structures.h File Reference
Various utility- and helper-functions for secondary structure parsing, converting, etc. More...
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Data Structures | |
| struct | vrna_elem_prob_s |
| Data structure representing a single entry of an element probability list (e.g. list of pair probabilities) More... | |
| struct | vrna_hx_s |
| Data structure representing an entry of a helix list. More... | |
Macros | |
| #define | VRNA_BRACKETS_ALPHA 4U |
| Bitflag to indicate secondary structure notations using uppercase/lowercase letters from the latin alphabet. More... | |
| #define | VRNA_BRACKETS_RND 8U |
Bitflag to indicate secondary structure notations using round brackets (parenthesis), () More... | |
| #define | VRNA_BRACKETS_CLY 16U |
Bitflag to indicate secondary structure notations using curly brackets, {} More... | |
| #define | VRNA_BRACKETS_ANG 32U |
Bitflag to indicate secondary structure notations using angular brackets, <> More... | |
| #define | VRNA_BRACKETS_SQR 64U |
Bitflag to indicate secondary structure notations using square brackets, [] More... | |
| #define | VRNA_BRACKETS_DEFAULT |
| Default bitmask to indicate secondary structure notation using any pair of brackets. More... | |
| #define | VRNA_BRACKETS_ANY |
| Bitmask to indicate secondary structure notation using any pair of brackets or uppercase/lowercase alphabet letters. More... | |
| #define | VRNA_PLIST_TYPE_BASEPAIR 0 |
| A Base Pair element. | |
| #define | VRNA_PLIST_TYPE_GQUAD 1 |
| A G-Quadruplex element. | |
| #define | VRNA_PLIST_TYPE_H_MOTIF 2 |
| A Hairpin loop motif element. | |
| #define | VRNA_PLIST_TYPE_I_MOTIF 3 |
| An Internal loop motif element. | |
| #define | VRNA_PLIST_TYPE_UD_MOTIF 4 |
| An Unstructured Domain motif element. | |
| #define | VRNA_PLIST_TYPE_STACK 5 |
| A Base Pair stack element. | |
| #define | VRNA_STRUCTURE_TREE_HIT 1U |
| Homeomorphically Irreducible Tree (HIT) representation of a secondary structure. More... | |
| #define | VRNA_STRUCTURE_TREE_SHAPIRO_SHORT 2U |
| (short) Coarse Grained representation of a secondary structure More... | |
| #define | VRNA_STRUCTURE_TREE_SHAPIRO 3U |
| (full) Coarse Grained representation of a secondary structure More... | |
| #define | VRNA_STRUCTURE_TREE_SHAPIRO_EXT 4U |
| (extended) Coarse Grained representation of a secondary structure More... | |
| #define | VRNA_STRUCTURE_TREE_SHAPIRO_WEIGHT 5U |
| (weighted) Coarse Grained representation of a secondary structure More... | |
| #define | VRNA_STRUCTURE_TREE_EXPANDED 6U |
| Expanded Tree representation of a secondary structure. More... | |
Typedefs | |
| typedef struct vrna_hx_s | vrna_hx_t |
| Convenience typedef for data structure vrna_hx_s. | |
| typedef struct vrna_elem_prob_s | vrna_ep_t |
| Convenience typedef for data structure vrna_elem_prob_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... | |
| void | vrna_db_flatten (char *structure, unsigned int options) |
| Substitute pairs of brackets in a string with parenthesis. More... | |
| 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. More... | |
| char * | vrna_db_from_ptable (short *pt) |
| Convert a pair table into dot-parenthesis notation. More... | |
| char * | vrna_db_from_WUSS (const char *wuss) |
| Convert a WUSS annotation string to dot-bracket format. More... | |
| char * | vrna_db_from_plist (vrna_ep_t *pairs, unsigned int n) |
| Convert a list of base pairs into dot-bracket notation. More... | |
| char * | vrna_db_to_element_string (const char *structure) |
| Convert a secondary structure in dot-bracket notation to a nucleotide annotation of loop contexts. More... | |
| char * | vrna_db_pk_remove (const char *structure, unsigned int options) |
| Remove pseudo-knots from an input structure. More... | |
| short * | vrna_ptable (const char *structure) |
| Create a pair table from a dot-bracket notation of a secondary structure. More... | |
| short * | vrna_ptable_from_string (const char *string, unsigned int options) |
| Create a pair table for a secondary structure string. 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... | |
| short * | vrna_pt_pk_remove (const short *ptable, unsigned int options) |
| Remove pseudo-knots from a pair table. More... | |
| vrna_ep_t * | vrna_plist (const char *struc, float pr) |
| Create a vrna_ep_t from a dot-bracket string. More... | |
| 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. More... | |
| vrna_hx_t * | vrna_hx_from_ptable (short *pt) |
| Convert a pair table representation of a secondary structure into a helix list. More... | |
| vrna_hx_t * | vrna_hx_merge (const vrna_hx_t *list, int maxdist) |
| Create a merged helix list from another helix list. | |
| int * | vrna_loopidx_from_ptable (const short *pt) |
| Get a loop index representation of a structure. | |
| 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... | |
| char * | vrna_db_to_tree_string (const char *structure, unsigned int type) |
| Convert a Dot-Bracket structure string into tree string representation. More... | |
| char * | vrna_tree_string_unweight (const char *structure) |
| Remove weights from a linear string tree representation of a secondary structure. More... | |
| char * | vrna_tree_string_to_db (const char *tree) |
| Convert a linear tree string representation of a secondary structure back to Dot-Bracket notation. More... | |
| void | assign_plist_from_db (vrna_ep_t **pl, const char *struc, float pr) |
| Create a vrna_ep_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_ep_t **pl, FLT_OR_DBL *probs, int length, double cutoff) |
| Create a vrna_ep_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.
