Deprecated Interface for Secondary Structure Utilities
Defines
-
STRUC
- #include <ViennaRNA/RNAstruct.h>
Functions
-
char *b2HIT(const char *structure)
- #include <ViennaRNA/RNAstruct.h>
Converts the full structure from bracket notation to the HIT notation including root.
- Deprecated:
See vrna_db_to_tree_string() and VRNA_STRUCTURE_TREE_HIT for a replacement
- Parameters:
structure –
- Returns:
-
char *b2C(const char *structure)
- #include <ViennaRNA/RNAstruct.h>
Converts the full structure from bracket notation to the a coarse grained notation using the ‘H’ ‘B’ ‘I’ ‘M’ and ‘R’ identifiers.
- Deprecated:
See vrna_db_to_tree_string() and VRNA_STRUCTURE_TREE_SHAPIRO_SHORT for a replacement
- Parameters:
structure –
- Returns:
-
char *b2Shapiro(const char *structure)
- #include <ViennaRNA/RNAstruct.h>
Converts the full structure from bracket notation to the weighted coarse grained notation using the ‘H’ ‘B’ ‘I’ ‘M’ ‘S’ ‘E’ and ‘R’ identifiers.
- Deprecated:
See vrna_db_to_tree_string() and VRNA_STRUCTURE_TREE_SHAPIRO_WEIGHT for a replacement
- Parameters:
structure –
- Returns:
-
char *add_root(const char *structure)
- #include <ViennaRNA/RNAstruct.h>
Adds a root to an un-rooted tree in any except bracket notation.
- Parameters:
structure –
- Returns:
-
char *expand_Shapiro(const char *coarse)
- #include <ViennaRNA/RNAstruct.h>
Inserts missing ‘S’ identifiers in unweighted coarse grained structures as obtained from b2C().
- Parameters:
coarse –
- Returns:
-
char *expand_Full(const char *structure)
- #include <ViennaRNA/RNAstruct.h>
Convert the full structure from bracket notation to the expanded notation including root.
- Parameters:
structure –
- Returns:
-
char *unexpand_Full(const char *ffull)
- #include <ViennaRNA/RNAstruct.h>
Restores the bracket notation from an expanded full or HIT tree, that is any tree using only identifiers ‘U’ ‘P’ and ‘R’.
- Parameters:
ffull –
- Returns:
-
char *unweight(const char *wcoarse)
- #include <ViennaRNA/RNAstruct.h>
Strip weights from any weighted tree.
- Parameters:
wcoarse –
- Returns:
-
void unexpand_aligned_F(char *align[2])
- #include <ViennaRNA/RNAstruct.h>
Converts two aligned structures in expanded notation.
Takes two aligned structures as produced by tree_edit_distance() function back to bracket notation with ‘_’ as the gap character. The result overwrites the input.
- Parameters:
align –
-
void parse_structure(const char *structure)
- #include <ViennaRNA/RNAstruct.h>
Collects a statistic of structure elements of the full structure in bracket notation.
The function writes to the following global variables: loop_size, loop_degree, helix_size, loops, pairs, unpaired
- Parameters:
structure –
-
char *pack_structure(const char *struc)
- #include <ViennaRNA/structures/dotbracket.h>
Pack secondary secondary structure, 5:1 compression using base 3 encoding.
Returns a binary string encoding of the secondary structure using a 5:1 compression scheme. The string is NULL terminated and can therefore be used with standard string functions such as strcmp(). Useful for programs that need to keep many structures in memory.
- Deprecated:
Use vrna_db_pack() as a replacement
- Parameters:
struc – The secondary structure in dot-bracket notation
- Returns:
The binary encoded structure
-
char *unpack_structure(const char *packed)
- #include <ViennaRNA/structures/dotbracket.h>
Unpack secondary structure previously packed with pack_structure()
Translate a compressed binary string produced by pack_structure() back into the familiar dot-bracket notation.
- Deprecated:
Use vrna_db_unpack() as a replacement
- Parameters:
packed – The binary encoded packed secondary structure
- Returns:
The unpacked secondary structure in dot-bracket notation
-
void parenthesis_structure(char *structure, vrna_bp_stack_t *bp, int length)
- #include <ViennaRNA/structures/dotbracket.h>
Create a dot-backet/parenthesis structure from backtracking stack.
