RNAlib-2.5.1
structures.h
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1#ifndef VIENNA_RNA_PACKAGE_STRUCT_UTILS_H
2#define VIENNA_RNA_PACKAGE_STRUCT_UTILS_H
3
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)))
9# else
10# define DEPRECATED(func, msg) func
11# endif
12#else
13# define DEPRECATED(func, msg) func
14#endif
15
33typedef struct vrna_hx_s vrna_hx_t;
34
35
41
42
73#define VRNA_BRACKETS_ALPHA 4U
74
75
81#define VRNA_BRACKETS_RND 8U
82
83
89#define VRNA_BRACKETS_CLY 16U
90
91
97#define VRNA_BRACKETS_ANG 32U
98
99
105#define VRNA_BRACKETS_SQR 64U
106
107
119#define VRNA_BRACKETS_DEFAULT \
120 (VRNA_BRACKETS_RND | \
121 VRNA_BRACKETS_CLY | \
122 VRNA_BRACKETS_ANG | \
123 VRNA_BRACKETS_SQR)
124
125
132#define VRNA_BRACKETS_ANY \
133 (VRNA_BRACKETS_RND | \
134 VRNA_BRACKETS_CLY | \
135 VRNA_BRACKETS_ANG | \
136 VRNA_BRACKETS_SQR | \
137 VRNA_BRACKETS_ALPHA)
138
139
140#include <stdio.h>
141
143
156char *
157vrna_db_pack(const char *struc);
158
159
170char *
171vrna_db_unpack(const char *packed);
172
173
189void
190vrna_db_flatten(char *structure,
191 unsigned int options);
192
193
213void
215 const char target[3],
216 unsigned int options);
217
218
236char *
237vrna_db_from_ptable(const short *pt);
238
239
249char *
251 unsigned int n);
252
253
260char *
261vrna_db_to_element_string(const char *structure);
262
263
295char *
296vrna_db_pk_remove(const char *structure,
297 unsigned int options);
298
299/* End dot-bracket interface */
318short *
319vrna_ptable(const char *structure);
320
321
341short *
342vrna_ptable_from_string(const char *structure,
343 unsigned int options);
344
345
363short *
364vrna_pt_pk_get(const char *structure);
365
366
373short *
374vrna_ptable_copy(const short *pt);
375
376
381short *
382vrna_pt_ali_get(const char *structure);
383
384
392short *
393vrna_pt_snoop_get(const char *structure);
394
395
412short *
413vrna_pt_pk_remove(const short *ptable,
414 unsigned int options);
415
416
417/* End pair table interface */
429#define VRNA_PLIST_TYPE_BASEPAIR 0
430
431
435#define VRNA_PLIST_TYPE_GQUAD 1
436
437
441#define VRNA_PLIST_TYPE_H_MOTIF 2
442
443
447#define VRNA_PLIST_TYPE_I_MOTIF 3
448
449
453#define VRNA_PLIST_TYPE_UD_MOTIF 4
454
455
459#define VRNA_PLIST_TYPE_STACK 5
460
461
465#define VRNA_PLIST_TYPE_UNPAIRED 6
466
467
471#define VRNA_PLIST_TYPE_TRIPLE 7
472
473
483 int i;
484 int j;
485 float p;
486 int type;
487};
488
504vrna_ep_t *vrna_plist(const char *struc,
505 float pr);
506
507
525 double cut_off);
526
527
528/* End pair list interface */
596char *
597vrna_db_from_WUSS(const char *wuss);
598
599
600/* End WUSS notation interface */
648char *
649vrna_abstract_shapes(const char *structure,
650 unsigned int level);
651
652
668char *
670 unsigned int level);
671
672
673/* End abstract shapes interface */
685struct vrna_hx_s {
686 unsigned int start;
687 unsigned int end;
688 unsigned int length;
689 unsigned int up5;
690 unsigned int up3;
691};
692
693
700vrna_hx_t *
702
703
707vrna_hx_t *
709 int maxdist);
710
711
712/* End helix list interface */
719int *
721
722
741int
742vrna_bp_distance_pt(const short *pt1,
743 const short *pt2);
744
759int
760vrna_bp_distance(const char *str1,
761 const char *str2);
762
763
764double
765vrna_dist_mountain(const char *str1,
766 const char *str2,
767 unsigned int p);
768
769
770/* End metrics interface */
779unsigned int *
780vrna_refBPcnt_matrix(const short *reference_pt,
781 unsigned int turn);
782
783
791unsigned int *
792vrna_refBPdist_matrix(const short *pt1,
793 const short *pt2,
794 unsigned int turn);
795
796
800char *
802 unsigned int length);
803
804
808char
809vrna_bpp_symbol(const float *x);
810
811
823char *
825 unsigned int length);
826
827
828void
829vrna_letter_structure(char *structure,
830 vrna_bp_stack_t *bp,
831 unsigned int length);
832
833
919#define VRNA_STRUCTURE_TREE_HIT 1U
920
921
926#define VRNA_STRUCTURE_TREE_SHAPIRO_SHORT 2U
927
928
933#define VRNA_STRUCTURE_TREE_SHAPIRO 3U
934
935
940#define VRNA_STRUCTURE_TREE_SHAPIRO_EXT 4U
941
942
947#define VRNA_STRUCTURE_TREE_SHAPIRO_WEIGHT 5U
948
953#define VRNA_STRUCTURE_TREE_EXPANDED 6U
