RNAlib-2.4.4
unstructured_domains.h
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1 #ifndef VIENNA_RNA_PACKAGE_UNSTRUCTURED_DOMAIN_H
2 #define VIENNA_RNA_PACKAGE_UNSTRUCTURED_DOMAIN_H
3 
70 
72 
74 
93 typedef int (vrna_callback_ud_energy)(vrna_fold_compound_t *vc, int i, int j, unsigned int loop_type, void *data);
94 
113 typedef FLT_OR_DBL (vrna_callback_ud_exp_energy)(vrna_fold_compound_t *vc, int i, int j, unsigned int loop_type, void *data);
114 
125 typedef void (vrna_callback_ud_production)(vrna_fold_compound_t *vc, void *data);
126 
138 
139 
149 typedef 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);
150 
160 typedef 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);
161 
162 
167 #define VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP 1U
168 
173 #define VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP 2U
174 
179 #define VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP 4U
180 
185 #define VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP 8U
186 
191 #define VRNA_UNSTRUCTURED_DOMAIN_MOTIF 16U
192 
197 #define VRNA_UNSTRUCTURED_DOMAIN_ALL_LOOPS (VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP | VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP)
198 
204 
205  /*
206  **********************************
207  Keep track of all added motifs
208  **********************************
209  */
211  unsigned int *uniq_motif_size;
214  char **motif;
215  unsigned int *motif_size;
216  double *motif_en;
217  unsigned int *motif_type;
219  /*
220  **********************************
221  Grammar extension for ligand
222  binding
223  **********************************
224  */
232  void *data;
236 };
237 
238 
240  int start;
241  int number;
242 };
243 
244 
270  const char *motif,
271  double motif_en,
272  unsigned int loop_type);
273 
274 
280  int i,
281  unsigned int loop_type);
282 
283 
284 int *
285 vrna_ud_get_motifs_at(vrna_fold_compound_t *vc,
286  int i,
287  unsigned int loop_type);
288 
289 
291 vrna_ud_detect_motifs(vrna_fold_compound_t *vc,
292  const char *structure);
293 
294 
306 
324  void *data,
325  vrna_callback_free_auxdata *free_cb);
326 
364 
365 
392  vrna_callback_ud_exp_energy *exp_e_cb);
393 
394 
398 
399 #endif
vrna_callback_ud_energy * energy_cb
Callback to evaluate free energy of ligand binding to a particular unpaired stretch.
Definition: unstructured_domains.h:230
double * motif_en
Ligand binding free energy contribution.
Definition: unstructured_domains.h:216
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.
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:231
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.
unsigned int * motif_type
Type of motif, i.e. loop type the ligand binds to.
Definition: unstructured_domains.h:217
void * data
Auxiliary data structure passed to energy evaluation callbacks.
Definition: unstructured_domains.h:232
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:229
void vrna_ud_set_prob_cb(vrna_fold_compound_t *vc, vrna_callback_ud_probs_add *setter, vrna_callback_ud_probs_get *getter)
Data structure to store all functionality for ligand binding.
Definition: unstructured_domains.h:203
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:43
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:131
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:93
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:149
vrna_callback_free_auxdata * free_data
Callback to free auxiliary data structure.
Definition: unstructured_domains.h:233
Definition: unstructured_domains.h:239
unsigned int * motif_size
Motif lengths.
Definition: unstructured_domains.h:215
Various data structures and pre-processor macros.
int uniq_motif_count
The unique number of motifs of different lengths.
Definition: unstructured_domains.h:210
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:113
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:160
char ** motif
Motif sequences.
Definition: unstructured_domains.h:214
unsigned int * uniq_motif_size
An array storing a unique list of motif lengths.
Definition: unstructured_domains.h:211
vrna_callback_ud_probs_add * probs_add
Callback to store/add outside partition function.
Definition: unstructured_domains.h:234
void vrna_ud_add_motif(vrna_fold_compound_t *vc, const char *motif, double motif_en, unsigned int loop_type)
Add an unstructured domain motif, e.g. for ligand binding.
int motif_count
Total number of distinguished motifs.
Definition: unstructured_domains.h:213
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_callback_free_auxdata(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition: fold_compound.h:46
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_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:125
void vrna_ud_remove(vrna_fold_compound_t *vc)
Remove ligand binding to unpaired stretches.
vrna_callback_ud_probs_get * probs_get
Callback to retrieve outside partition function.
Definition: unstructured_domains.h:235
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:137
vrna_callback_ud_production * prod_cb
Callback to ligand binding production rule, i.e. create/fill DP free energy matrices.
Definition: unstructured_domains.h:225