1 #ifndef __VIENNA_RNA_PACKAGE_CONSTRAINTS_H__
2 #define __VIENNA_RNA_PACKAGE_CONSTRAINTS_H__
32 #define VRNA_CONSTRAINT_PIPE 1U
40 #define VRNA_CONSTRAINT_DOT 2U
47 #define VRNA_CONSTRAINT_X 4U
54 #define VRNA_CONSTRAINT_ANG_BRACK 8U
61 #define VRNA_CONSTRAINT_RND_BRACK 16U
72 #define VRNA_CONSTRAINT_INTRAMOLECULAR 2048U
83 #define VRNA_CONSTRAINT_INTERMOLECULAR 4096U
91 #define VRNA_CONSTRAINT_MULTILINE 32U
98 #define VRNA_CONSTRAINT_NO_HEADER 64U
105 #define VRNA_CONSTRAINT_ALL 128U
113 #define VRNA_CONSTRAINT_DB 256U
121 #define VRNA_CONSTRAINT_FILE 512U
129 #define VRNA_CONSTRAINT_IINDX 1024U
137 #define VRNA_CONSTRAINT_SOFT_MFE 8192U
145 #define VRNA_CONSTRAINT_SOFT_PF 16384U
154 #define VRNA_CONSTRAINT_SOFT_UP 32768U
162 #define VRNA_CONSTRAINT_SOFT_BP 65536U
170 #define VRNA_CONSTRAINT_UNGAP 131072U
178 #define VRNA_HC_CONTEXT_EXT_LOOP (char)0x01
185 #define VRNA_HC_CONTEXT_HP_LOOP (char)0x02
192 #define VRNA_HC_CONTEXT_INT_LOOP (char)0x04
199 #define VRNA_HC_CONTEXT_MB_LOOP (char)0x08
206 #define VRNA_HC_CONTEXT_INT_LOOP_ENC (char)0x10
213 #define VRNA_HC_CONTEXT_MB_LOOP_ENC (char)0x20
215 #define VRNA_HC_CONTEXT_ALL_LOOPS VRNA_HC_CONTEXT_EXT_LOOP \
216 | VRNA_HC_CONTEXT_HP_LOOP \
217 | VRNA_HC_CONTEXT_INT_LOOP \
218 | VRNA_HC_CONTEXT_INT_LOOP_ENC \
219 | VRNA_HC_CONTEXT_MB_LOOP \
220 | VRNA_HC_CONTEXT_MB_LOOP_ENC
222 #define VRNA_HC_CONTEXT_ENFORCE (char)0x40
230 #define VRNA_DECOMP_PAIR_HP 1
238 #define VRNA_DECOMP_PAIR_IL 2
244 #define VRNA_DECOMP_PAIR_ML 3
250 #define VRNA_DECOMP_ML_ML_ML 5
256 #define VRNA_DECOMP_ML_UP_3 4
262 #define VRNA_DECOMP_ML_UP_5 6
268 #define VRNA_DECOMP_ML_UP 11
274 #define VRNA_DECOMP_EXT_EXT 9
280 #define VRNA_DECOMP_EXT_UP_3 7
286 #define VRNA_DECOMP_EXT_UP_5 10
292 #define VRNA_DECOMP_EXT_UP 8
298 #define VRNA_DECOMP_EXT_STEM_UP 12
351 unsigned int idx_type);
372 unsigned int option);
397 const char *constraint,
398 unsigned int options);
448 int parse_soft_constraints_file(
const char *file_name,
450 double default_value,
466 int convert_shape_reactivities_to_probabilities(
const char *shape_conversion,
469 double default_value);
489 const double *constraints,
490 unsigned int options);
493 const double **constraints,
494 unsigned int options);
497 const char **shape_files,
498 const int *shape_file_association,
501 unsigned int options);
504 const double **constraints,
505 unsigned int options);
508 const double **constraints,
509 unsigned int options);
512 const double **constraints,
513 unsigned int options);
516 const double *constraints,
517 unsigned int options);
520 const double *constraints,
521 unsigned int options);
524 const double *constraints,
525 unsigned int options);
528 const double *constraints,
529 unsigned int options);
532 const double *constraints,
533 unsigned int options);
536 const double *constraints,
537 unsigned int options);
544 int parse_soft_constraints_shape_method(
const char *method_string,
The soft constraints data structure.
Definition: data_structures.h:323
void print_tty_constraint_full(void)
Print structure constraint characters to stdout (full constraint support)
void getConstraint(char **cstruc, const char **lines, unsigned int option)
Get a hard constraint from pseudo dot-bracket notation as specified in the ViennaRNA Package extensio...
The hard constraints data structure.
Definition: data_structures.h:300
void vrna_hc_reset(vrna_fold_compound *vc)
Reset hard constraints to default values.
void print_tty_constraint(unsigned int option)
Print structure constraint characters to stdout. (constraint support is specified by option parameter...
Definition: data_structures.h:359
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
void vrna_hc_free(hard_constraintT *hc)
Free the memory allocated by a hard_constraintT data structure.
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 vrna_hc_add(vrna_fold_compound *vc, const char *constraint, unsigned int options)
Add hard constraints to a vrna_fold_compound data structure.