RNAlib-2.4.5
constraints_soft.h
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1 #ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_H
2 #define VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_H
3 
5 
28 typedef struct vrna_sc_s vrna_sc_t;
29 
62 typedef int (vrna_callback_sc_energy)(int i,
63  int j,
64  int k,
65  int l,
66  unsigned char d,
67  void *data);
68 
102  int j,
103  int k,
104  int l,
105  unsigned char d,
106  void *data);
107 
135  int j,
136  int k,
137  int l,
138  unsigned char d,
139  void *data);
140 
141 
142 typedef enum {
149 
150 
154 typedef struct {
155  unsigned int interval_start;
156  unsigned int interval_end;
157  int e;
159 
160 
166 struct vrna_sc_s {
167  vrna_sc_type_e type;
168  unsigned int n;
169 
170  unsigned char state;
171 
172  int **energy_up;
175  int *up_storage;
178 #ifndef VRNA_DISABLE_C11_FEATURES
179  /* C11 support for unnamed unions/structs */
180  union {
181  struct {
182 #endif
183  int *energy_bp;
185 #ifndef VRNA_DISABLE_C11_FEATURES
186  /* C11 support for unnamed unions/structs */
187  };
188  struct {
189 #endif
192 #ifndef VRNA_DISABLE_C11_FEATURES
193  /* C11 support for unnamed unions/structs */
194  };
195  };
196 #endif
197 
201  /* generic soft contraints below */
219  void *data;
223  vrna_callback_free_auxdata *free_data;
224 };
225 
243 
244 
245 void
246 vrna_sc_prepare(vrna_fold_compound_t *vc,
247  unsigned int options);
248 
249 
250 void
251 vrna_sc_update(vrna_fold_compound_t *vc,
252  unsigned int i,
253  unsigned int options);
254 
255 
271  const FLT_OR_DBL **constraints,
272  unsigned int options);
273 
274 
289  int i,
290  int j,
291  FLT_OR_DBL energy,
292  unsigned int options);
293 
294 
310  const FLT_OR_DBL *constraints,
311  unsigned int options);
312 
313 
327  int i,
328  FLT_OR_DBL energy,
329  unsigned int options);
330 
331 
332 void vrna_sc_set_stack(vrna_fold_compound_t *vc,
333  const FLT_OR_DBL *constraints,
334  unsigned int options);
335 
336 
337 void vrna_sc_add_stack(vrna_fold_compound_t *vc,
338  int i,
339  FLT_OR_DBL energy,
340  unsigned int options);
341 
342 
353 
354 
362 void vrna_sc_free(vrna_sc_t *sc);
363 
364 
377  void *data,
378  vrna_callback_free_auxdata *free_data);
379 
380 
398 
399 
419 
420 
439 
440 
441 #endif
A base pair constraint.
Definition: constraints_soft.h:154
void vrna_sc_free(vrna_sc_t *sc)
Free memory occupied by a vrna_sc_t data structure.
Default Soft Constraints.
Definition: constraints_soft.h:143
int() vrna_callback_sc_energy(int i, int j, int k, int l, unsigned char d, void *data)
Callback to retrieve pseudo energy contribution for soft constraint feature.
Definition: constraints_soft.h:62
FLT_OR_DBL ** exp_energy_bp_local
Boltzmann Factors of the energy contribution for base pairs (sliding window approach) ...
Definition: constraints_soft.h:191
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
vrna_basepair_t *() vrna_callback_sc_backtrack(int i, int j, int k, int l, unsigned char d, void *data)
Callback to retrieve auxiliary base pairs for soft constraint feature.
Definition: constraints_soft.h:134
int * energy_stack
Pseudo Energy contribution per base pair involved in a stack.
Definition: constraints_soft.h:198
vrna_callback_sc_backtrack * bt
A function pointer used to obtain backtraced base pairs in loop regions that were altered by soft con...