954
955
985char *
986vrna_db_to_tree_string(const char *structure,
987 unsigned int type);
988
989
1001char *
1002vrna_tree_string_unweight(const char *structure);
1003
1004
1016char *
1017vrna_tree_string_to_db(const char *tree);
1018
1019
1020/* End tree representations */
1023#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
1024
1025/*###########################################*/
1026/*# deprecated functions below #*/
1027/*###########################################*/
1028
1048DEPRECATED(void assign_plist_from_db(vrna_ep_t **pl,
1049 const char *struc,
1050 float pr),
1051 "Use vrna_plist() instead");
1052
1066DEPRECATED(char *pack_structure(const char *struc),
1067 "Use vrna_db_pack() instead");
1068
1080DEPRECATED(char *unpack_structure(const char *packed),
1081 "Use vrna_db_unpack() instead");
1082
1095DEPRECATED(short *make_pair_table(const char *structure),
1096 "Use vrna_ptable() instead");
1097
1098DEPRECATED(short *make_pair_table_pk(const char *structure),
1099 "Use vrna_ptable_from_string() instead");
1100
1110DEPRECATED(short *copy_pair_table(const short *pt),
1111 "Use vrna_ptable_copy() instead");
1112
1119DEPRECATED(short *alimake_pair_table(const char *structure),
1120 "Use vrna_pt_ali_get() instead");
1121
1129DEPRECATED(short *make_pair_table_snoop(const char *structure),
1130 "Use vrna_pt_snoop_get() instead");
1131
1132DEPRECATED(int *make_loop_index_pt(short *pt),
1133 "Use vrna_loopidx_from_ptable() instead");
1134
1148DEPRECATED(int bp_distance(const char *str1,
1149 const char *str2),
1150 "Use vrna_bp_distance() instead");
1151
1161DEPRECATED(unsigned int *make_referenceBP_array(short *reference_pt,
1162 unsigned int turn),
1163 "Use vrna_refBPcnt_matrix() instead");
1164
1174DEPRECATED(unsigned int *compute_BPdifferences(short *pt1,
1175 short *pt2,
1176 unsigned int turn),
1177 "Use vrna_refBPdist_matrix() instead");
1178
1199DEPRECATED(void assign_plist_from_pr(vrna_ep_t **pl,
1200 FLT_OR_DBL *probs,
1201 int length,
1202 double cutoff),
1203 "Use vrna_plist_from_probs() instead");
1204
1213DEPRECATED(void parenthesis_structure(char *structure,
1214 vrna_bp_stack_t *bp,
1215 int length),
1216 "Use vrna_parenthesis_structure() instead");
1217
1227DEPRECATED(void parenthesis_zuker(char *structure,
1228 vrna_bp_stack_t *bp,
1229 int length),
1230 "Use vrna_parenthesis_zuker() instead");
1231
1232DEPRECATED(void letter_structure(char *structure,
1233 vrna_bp_stack_t *bp,
1234 int length),
1235 "Use vrna_letter_structure() instead");
1236
1242DEPRECATED(void bppm_to_structure(char *structure,
1243 FLT_OR_DBL *pr,
1244 unsigned int length),
1245 "Use vrna_db_from_probs() instead");
1246
1252DEPRECATED(char bppm_symbol(const float *x),
1253 "Use vrna_bpp_symbol() instead");
1254
1255#endif
1256
1261#endif
Various data structures and pre-processor macros.
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
Base pair stack element.
Definition: basic.h:143
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:148
void assign_plist_from_pr(vrna_ep_t **pl, FLT_OR_DBL *probs, int length, double cutoff)
Create a vrna_ep_t from a probability matrix.
void assign_plist_from_db(vrna_ep_t **pl, const char *struc, float pr)
Create a vrna_ep_t from a dot-bracket string.
vrna_ep_t * vrna_plist_from_probs(vrna_fold_compound_t *vc, double cut_off)
Create a vrna_ep_t from base pair probability matrix.
char * vrna_abstract_shapes_pt(const short *pt, unsigned int level)
Convert a secondary structure to its abstract shapes representation.
char * vrna_abstract_shapes(const char *structure, unsigned int level)
Convert a secondary structure in dot-bracket notation to its abstract shapes representation.
void bppm_to_structure(char *structure, FLT_OR_DBL *pr, unsigned int length)
Create a dot-bracket like structure string from base pair probability matrix.
short * copy_pair_table(const short *pt)
Get an exact copy of a pair table.
char * unpack_structure(const char *packed)
Unpack secondary structure previously packed with pack_structure()
char bppm_symbol(const float *x)
Get a pseudo dot bracket notation for a given probability information.