- Deprecated:
use vrna_parenthesis_structure() instead
Note
This function is threadsafe
-
void parenthesis_zuker(char *structure, vrna_bp_stack_t *bp, int length)
- #include <ViennaRNA/structures/dotbracket.h>
Create a dot-backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.c.
- Deprecated:
use vrna_parenthesis_zuker instead
Note
This function is threadsafe
-
void bppm_to_structure(char *structure, FLT_OR_DBL *pr, unsigned int length)
- #include <ViennaRNA/structures/dotbracket.h>
Create a dot-bracket like structure string from base pair probability matrix.
- Deprecated:
Use vrna_db_from_probs() instead!
-
char bppm_symbol(const float *x)
- #include <ViennaRNA/structures/dotbracket.h>
Get a pseudo dot bracket notation for a given probability information.
- Deprecated:
Use vrna_bpp_symbol() instead!
-
int bp_distance(const char *str1, const char *str2)
- #include <ViennaRNA/structures/metrics.h>
Compute the “base pair” distance between two secondary structures s1 and s2.
The sequences should have the same length. dist = number of base pairs in one structure but not in the other same as edit distance with open-pair close-pair as move-set
- Deprecated:
Use vrna_bp_distance instead
- Parameters:
str1 – First structure in dot-bracket notation
str2 – Second structure in dot-bracket notation
- Returns:
The base pair distance between str1 and str2
-
short *make_pair_table(const char *structure)
- #include <ViennaRNA/structures/pairtable.h>
Create a pair table of a secondary structure.
Returns a newly allocated table, such that table[i]=j if (i.j) pair or 0 if i is unpaired, table[0] contains the length of the structure.
- Deprecated:
Use vrna_ptable() instead
- Parameters:
structure – The secondary structure in dot-bracket notation
- Returns:
A pointer to the created pair_table
-
short *copy_pair_table(const short *pt)
- #include <ViennaRNA/structures/pairtable.h>
Get an exact copy of a pair table.
- Deprecated:
Use vrna_ptable_copy() instead
- Parameters:
pt – The pair table to be copied
- Returns:
A pointer to the copy of ‘pt’
-
short *alimake_pair_table(const char *structure)
- #include <ViennaRNA/structures/pairtable.h>
Pair table for snoop align
- Deprecated:
Use vrna_pt_ali_get() instead!
-
short *make_pair_table_snoop(const char *structure)
- #include <ViennaRNA/structures/pairtable.h>
returns a newly allocated table, such that: table[i]=j if (i.j) pair or 0 if i is unpaired, table[0] contains the length of the structure. The special pseudoknotted H/ACA-mRNA structure is taken into account.
- Deprecated:
Use vrna_pt_snoop_get() instead!
-
unsigned int *make_referenceBP_array(short *reference_pt, unsigned int turn)
- #include <ViennaRNA/structures/utils.h>
Make a reference base pair count matrix.
Get an upper triangular matrix containing the number of basepairs of a reference structure for each interval [i,j] with i<j. Access it via iindx!!!
- Deprecated:
Use vrna_refBPcnt_matrix() instead
-
unsigned int *compute_BPdifferences(short *pt1, short *pt2, unsigned int turn)
- #include <ViennaRNA/structures/utils.h>
Make a reference base pair distance matrix.
Get an upper triangular matrix containing the base pair distance of two reference structures for each interval [i,j] with i<j. Access it via iindx!!!
- Deprecated:
Use vrna_refBPdist_matrix() instead
Variables
-
int loop_size[2000]
contains a list of all loop sizes. loop_size[0] contains the number of external bases.
-
int helix_size[2000]
contains a list of all stack sizes.
-
int loop_degree[2000]
contains the corresponding list of loop degrees.
-
int loops
contains the number of loops ( and therefore of stacks ).
-
int unpaired
contains the number of unpaired bases.
-
int pairs
contains the number of base pairs in the last parsed structure.
-
STRUC