structure_utils.h File Reference
Utilities » Parsing, Converting, and Comparing - Functions to Manipulate Secondary Structures

Various utility- and helper-functions for secondary structure parsing, converting, etc. More...

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## Data Structures

struct | vrna_hx_s

## Functions

char * | vrna_db_pack (const char *struc)
| Pack secondary secondary structure, 5:1 compression using base 3 encoding. More...
char * | vrna_db_unpack (const char *packed)
| Unpack secondary structure previously packed with vrna_db_pack() More...
short * | vrna_ptable (const char *structure)
| Create a pair table of a secondary structure. More...
short * | vrna_pt_pk_get (const char *structure)
| Create a pair table of a secondary structure (pseudo-knot version) More...
short * | vrna_ptable_copy (const short *pt)
| Get an exact copy of a pair table. More...
short * | vrna_pt_ali_get (const char *structure)
| Create a pair table of a secondary structure (snoop align version)
short * | vrna_pt_snoop_get (const char *structure)
| Create a pair table of a secondary structure (snoop version) More...
int * | vrna_loopidx_from_ptable (const short *pt)
| Get a loop index representation of a structure.
char * | vrna_db_from_ptable (short *pt)
| Convert a pair table into dot-parenthesis notation. More...
int | vrna_bp_distance (const char *str1, const char *str2)
| Compute the "base pair" distance between two secondary structures s1 and s2. More...
unsigned int * | vrna_refBPcnt_matrix (const short *reference_pt, unsigned int turn)
| Make a reference base pair count matrix. More...
unsigned int * | vrna_refBPdist_matrix (const short *pt1, const short *pt2, unsigned int turn)
| Make a reference base pair distance matrix. More...
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.
char | vrna_bpp_symbol (const float *x)
| Get a pseudo dot bracket notation for a given probability information.
char * | vrna_db_from_bp_stack (vrna_bp_stack_t *bp, unsigned int length)
| Create a dot-backet/parenthesis structure from backtracking stack. More...
vrna_plist_t * | vrna_plist (const char *struc, float pr)
| Create a vrna_plist_t from a dot-bracket string. More...
vrna_plist_t * | vrna_plist_from_probs (vrna_fold_compound_t *vc, double cut_off)
| Create a vrna_plist_t from base pair probability matrix. More...
char * | vrna_db_from_plist (vrna_plist_t *pairs, unsigned int n)
| Convert a list of base pairs into dot-bracket notation. More...
void | assign_plist_from_db (vrna_plist_t **pl, const char *struc, float pr)
| Create a vrna_plist_t from a dot-bracket string. More...
char * | pack_structure (const char *struc)
| Pack secondary secondary structure, 5:1 compression using base 3 encoding. More...
char * | unpack_structure (const char *packed)
| Unpack secondary structure previously packed with pack_structure() More...
short * | make_pair_table (const char *structure)
| Create a pair table of a secondary structure. More...
short * | copy_pair_table (const short *pt)
| Get an exact copy of a pair table. More...
short * | alimake_pair_table (const char *structure)
short * | make_pair_table_snoop (const char *structure)
int | bp_distance (const char *str1, const char *str2)
| Compute the "base pair" distance between two secondary structures s1 and s2. More...
unsigned int * | make_referenceBP_array (short *reference_pt, unsigned int turn)
| Make a reference base pair count matrix. More...
unsigned int * | compute_BPdifferences (short *pt1, short *pt2, unsigned int turn)
| Make a reference base pair distance matrix. More...
void | assign_plist_from_pr (vrna_plist_t **pl, FLT_OR_DBL *probs, int length, double cutoff)
| Create a vrna_plist_t from a probability matrix. More...
void | parenthesis_structure (char *structure, vrna_bp_stack_t *bp, int length)
| Create a dot-backet/parenthesis structure from backtracking stack. More...
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 calculation in cofold.c. More...
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. More...
char | bppm_symbol (const float *x)
| Get a pseudo dot bracket notation for a given probability information. More...

## Detailed Description

Various utility- and helper-functions for secondary structure parsing, converting, etc.