1#ifndef VIENNA_RNA_PACKAGE_STRUCT_UTILS_H
2#define VIENNA_RNA_PACKAGE_STRUCT_UTILS_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
73#define VRNA_BRACKETS_ALPHA 4U
81#define VRNA_BRACKETS_RND 8U
89#define VRNA_BRACKETS_CLY 16U
97#define VRNA_BRACKETS_ANG 32U
105#define VRNA_BRACKETS_SQR 64U
119#define VRNA_BRACKETS_DEFAULT \
120 (VRNA_BRACKETS_RND | \
121 VRNA_BRACKETS_CLY | \
122 VRNA_BRACKETS_ANG | \
132#define VRNA_BRACKETS_ANY \
133 (VRNA_BRACKETS_RND | \
134 VRNA_BRACKETS_CLY | \
135 VRNA_BRACKETS_ANG | \
136 VRNA_BRACKETS_SQR | \
191 unsigned int options);
215 const char target[3],
216 unsigned int options);
297 unsigned int options);
343 unsigned int options);
414 unsigned int options);
429#define VRNA_PLIST_TYPE_BASEPAIR 0
435#define VRNA_PLIST_TYPE_GQUAD 1
441#define VRNA_PLIST_TYPE_H_MOTIF 2
447#define VRNA_PLIST_TYPE_I_MOTIF 3
453#define VRNA_PLIST_TYPE_UD_MOTIF 4
459#define VRNA_PLIST_TYPE_STACK 5
465#define VRNA_PLIST_TYPE_UNPAIRED 6
471#define VRNA_PLIST_TYPE_TRIPLE 7
765vrna_dist_mountain(
const char *str1,
802 unsigned int length);
825 unsigned int length);
829vrna_letter_structure(
char *structure,
831 unsigned int length);
919#define VRNA_STRUCTURE_TREE_HIT 1U
926#define VRNA_STRUCTURE_TREE_SHAPIRO_SHORT 2U
933#define VRNA_STRUCTURE_TREE_SHAPIRO 3U
940#define VRNA_STRUCTURE_TREE_SHAPIRO_EXT 4U
947#define VRNA_STRUCTURE_TREE_SHAPIRO_WEIGHT 5U
953#define VRNA_STRUCTURE_TREE_EXPANDED 6U
1023#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
1051 "Use vrna_plist() instead");
1067 "Use vrna_db_pack() instead");
1081 "Use vrna_db_unpack() instead");
1096 "Use vrna_ptable() instead");
1098DEPRECATED(
short *make_pair_table_pk(
const char *structure),
1099 "Use vrna_ptable_from_string() instead");
1111 "Use vrna_ptable_copy() instead");
1120 "Use vrna_pt_ali_get() instead");
1130 "Use vrna_pt_snoop_get() instead");
1132DEPRECATED(
int *make_loop_index_pt(
short *pt),
1133 "Use vrna_loopidx_from_ptable() instead");
1150 "Use vrna_bp_distance() instead");
1163 "Use vrna_refBPcnt_matrix() instead");
1177 "Use vrna_refBPdist_matrix() instead");
1203 "Use vrna_plist_from_probs() instead");
1216 "Use vrna_parenthesis_structure() instead");
1230 "Use vrna_parenthesis_zuker() instead");
1232DEPRECATED(
void letter_structure(
char *structure,
1235 "Use vrna_letter_structure() instead");
1244 unsigned int length),
1245 "Use vrna_db_from_probs() instead");
1253 "Use vrna_bpp_symbol() instead");
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.