Go to the documentation of this file. 1 #ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_HARD_H
2 #define VIENNA_RNA_PACKAGE_CONSTRAINTS_HARD_H
4 #ifdef VRNA_WARN_DEPRECATED
5 # if defined(__clang__)
6 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
7 # elif defined(__GNUC__)
8 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
10 # define DEPRECATED(func, msg) func
13 # define DEPRECATED(func, msg) func
44 typedef struct vrna_hc_depot_s vrna_hc_depot_t;
89 #define VRNA_CONSTRAINT_NO_HEADER 0
99 #define VRNA_CONSTRAINT_DB 16384U
112 #define VRNA_CONSTRAINT_DB_ENFORCE_BP 32768U
125 #define VRNA_CONSTRAINT_DB_PIPE 65536U
135 #define VRNA_CONSTRAINT_DB_DOT 131072U
144 #define VRNA_CONSTRAINT_DB_X 262144U
151 #define VRNA_CONSTRAINT_DB_ANG_BRACK 524288U
160 #define VRNA_CONSTRAINT_DB_RND_BRACK 1048576U
173 #define VRNA_CONSTRAINT_DB_INTRAMOL 2097152U
186 #define VRNA_CONSTRAINT_DB_INTERMOL 4194304U
198 #define VRNA_CONSTRAINT_DB_GQUAD 8388608U
200 #define VRNA_CONSTRAINT_DB_CANONICAL_BP 16777216U
210 #define VRNA_CONSTRAINT_DB_WUSS 33554432U
224 #define VRNA_CONSTRAINT_DB_DEFAULT \
225 (VRNA_CONSTRAINT_DB \
226 | VRNA_CONSTRAINT_DB_PIPE \
227 | VRNA_CONSTRAINT_DB_DOT \
228 | VRNA_CONSTRAINT_DB_X \
229 | VRNA_CONSTRAINT_DB_ANG_BRACK \
230 | VRNA_CONSTRAINT_DB_RND_BRACK \
231 | VRNA_CONSTRAINT_DB_INTRAMOL \
232 | VRNA_CONSTRAINT_DB_INTERMOL \
233 | VRNA_CONSTRAINT_DB_GQUAD \
242 #define VRNA_CONSTRAINT_CONTEXT_EXT_LOOP (unsigned char)0x01
250 #define VRNA_CONSTRAINT_CONTEXT_HP_LOOP (unsigned char)0x02
258 #define VRNA_CONSTRAINT_CONTEXT_INT_LOOP (unsigned char)0x04
266 #define VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC (unsigned char)0x08
274 #define VRNA_CONSTRAINT_CONTEXT_MB_LOOP (unsigned char)0x10
282 #define VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC (unsigned char)0x20
287 #define VRNA_CONSTRAINT_CONTEXT_ENFORCE (unsigned char)0x40
292 #define VRNA_CONSTRAINT_CONTEXT_NO_REMOVE (unsigned char)0x80
298 #define VRNA_CONSTRAINT_CONTEXT_NONE (unsigned char)0
303 #define VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_EXT_LOOP | \
304 VRNA_CONSTRAINT_CONTEXT_HP_LOOP | \
305 VRNA_CONSTRAINT_CONTEXT_INT_LOOP | \
306 VRNA_CONSTRAINT_CONTEXT_MB_LOOP)
311 #define VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC | \
312 VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC)
320 #define VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS | \
321 VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS)
324 #define VRNA_CONSTRAINT_WINDOW_UPDATE_5 1U
326 #define VRNA_CONSTRAINT_WINDOW_UPDATE_3 2U
373 #ifndef VRNA_DISABLE_C11_FEATURES
382 #ifndef VRNA_DISABLE_C11_FEATURES
386 unsigned char **matrix_local;
387 #ifndef VRNA_DISABLE_C11_FEATURES
425 vrna_hc_depot_t *depot;
499 unsigned int options);
504 unsigned int options);
523 unsigned char option);
530 unsigned char option);
568 unsigned char option);
574 unsigned int strand_i,
576 unsigned int strand_j,
577 unsigned char option);
599 unsigned char option);
660 const char *constraint,
661 unsigned int options);
664 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
674 "Use vrna_message_constraint_options() instead");
683 "Use vrna_message_constraint_options_all() instead");
702 unsigned int idx_type),
703 "Use the new API and the hard constraint framework instead");
int * up_hp
A linear array that holds the number of allowed unpaired nucleotides in a hairpin loop.