Definition: constraints_soft.h:207
vrna_sc_type_e
Definition: constraints_soft.h:142
vrna_sc_bp_storage_t ** bp_storage
Storage container for energy contributions per base pair.
Definition: constraints_soft.h:176
vrna_callback_sc_energy * f
A function pointer used for pseudo energy contribution in MFE calculations.
Definition: constraints_soft.h:202
void vrna_sc_add_exp_f(vrna_fold_compound_t *vc, vrna_callback_sc_exp_energy *exp_f)
Bind a function pointer for generic soft constraint feature (PF version)
Various data structures and pre-processor macros.
FLT_OR_DBL * exp_energy_bp
Boltzmann Factors of the energy contribution for base pairs.
Definition: constraints_soft.h:184
Base pair data structure used in subopt.c.
Definition: data_structures.h:103
FLT_OR_DBL ** exp_energy_up
Boltzmann Factors of the energy contributions for unpaired sequence stretches.
Definition: constraints_soft.h:173
Soft Constraints suitable for local structure prediction using window approach.
Definition: constraints_soft.h:144
The soft constraints data structure.
Definition: constraints_soft.h:166
vrna_callback_sc_exp_energy * exp_f
A function pointer used for pseudo energy contribution boltzmann factors in PF calculations.
Definition: constraints_soft.h:213
int ** energy_up
Energy contribution for stretches of unpaired nucleotides.
Definition: constraints_soft.h:172
FLT_OR_DBL() vrna_callback_sc_exp_energy(int i, int j, int k, int l, unsigned char d, void *data)
Callback to retrieve pseudo energy contribution as Boltzmann Factors for soft constraint feature...
Definition: constraints_soft.h:101
void vrna_sc_set_bp(vrna_fold_compound_t *vc, const FLT_OR_DBL **constraints, unsigned int options)
Set soft constraints for paired nucleotides.
void vrna_sc_add_bp(vrna_fold_compound_t *vc, int i, int j, FLT_OR_DBL energy, unsigned int options)
Add soft constraints for paired nucleotides.
int * up_storage
Storage container for energy contributions per unpaired nucleotide.
Definition: constraints_soft.h:175
FLT_OR_DBL * exp_energy_stack
Boltzmann weighted pseudo energy contribution per nucleotide involved in a stack. ...
Definition: constraints_soft.h:199
void() vrna_callback_free_auxdata(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition: fold_compound.h:46
int ** energy_bp_local
Energy contribution for base pairs (sliding window approach)
Definition: constraints_soft.h:190
void vrna_sc_add_data(vrna_fold_compound_t *vc, void *data, vrna_callback_free_auxdata *free_data)
Add an auxiliary data structure for the generic soft constraints callback function.
void vrna_sc_init(vrna_fold_compound_t *vc)
Initialize an empty soft constraints data structure within a vrna_fold_compound_t.
int * energy_bp
Energy contribution for base pairs.
Definition: constraints_soft.h:183
void vrna_sc_add_bt(vrna_fold_compound_t *vc, vrna_callback_sc_backtrack *f)
Bind a backtracking function pointer for generic soft constraint feature.
void vrna_sc_remove(vrna_fold_compound_t *vc)
Remove soft constraints from vrna_fold_compound_t.
void vrna_sc_add_up(vrna_fold_compound_t *vc, int i, FLT_OR_DBL energy, unsigned int options)
Add soft constraints for unpaired nucleotides.
void vrna_sc_set_up(vrna_fold_compound_t *vc, const FLT_OR_DBL *constraints, unsigned int options)
Set soft constraints for unpaired nucleotides.
void vrna_sc_add_f(vrna_fold_compound_t *vc, vrna_callback_sc_energy *f)
Bind a function pointer for generic soft constraint feature (MFE version)
void * data
A pointer to the data object provided for for pseudo energy contribution functions of the generic sof...
Definition: constraints_soft.h:219