int pairs
contains the number of base pairs in the last parsed structure.
int bp_distance(const char *str1, const char *str2)
Compute the "base pair" distance between two secondary structures s1 and s2.
short * alimake_pair_table(const char *structure)
char * pack_structure(const char *struc)
Pack secondary secondary structure, 5:1 compression using base 3 encoding.
short * make_pair_table(const char *structure)
Create a pair table of a secondary structure.
short * make_pair_table_snoop(const char *structure)
void parenthesis_zuker(char *structure, vrna_bp_stack_t *bp, int length)
Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calcul...
void parenthesis_structure(char *structure, vrna_bp_stack_t *bp, int length)
Create a dot-backet/parenthesis structure from backtracking stack.
unsigned int * make_referenceBP_array(short *reference_pt, unsigned int turn)
Make a reference base pair count matrix.
unsigned int * compute_BPdifferences(short *pt1, short *pt2, unsigned int turn)
Make a reference base pair distance matrix.
char * vrna_db_to_element_string(const char *structure)
Convert a secondary structure in dot-bracket notation to a nucleotide annotation of loop contexts.
char * vrna_db_from_plist(vrna_ep_t *pairs, unsigned int n)
Convert a list of base pairs into dot-bracket notation.
char * vrna_db_from_ptable(const short *pt)
Convert a pair table into dot-parenthesis notation.
void vrna_db_flatten_to(char *string, const char target[3], unsigned int options)
Substitute pairs of brackets in a string with another type of pair characters.
char * vrna_db_pk_remove(const char *structure, unsigned int options)
Remove pseudo-knots from an input structure.
char * vrna_db_unpack(const char *packed)
Unpack secondary structure previously packed with vrna_db_pack()
char * vrna_db_pack(const char *struc)
Pack secondary secondary structure, 5:1 compression using base 3 encoding.
void vrna_db_flatten(char *structure, unsigned int options)
Substitute pairs of brackets in a string with parenthesis.
vrna_hx_t * vrna_hx_from_ptable(short *pt)
Convert a pair table representation of a secondary structure into a helix list.
vrna_hx_t * vrna_hx_merge(const vrna_hx_t *list, int maxdist)
Create a merged helix list from another helix list.
Data structure representing an entry of a helix list.
Definition: structures.h:685
int vrna_bp_distance(const char *str1, const char *str2)
Compute the "base pair" distance between two secondary structures s1 and s2.
int vrna_bp_distance_pt(const short *pt1, const short *pt2)
Compute the "base pair" distance between two pair tables pt1 and pt2 of secondary structures.
short * vrna_pt_pk_get(const char *structure)
Create a pair table of a secondary structure (pseudo-knot version)
short * vrna_pt_snoop_get(const char *structure)
Create a pair table of a secondary structure (snoop version)
short * vrna_pt_pk_remove(const short *ptable, unsigned int options)
Remove pseudo-knots from a pair table.
short * vrna_ptable_from_string(const char *structure, unsigned int options)
Create a pair table for a secondary structure string.
short * vrna_pt_ali_get(const char *structure)
Create a pair table of a secondary structure (snoop align version)
short * vrna_ptable(const char *structure)
Create a pair table from a dot-bracket notation of a secondary structure.
short * vrna_ptable_copy(const short *pt)
Get an exact copy of a pair table.
int i
Start position (usually 5' nucleotide that starts the element, e.g. base pair)
Definition: structures.h:483
int type
Type of the element.
Definition: structures.h:486
float p
Probability of the element.
Definition: structures.h:485
int j
End position (usually 3' nucleotide that ends the element, e.g. base pair)
Definition: structures.h:484
vrna_ep_t * vrna_plist(const char *struc, float pr)
Create a vrna_ep_t from a dot-bracket string.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:482
char * vrna_tree_string_to_db(const char *tree)
Convert a linear tree string representation of a secondary structure back to Dot-Bracket notation.
char * vrna_tree_string_unweight(const char *structure)
Remove weights from a linear string tree representation of a secondary structure.
char * vrna_db_to_tree_string(const char *structure, unsigned int type)
Convert a Dot-Bracket structure string into tree string representation.
char * vrna_db_from_WUSS(const char *wuss)
Convert a WUSS annotation string to dot-bracket format.
char vrna_bpp_symbol(const float *x)
Get a pseudo dot bracket notation for a given probability information.
unsigned int * vrna_refBPdist_matrix(const short *pt1, const short *pt2, unsigned int turn)
Make a reference base pair distance matrix.
char * vrna_db_from_bp_stack(vrna_bp_stack_t *bp, unsigned int length)
Create a dot-backet/parenthesis structure from backtracking stack.
int * vrna_loopidx_from_ptable(const short *pt)
Get a loop index representation of a structure.
char * vrna_db_from_probs(const FLT_OR_DBL *pr, unsigned int length)
Create a dot-bracket like structure string from base pair probability matrix.
unsigned int * vrna_refBPcnt_matrix(const short *reference_pt, unsigned int turn)
Make a reference base pair count matrix.