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Parsing, Converting, and Comparing - Functions to Manipulate Secondary Structures
Utilities
Collaboration diagram for Parsing, Converting, and Comparing - Functions to Manipulate Secondary Structures:

## Files
file | RNAstruct.h
| Parsing and Coarse Graining of Structures.
file | structure_utils.h
| Various utility- and helper-functions for secondary structure parsing, converting, etc.

## Data Structures
struct | vrna_hx_s
| Data structure representing an entry of a helix list. More...

## Typedefs
typedef struct vrna_hx_s | vrna_hx_t
| Convenience typedef for data structure vrna_hx_s.

## 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 * | 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...
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 | 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 [STRUC]
| contains a list of all loop sizes. loop_size[0] contains the number of external bases.
int | helix_size [STRUC]
| contains a list of all stack sizes.
int | loop_degree [STRUC]
| 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.

## Detailed Description

## Data Structure Documentation

struct vrna_hx_s

Data structure representing an entry of a helix list.

## Function Documentation

char* b2HIT | ( | const char * | structure | ) |

`#include <ViennaRNA/RNAstruct.h>`

Converts the full structure from bracket notation to the HIT notation including root.

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.

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.

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 |

Returns

char* vrna_db_pack | ( | const char * | struc | ) |

`#include <ViennaRNA/structure_utils.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.

See also
  vrna_db_unpack()

Parameters

  struc | The secondary structure in dot-bracket notation

Returns
  The binary encoded structure

char* vrna_db_unpack | ( | const char * | packed | ) |

`#include <ViennaRNA/structure_utils.h>`

Unpack secondary structure previously packed with vrna_db_pack()

Translate a compressed binary string produced by vrna_db_pack() back into the familiar dot-bracket notation.

See also
  vrna_db_pack()

Parameters

  packed | The binary encoded packed secondary structure

Returns
  The unpacked secondary structure in dot-bracket notation

short* vrna_ptable | ( | const char * | structure | ) |

`#include <ViennaRNA/structure_utils.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.

Parameters

  structure | The secondary structure in dot-bracket notation

Returns
  A pointer to the created pair_table

short* vrna_pt_pk_get | ( | const char * | structure | ) |

`#include <ViennaRNA/structure_utils.h>`

Create a pair table of a secondary structure (pseudo-knot version)

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.

In contrast to vrna_ptable() this function also recognizes the base pairs denoted by '[' and ']' brackets.

Parameters

  structure | The secondary structure in (extended) dot-bracket notation

Returns
  A pointer to the created pair_table

short* vrna_ptable_copy | ( | const short * | pt | ) |

`#include <ViennaRNA/structure_utils.h>`

Get an exact copy of a pair table.

Parameters

  pt | The pair table to be copied

Returns
  A pointer to the copy of 'pt'

short* vrna_pt_snoop_get | ( | const char * | structure | ) |

`#include <ViennaRNA/structure_utils.h>`

Create a pair table of a secondary structure (snoop version)

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.

char* vrna_db_from_ptable | ( | short * | pt | ) |

`#include <ViennaRNA/structure_utils.h>`

Convert a pair table into dot-parenthesis notation.

Parameters

  pt | The pair table to be copied

Returns
  A char pointer to the dot-bracket string

int vrna_bp_distance | ( | const char * | str1,
|  | const char * | str2
| ) |  |

`#include <ViennaRNA/structure_utils.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

Parameters

  str1 | First structure in dot-bracket notation
  str2 | Second structure in dot-bracket notation

Returns
  The base pair distance between str1 and str2

unsigned int* vrna_refBPcnt_matrix | ( | const short * | reference_pt,
|  | unsigned int | turn
| ) |  |

`#include <ViennaRNA/structure_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!!!

unsigned int* vrna_refBPdist_matrix | ( | const short * | pt1,
|  | const short * | pt2,
|  | unsigned int | turn
| ) |  |

`#include <ViennaRNA/structure_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!!!

char* vrna_db_from_bp_stack | ( | vrna_bp_stack_t * | bp,
|  | unsigned int | length
| ) |  |

`#include <ViennaRNA/structure_utils.h>`

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

This function is capable to create dot-bracket structures from suboptimal structure prediction sensu M. Zuker

Parameters

  bp | Base pair stack containing the traced base pairs
  length | The length of the structure

Returns
  The secondary structure in dot-bracket notation as provided in the input

vrna_plist_t* vrna_plist | ( | const char * | struc,
|  | float | pr
| ) |  |

`#include <ViennaRNA/structure_utils.h>`

Create a vrna_plist_t from a dot-bracket string.

The dot-bracket string is parsed and for each base pair an entry in the plist is created. The probability of each pair in the list is set by a function parameter.

The end of the plist is marked by sequence positions i as well as j equal to 0. This condition should be used to stop looping over its entries

Parameters

  struc | The secondary structure in dot-bracket notation
  pr | The probability for each base pair used in the plist

Returns
  The plist array

char* vrna_db_from_plist | ( | vrna_plist_t * | pairs,
|  | unsigned int | n
| ) |  |

`#include <ViennaRNA/structure_utils.h>`

Convert a list of base pairs into dot-bracket notation.

See also
  vrna_plist()

Parameters

  pairs | A vrna_plist_t containing the pairs to be included in the dot-bracket string
  n | The length of the structure (number of nucleotides)

Returns
  The dot-bracket string containing the provided base pairs

void assign_plist_from_db | ( | vrna_plist_t ** | pl,
|  | const char * | struc,
|  | float | pr
| ) |  |

`#include <ViennaRNA/structure_utils.h>`

Create a vrna_plist_t from a dot-bracket string.

The dot-bracket string is parsed and for each base pair an entry in the plist is created. The probability of each pair in the list is set by a function parameter.

The end of the plist is marked by sequence positions i as well as j equal to 0. This condition should be used to stop looping over its entries

Deprecated:
  Use vrna_plist() instead

Parameters

  pl | A pointer to the vrna_plist_t that is to be created
  struc | The secondary structure in dot-bracket notation
  pr | The probability for each base pair

char* pack_structure | ( | const char * | struc | ) |

`#include <ViennaRNA/structure_utils.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/structure_utils.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

short* make_pair_table | ( | const char * | structure | ) |

`#include <ViennaRNA/structure_utils.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/structure_utils.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/structure_utils.h>`

Pair table for snoop align

Deprecated:
  Use vrna_pt_ali_get() instead!

short* make_pair_table_snoop | ( | const char * | structure | ) |

`#include <ViennaRNA/structure_utils.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!

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

`#include <ViennaRNA/structure_utils.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

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

`#include <ViennaRNA/structure_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/structure_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

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

`#include <ViennaRNA/structure_utils.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/structure_utils.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/structure_utils.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/structure_utils.h>`

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

Deprecated:
  Use vrna_bpp_symbol() instead!