1#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_H
2#define VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_H
73DEPRECATED(
typedef int (vrna_callback_sc_energy)(
int i,
79 "Use vrna_sc_f instead!");
128DEPRECATED(
typedef FLT_OR_DBL (vrna_callback_sc_exp_energy)(
int i,
134 "Use vrna_sc_exp_f instead!");
184 "Use vrna_sc_bt_f instead");
203 unsigned int interval_start;
204 unsigned int interval_end;
226#ifndef VRNA_DISABLE_C11_FEATURES
233#ifndef VRNA_DISABLE_C11_FEATURES
240#ifndef VRNA_DISABLE_C11_FEATURES
272 vrna_auxdata_prepare_f prepare_data;
299 unsigned int options);
305 unsigned int options);
326 unsigned int options);
348 unsigned int options);
369 unsigned int options);
389 unsigned int options);
395 unsigned int options);
401 unsigned int options);
408 unsigned int options);
415 unsigned int options);
463 vrna_auxdata_prepare_f prepare_cb,
497 vrna_sc_exp_direct_f cb_exp,
499 vrna_auxdata_prepare_f prepare_cb,
501 unsigned int decomp_type);
Functions and data structures for constraining secondary structure predictions and evaluation.
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
Base pair data structure used in subopt.c.
Definition basic.h:104
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
vrna_sc_f f
A function pointer used for pseudo energy contribution in MFE calculations.
Definition soft.h:250
int * up_storage
Storage container for energy contributions per unpaired nucleotide.
Definition soft.h:223
vrna_sc_exp_f exp_f
A function pointer used for pseudo energy contribution boltzmann factors in PF calculations.
Definition soft.h:261
FLT_OR_DBL * exp_energy_stack
Boltzmann weighted pseudo energy contribution per nucleotide involved in a stack.
Definition soft.h:247
int ** energy_up
Energy contribution for stretches of unpaired nucleotides.
Definition soft.h:220
FLT_OR_DBL * exp_energy_bp
Boltzmann Factors of the energy contribution for base pairs.
Definition soft.h:232
FLT_OR_DBL ** exp_energy_bp_local
Boltzmann Factors of the energy contribution for base pairs (sliding window approach)
Definition soft.h:239
void * data
A pointer to the data object provided for for pseudo energy contribution functions of the generic sof...
Definition soft.h:267
vrna_sc_bp_storage_t ** bp_storage
Storage container for energy contributions per base pair.
Definition soft.h:224
int * energy_stack
Pseudo Energy contribution per base pair involved in a stack.
Definition soft.h:246
int * energy_bp
Energy contribution for base pairs.
Definition soft.h:231
FLT_OR_DBL ** exp_energy_up
Boltzmann Factors of the energy contributions for unpaired sequence stretches.
Definition soft.h:221
int ** energy_bp_local
Energy contribution for base pairs (sliding window approach)
Definition soft.h:238
vrna_sc_bt_f bt
A function pointer used to obtain backtraced base pairs in loop regions that were altered by soft con...
Definition soft.h:255
int vrna_sc_add_data(vrna_fold_compound_t *fc, void *data, vrna_auxdata_free_f free_data)
Add an auxiliary data structure for the generic soft constraints callback function.
int vrna_sc_add_exp_f(vrna_fold_compound_t *fc, vrna_sc_exp_f exp_f)
Bind a function pointer for generic soft constraint feature (PF version)
int vrna_sc_add_f(vrna_fold_compound_t *fc, vrna_sc_f f)
Bind a function pointer for generic soft constraint feature (MFE version)
FLT_OR_DBL(* vrna_sc_exp_f)(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 soft.h:121
int vrna_sc_set_bp(vrna_fold_compound_t *fc, const FLT_OR_DBL **constraints, unsigned int options)
Set soft constraints for paired nucleotides.
void vrna_sc_free(vrna_sc_t *sc)
Free memory occupied by a vrna_sc_t data structure.
vrna_basepair_t *(* vrna_sc_bt_f)(int i, int j, int k, int l, unsigned char d, void *data)
Callback to retrieve auxiliary base pairs for soft constraint feature.
Definition soft.h:171
int vrna_sc_add_bt(vrna_fold_compound_t *fc, vrna_sc_bt_f f)
Bind a backtracking function pointer for generic soft constraint feature.
void vrna_sc_init(vrna_fold_compound_t *fc)
Initialize an empty soft constraints data structure within a vrna_fold_compound_t.
void vrna_sc_remove(vrna_fold_compound_t *fc)
Remove soft constraints from vrna_fold_compound_t.
int vrna_sc_add_bp(vrna_fold_compound_t *fc, int i, int j, FLT_OR_DBL energy, unsigned int options)
Add soft constraints for paired nucleotides.
int(* vrna_sc_f)(int i, int j, int k, int l, unsigned char d, void *data)
Callback to retrieve pseudo energy contribution for soft constraint feature.
Definition soft.h:66
int vrna_sc_set_up(vrna_fold_compound_t *fc, const FLT_OR_DBL *constraints, unsigned int options)
Set soft constraints for unpaired nucleotides.
int vrna_sc_add_up(vrna_fold_compound_t *fc, int i, FLT_OR_DBL energy, unsigned int options)
Add soft constraints for unpaired nucleotides.
The soft constraints data structure.
Definition soft.h:214
vrna_sc_type_e
The type of a soft constraint.
Definition soft.h:190
@ VRNA_SC_DEFAULT
Default Soft Constraints.
Definition soft.h:191
@ VRNA_SC_WINDOW
Soft Constraints suitable for local structure prediction using window approach.
Definition soft.h:192
A base pair constraint.
Definition soft.h:202