RNAlib-2.4.0
unstructured_domains.h
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1 #ifndef VIENNA_RNA_PACKAGE_UNSTRUCTURED_DOMAIN_H
2 #define VIENNA_RNA_PACKAGE_UNSTRUCTURED_DOMAIN_H
3 
64 
66 
68 
87 typedef int (vrna_callback_ud_energy)(vrna_fold_compound_t *vc, int i, int j, unsigned int loop_type, void *data);
88 
107 typedef FLT_OR_DBL (vrna_callback_ud_exp_energy)(vrna_fold_compound_t *vc, int i, int j, unsigned int loop_type, void *data);
108 
119 typedef void (vrna_callback_ud_production)(vrna_fold_compound_t *vc, void *data);
120 
132 
133 
143 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);
144 
154 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);
155 
156 
161 #define VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP 1U
162 
167 #define VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP 2U
168 
173 #define VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP 4U
174 
179 #define VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP 8U
180 
185 #define VRNA_UNSTRUCTURED_DOMAIN_MOTIF 16U
186 
191 #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)
192 
198 
199  /*
200  **********************************
201  Keep track of all added motifs
202  **********************************
203  */
205  unsigned int *uniq_motif_size;
208  char **motif;
209  unsigned int *motif_size;
210  double *motif_en;
211  unsigned int *motif_type;
213  /*
214  **********************************
215  Grammar extension for ligand
216  binding
217  **********************************
218  */
226  void *data;
230 };
231 
232 
234  int start;
235  int number;
236 };
237 
238 
264  const char *motif,
265  double motif_en,
266  unsigned int loop_type);
267 
268 
274  int i,
275  unsigned int loop_type);
276 
277 
278 int *
279 vrna_ud_get_motifs_at(vrna_fold_compound_t *vc,
280  int i,
281  unsigned int loop_type);
282 
283 
285 vrna_ud_detect_motifs(vrna_fold_compound_t *vc,
286  const char *structure);
287 
288 
300 
318  void *data,
319  vrna_callback_free_auxdata *free_cb);
320 
358 
359 
386  vrna_callback_ud_exp_energy *exp_e_cb);
387 
388 
392 
393 #endif
vrna_callback_ud_energy * energy_cb
Callback to evaluate free energy of ligand binding to a particular unpaired stretch.
Definition: unstructured_domains.h:224
double * motif_en
Ligand binding free energy contribution.
Definition: unstructured_domains.h:210
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:225
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:131
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:211
void * data
Auxiliary data structure passed to energy evaluation callbacks.
Definition: unstructured_domains.h:226
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:223
void vrna_ud_set_prob_cb(vrna_fold_compound_t *vc, vrna_callback_ud_probs_add *setter, vrna_callback_ud_probs_get *getter)
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:143
Data structure to store all functionality for ligand binding.
Definition: unstructured_domains.h:197
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:48
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:107
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:463
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:87
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:119
vrna_callback_free_auxdata * free_data
Callback to free auxiliary data structure.
Definition: unstructured_domains.h:227
Definition: unstructured_domains.h:233
unsigned int * motif_size
Motif lengths.
Definition: unstructured_domains.h:209
Various data structures and pre-processor macros.
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:154
int uniq_motif_count
The unique number of motifs of different lengths.
Definition: unstructured_domains.h:204
char ** motif
Motif sequences.
Definition: unstructured_domains.h:208
unsigned int * uniq_motif_size
An array storing a unique list of motif lengths.
Definition: unstructured_domains.h:205
void( vrna_callback_free_auxdata)(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition: data_structures.h:71
vrna_callback_ud_probs_add * probs_add
Callback to store/add outside partition function.
Definition: unstructured_domains.h:228
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:207
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_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_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:229
vrna_callback_ud_production * prod_cb
Callback to ligand binding production rule, i.e. create/fill DP free energy matrices.
Definition: unstructured_domains.h:219