RNAlib-2.5.1
Deprecated Interface for Secondary Structure Utilities

Detailed Description

+ Collaboration diagram for Deprecated Interface for Secondary Structure Utilities:

Files

file  RNAstruct.h
 Parsing and Coarse Graining of Structures.
 

Functions

char * b2HIT (const char *structure)
 Converts the full structure from bracket notation to the HIT notation including root. More...
 
char * b2C (const char *structure)
 Converts the full structure from bracket notation to the a coarse grained notation using the 'H' 'B' 'I' 'M' and 'R' identifiers. More...
 
char * b2Shapiro (const char *structure)
 Converts the full structure from bracket notation to the weighted coarse grained notation using the 'H' 'B' 'I' 'M' 'S' 'E' and 'R' identifiers. More...
 
char * add_root (const char *structure)
 Adds a root to an un-rooted tree in any except bracket notation. More...
 
char * expand_Shapiro (const char *coarse)
 Inserts missing 'S' identifiers in unweighted coarse grained structures as obtained from b2C(). More...
 
char * expand_Full (const char *structure)
 Convert the full structure from bracket notation to the expanded notation including root. More...
 
char * unexpand_Full (const char *ffull)
 Restores the bracket notation from an expanded full or HIT tree, that is any tree using only identifiers 'U' 'P' and 'R'. More...
 
char * unweight (const char *wcoarse)
 Strip weights from any weighted tree. More...
 
void unexpand_aligned_F (char *align[2])
 Converts two aligned structures in expanded notation. More...
 
void parse_structure (const char *structure)
 Collects a statistic of structure elements of the full structure in bracket notation. 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 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...
 

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.
 

Function Documentation

◆ b2HIT()

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

◆ b2C()

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

◆ b2Shapiro()

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

◆ add_root()

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

◆ expand_Shapiro()

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

◆ expand_Full()

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

◆ unexpand_Full()

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

◆ unweight()

char * unweight ( const char *  wcoarse)

#include <ViennaRNA/RNAstruct.h>

Strip weights from any weighted tree.

Parameters
wcoarse
Returns

◆ unexpand_aligned_F()

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

◆ parse_structure()

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

◆ pack_structure()

char * pack_structure ( const char *  struc)

#include <ViennaRNA/utils/structures.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
strucThe secondary structure in dot-bracket notation
Returns
The binary encoded structure

◆ unpack_structure()

char * unpack_structure ( const char *  packed)

#include <ViennaRNA/utils/structures.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
packedThe binary encoded packed secondary structure
Returns
The unpacked secondary structure in dot-bracket notation

◆ make_pair_table()

short * make_pair_table ( const char *  structure)

#include <ViennaRNA/utils/structures.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
structureThe secondary structure in dot-bracket notation
Returns
A pointer to the created pair_table

◆ copy_pair_table()

short * copy_pair_table ( const short *  pt)

#include <ViennaRNA/utils/structures.h>

Get an exact copy of a pair table.

Deprecated:
Use vrna_ptable_copy() instead
Parameters
ptThe pair table to be copied
Returns
A pointer to the copy of 'pt'

◆ alimake_pair_table()

short * alimake_pair_table ( const char *  structure)

#include <ViennaRNA/utils/structures.h>

Pair table for snoop align

Deprecated:
Use vrna_pt_ali_get() instead!

◆ make_pair_table_snoop()

short * make_pair_table_snoop ( const char *  structure)

#include <ViennaRNA/utils/structures.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!

◆ bp_distance()

int bp_distance ( const char *  str1,
const char *  str2 
)

#include <ViennaRNA/utils/structures.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
str1First structure in dot-bracket notation
str2Second structure in dot-bracket notation
Returns
The base pair distance between str1 and str2

◆ make_referenceBP_array()

unsigned int * make_referenceBP_array ( short *  reference_pt,
unsigned int  turn 
)

#include <ViennaRNA/utils/structures.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

◆ compute_BPdifferences()

unsigned int * compute_BPdifferences ( short *  pt1,
short *  pt2,
unsigned int  turn 
)

#include <ViennaRNA/utils/structures.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

◆ parenthesis_structure()

void parenthesis_structure ( char *  structure,
vrna_bp_stack_t bp,
int  length 
)

#include <ViennaRNA/utils/structures.h>

Create a dot-backet/parenthesis structure from backtracking stack.

Deprecated:
use vrna_parenthesis_structure() instead
Note
This function is threadsafe

◆ parenthesis_zuker()

void parenthesis_zuker ( char *  structure,
vrna_bp_stack_t bp,
int  length 
)

#include <ViennaRNA/utils/structures.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

◆ bppm_to_structure()

void bppm_to_structure ( char *  structure,
FLT_OR_DBL pr,
unsigned int  length 
)

#include <ViennaRNA/utils/structures.h>

Create a dot-bracket like structure string from base pair probability matrix.

Deprecated:
Use vrna_db_from_probs() instead!

◆ bppm_symbol()

char bppm_symbol ( const float *  x)

#include <ViennaRNA/utils/structures.h>

Get a pseudo dot bracket notation for a given probability information.

Deprecated:
Use vrna_bpp_symbol() instead!