RNAlib-2.2.7
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Various utility- and helper-functions for secondary structure parsing, converting, etc. More...
Go to the source code of this file.
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... | |
Various utility- and helper-functions for secondary structure parsing, converting, etc.