Definition: hard.h:395
void vrna_hc_add_bp_nonspecific(vrna_fold_compound_t *vc, int i, int d, unsigned char option)
Enforce a nucleotide to be paired (upstream/downstream)
A single hard constraint for a single nucleotide.
Definition: hard.h:433
vrna_hc_type_e
The hard constraints type.
Definition: hard.h:334
vrna_callback_free_auxdata * free_data
A pointer to a function to free memory occupied by auxiliary data.
Definition: hard.h:414
void vrna_hc_free(vrna_hc_t *hc)
Free the memory allocated by a vrna_hc_t data structure.
void vrna_hc_add_f(vrna_fold_compound_t *vc, vrna_callback_hc_evaluate *f)
Add a function pointer pointer for the generic hard constraint feature.
The hard constraints data structure.
Definition: hard.h:367
int vrna_hc_add_up_batch(vrna_fold_compound_t *vc, vrna_hc_up_t *constraints)
Apply a list of hard constraints for single nucleotides.
void * data
A pointer to some structure where the user may store necessary data to evaluate its generic hard cons...
Definition: hard.h:409
void vrna_hc_add_data(vrna_fold_compound_t *vc, void *data, vrna_callback_free_auxdata *f)
Add an auxiliary data structure for the generic hard constraints callback function.
unsigned char() vrna_callback_hc_evaluate(int i, int j, int k, int l, unsigned char d, void *data)
Callback to evaluate whether or not a particular decomposition step is contributing to the solution s...
Definition: hard.h:77
Functions and data structures for constraining secondary structure predictions and evaluation.
void vrna_hc_init(vrna_fold_compound_t *vc)
Initialize/Reset hard constraints to default values.
@ VRNA_HC_WINDOW
Hard Constraints suitable for local structure prediction using window approach.
Definition: hard.h:336
int vrna_hc_add_bp(vrna_fold_compound_t *vc, int i, int j, unsigned char option)
Favorize/Enforce a certain base pair (i,j)
unsigned char * matrix
Upper triangular matrix that encodes where a base pair or unpaired nucleotide is allowed.
Definition: hard.h:378
int vrna_hc_add_from_db(vrna_fold_compound_t *vc, const char *constraint, unsigned int options)
Add hard constraints from pseudo dot-bracket notation.
int * up_int
A linear array that holds the number of allowed unpaired nucleotides in an interior loop.
Definition: hard.h:398
void vrna_message_constraint_options(unsigned int option)
Print a help message for pseudo dot-bracket structure constraint characters to stdout....
@ VRNA_HC_DEFAULT
Default Hard Constraints.
Definition: hard.h:335
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
void print_tty_constraint_full(void)
Print structure constraint characters to stdout (full constraint support)
vrna_callback_hc_evaluate * f
A function pointer that returns whether or not a certain decomposition may be evaluated.
Definition: hard.h:405
int position
The sequence position (1-based)
Definition: hard.h:434
void vrna_hc_add_up(vrna_fold_compound_t *vc, int i, unsigned char option)
Make a certain nucleotide unpaired.
void print_tty_constraint(unsigned int option)
Print structure constraint characters to stdout. (constraint support is specified by option parameter...
void vrna_message_constraint_options_all(void)
Print structure constraint characters to stdout (full constraint support)
void() vrna_callback_free_auxdata(void *data)
Callback to free memory allocated for auxiliary user-provided data.
Definition: fold_compound.h:46
The Basic Fold Compound API.
unsigned char options
The hard constraint option
Definition: hard.h:436
int * up_ml
A linear array that holds the number of allowed unpaired nucleotides in a multi branched loop.
Definition: hard.h:401
void constrain_ptypes(const char *constraint, unsigned int length, char *ptype, int *BP, int min_loop_size, unsigned int idx_type)
Insert constraining pair types according to constraint structure string.
int * up_ext
A linear array that holds the number of allowed unpaired nucleotides in an exterior loop.
Definition: hard.h:392