223
229 /*
230 **********************************
231 * Keep track of all motifs added
232 **********************************
233 */
235 unsigned int *uniq_motif_size;
238 char **motif;
239 char **motif_name;
240 unsigned int *motif_size;
241 double *motif_en;
242 unsigned int *motif_type;
244 /*
245 **********************************
246 * Grammar extension for ligand
247 * binding
248 **********************************
249 */
257 void *data;
261};
262
263
265 int start;
266 int number;
267};
268
269
291 const char *structure);
292
293
316 const char *structure,
317 vrna_ep_t *probability_list);
318
319
340 const char *structure);
341
342
369 const char *motif,
370 double motif_en,
371 const char *motif_name,
372 unsigned int loop_type);
373
374
380 int i,
381 unsigned int loop_type);
382
383
384int *
385vrna_ud_get_motifs_at(vrna_fold_compound_t *vc,
386 int i,
387 unsigned int loop_type);
388
389
391vrna_ud_detect_motifs(vrna_fold_compound_t *vc,
392 const char *structure);
393
394
406
407
425 void *data,
427
428
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467
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501
502#endif
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_callback_ud_probs_get * probs_get
Callback to retrieve outside partition function.
Definition: unstructured_domains.h:260
vrna_callback_ud_exp_production * exp_prod_cb
Callback to ligand binding production rule, i.e. create/fill DP partition function matrices.
Definition: unstructured_domains.h:254
vrna_callback_ud_energy * energy_cb
Callback to evaluate free energy of ligand binding to a particular unpaired stretch.
Definition: unstructured_domains.h:255
vrna_callback_free_auxdata * free_data
Callback to free auxiliary data structure.
Definition: unstructured_domains.h:258
unsigned int * uniq_motif_size
An array storing a unique list of motif lengths.
Definition: unstructured_domains.h:235
unsigned int * motif_type
Type of motif, i.e. loop type the ligand binds to.
Definition: unstructured_domains.h:242
vrna_callback_ud_probs_add * probs_add
Callback to store/add outside partition function.
Definition: unstructured_domains.h:259
int motif_count
Total number of distinguished motifs.
Definition: unstructured_domains.h:237
unsigned int * motif_size
Motif lengths.
Definition: unstructured_domains.h:240
void * data
Auxiliary data structure passed to energy evaluation callbacks.
Definition: unstructured_domains.h:257
double * motif_en
Ligand binding free energy contribution.
Definition: unstructured_domains.h:241
vrna_callback_ud_production * prod_cb
Callback to ligand binding production rule, i.e. create/fill DP free energy matrices.
Definition: unstructured_domains.h:250
char ** motif_name
Motif identifier/name.
Definition: unstructured_domains.h:239
vrna_callback_ud_exp_energy * exp_energy_cb
Callback to evaluate Boltzmann factor of ligand binding to a particular unpaired stretch.
Definition: unstructured_domains.h:256
int uniq_motif_count
The unique number of motifs of different lengths.
Definition: unstructured_domains.h:234
char ** motif
Motif sequences.
Definition: unstructured_domains.h:238
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.
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 (...
Definition: unstructured_domains.h:148
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.
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.
Definition: unstructured_domains.h:135
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.
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.
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.
Definition: unstructured_domains.h:95
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 seq...
Definition: unstructured_domains.h:119
vrna_ud_motif_t * vrna_ud_motifs_centroid(vrna_fold_compound_t *fc, const char *structure)
Detect unstructured domains in centroid structure.
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.
Definition: unstructured_domains.h:177
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.
Definition: unstructured_domains.h:161
void vrna_ud_set_data(vrna_fold_compound_t *vc, void *data, vrna_callback_free_auxdata *free_cb)
Attach an auxiliary data structure.
void vrna_ud_remove(vrna_fold_compound_t *vc)
Remove ligand binding to unpaired stretches.
Data structure to store all functionality for ligand binding.
Definition: unstructured_domains.h:228
void() vrna_callback_free_auxdata(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:148
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:482
Definition: unstructured_domains.h:264
void vrna_ud_set_prob_cb(vrna_fold_compound_t *vc, vrna_callback_ud_probs_add *setter, vrna_callback_ud_probs_get *getter)
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.
Various utility- and helper-functions for secondary structure parsing, converting,...