1#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_HARD_H
2#define VIENNA_RNA_PACKAGE_CONSTRAINTS_HARD_H
4#ifdef VRNA_WARN_DEPRECATED
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
42typedef struct vrna_hc_depot_s vrna_hc_depot_t;
85DEPRECATED(
typedef unsigned char (vrna_callback_hc_evaluate)(
int i,
91 "Use vrna_hc_eval_f instead!");
99#define VRNA_CONSTRAINT_NO_HEADER 0
109#define VRNA_CONSTRAINT_DB 16384U
122#define VRNA_CONSTRAINT_DB_ENFORCE_BP 32768U
135#define VRNA_CONSTRAINT_DB_PIPE 65536U
145#define VRNA_CONSTRAINT_DB_DOT 131072U
154#define VRNA_CONSTRAINT_DB_X 262144U
161#define VRNA_CONSTRAINT_DB_ANG_BRACK 524288U
170#define VRNA_CONSTRAINT_DB_RND_BRACK 1048576U
183#define VRNA_CONSTRAINT_DB_INTRAMOL 2097152U
196#define VRNA_CONSTRAINT_DB_INTERMOL 4194304U
208#define VRNA_CONSTRAINT_DB_GQUAD 8388608U
210#define VRNA_CONSTRAINT_DB_CANONICAL_BP 16777216U
220#define VRNA_CONSTRAINT_DB_WUSS 33554432U
234#define VRNA_CONSTRAINT_DB_DEFAULT \
235 (VRNA_CONSTRAINT_DB \
236 | VRNA_CONSTRAINT_DB_PIPE \
237 | VRNA_CONSTRAINT_DB_DOT \
238 | VRNA_CONSTRAINT_DB_X \
239 | VRNA_CONSTRAINT_DB_ANG_BRACK \
240 | VRNA_CONSTRAINT_DB_RND_BRACK \
241 | VRNA_CONSTRAINT_DB_INTRAMOL \
242 | VRNA_CONSTRAINT_DB_INTERMOL \
243 | VRNA_CONSTRAINT_DB_GQUAD \
252#define VRNA_CONSTRAINT_CONTEXT_EXT_LOOP (unsigned char)0x01
260#define VRNA_CONSTRAINT_CONTEXT_HP_LOOP (unsigned char)0x02
268#define VRNA_CONSTRAINT_CONTEXT_INT_LOOP (unsigned char)0x04
276#define VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC (unsigned char)0x08
284#define VRNA_CONSTRAINT_CONTEXT_MB_LOOP (unsigned char)0x10
292#define VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC (unsigned char)0x20
297#define VRNA_CONSTRAINT_CONTEXT_ENFORCE (unsigned char)0x40
302#define VRNA_CONSTRAINT_CONTEXT_NO_REMOVE (unsigned char)0x80
308#define VRNA_CONSTRAINT_CONTEXT_NONE (unsigned char)0
313#define VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_EXT_LOOP | \
314 VRNA_CONSTRAINT_CONTEXT_HP_LOOP | \
315 VRNA_CONSTRAINT_CONTEXT_INT_LOOP | \
316 VRNA_CONSTRAINT_CONTEXT_MB_LOOP)
321#define VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC | \
322 VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC)
330#define VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS | \
331 VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS)
334#define VRNA_CONSTRAINT_WINDOW_UPDATE_5 1U
336#define VRNA_CONSTRAINT_WINDOW_UPDATE_3 2U
383#ifndef VRNA_DISABLE_C11_FEATURES
389#ifndef VRNA_DISABLE_C11_FEATURES
393 unsigned char **matrix_local;
394#ifndef VRNA_DISABLE_C11_FEATURES
432 vrna_hc_depot_t *depot;
510 unsigned int options);
516 unsigned int options);
536 unsigned char option);
543 unsigned char option);
585 unsigned char option);
591 unsigned int strand_i,
593 unsigned int strand_j,
594 unsigned char option);
618 unsigned char option);
682 const char *constraint,
683 unsigned int options);
686#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
697 "Use vrna_message_constraint_options() instead");
707 "Use vrna_message_constraint_options_all() instead");
727 unsigned int idx_type),
728 "Use the new API and the hard constraint framework instead");
Functions and data structures for constraining secondary structure predictions and evaluation.
The Basic Fold Compound API.
void vrna_message_constraint_options(unsigned int option)
Print a help message for pseudo dot-bracket structure constraint characters to stdout....
void vrna_message_constraint_options_all(void)
Print structure constraint characters to stdout (full constraint support)
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:156
int * up_int
A linear array that holds the number of allowed unpaired nucleotides in an interior loop.
Definition: hard.h:405
unsigned char options
The hard constraint option
Definition: hard.h:443
int * up_ext
A linear array that holds the number of allowed unpaired nucleotides in an exterior loop.
Definition: hard.h:399
int position
The sequence position (1-based)
Definition: hard.h:441
int * up_hp
A linear array that holds the number of allowed unpaired nucleotides in a hairpin loop.
Definition: hard.h:402
int * up_ml
A linear array that holds the number of allowed unpaired nucleotides in a multi branched loop.
Definition: hard.h:408
vrna_auxdata_free_f free_data
A pointer to a function to free memory occupied by auxiliary data.
Definition: hard.h:421
vrna_hc_eval_f f
A function pointer that returns whether or not a certain decomposition may be evaluated.
Definition: hard.h:412
void * data
A pointer to some structure where the user may store necessary data to evaluate its generic hard cons...
Definition: hard.h:416
unsigned char(* vrna_hc_eval_f)(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:78
void vrna_hc_init(vrna_fold_compound_t *vc)
Initialize/Reset hard constraints to default values.
void vrna_hc_add_up(vrna_fold_compound_t *vc, int i, unsigned char option)
Make a certain nucleotide unpaired.
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.
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.
void vrna_hc_free(vrna_hc_t *hc)
Free the memory allocated by a vrna_hc_t data structure.
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)
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)
The hard constraints data structure.
Definition: hard.h:377
A single hard constraint for a single nucleotide.
Definition: hard.h:440
vrna_hc_type_e
The hard constraints type.
Definition: hard.h:344
@ VRNA_HC_DEFAULT
Default Hard Constraints.
Definition: hard.h:345
@ VRNA_HC_WINDOW
Hard Constraints suitable for local structure prediction using window approach.
Definition: hard.h:346
void vrna_hc_add_data(vrna_fold_compound_t *vc, void *data, vrna_auxdata_free_f f)
Add an auxiliary data structure for the generic hard constraints callback function.
void vrna_hc_add_f(vrna_fold_compound_t *vc, vrna_hc_eval_f f)
Add a function pointer pointer for the generic hard constraint feature.
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.
void print_tty_constraint(unsigned int option)
Print structure constraint characters to stdout. (constraint support is specified by option parameter...
void print_tty_constraint_full(void)
Print structure constraint characters to stdout (full constraint support)