RNAlib-2.5.1
Distance measures between Secondary Structures

Detailed Description

+ Collaboration diagram for Distance measures between Secondary Structures:

Functions

int vrna_bp_distance_pt (const short *pt1, const short *pt2)
 Compute the "base pair" distance between two pair tables pt1 and pt2 of secondary structures. More...
 
int vrna_bp_distance (const char *str1, const char *str2)
 Compute the "base pair" distance between two secondary structures s1 and s2. More...
 

Function Documentation

◆ vrna_bp_distance_pt()

int vrna_bp_distance_pt ( const short *  pt1,
const short *  pt2 
)

#include <ViennaRNA/utils/structures.h>

Compute the "base pair" distance between two pair tables pt1 and pt2 of secondary structures.

The pair tables 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

See also
vrna_bp_distance()
Parameters
pt1First structure in dot-bracket notation
pt2Second structure in dot-bracket notation
Returns
The base pair distance between pt1 and pt2
SWIG Wrapper Notes:
This function is available as an overloaded method bp_distance().

◆ vrna_bp_distance()

int vrna_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.

This is a wrapper around vrna_bp_distance_pt(). 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

See also
vrna_bp_distance_pt()
Parameters
str1First structure in dot-bracket notation
str2Second structure in dot-bracket notation
Returns
The base pair distance between str1 and str2
SWIG Wrapper Notes:
This function is available as an overloaded method bp_distance(). Note that the SWIG wrapper takes two structure in dot-bracket notation and converts them into pair tables using vrna_ptable_from_string(). The resulting pair tables are then internally passed to vrna_bp_distance_pt(). To control which kind of matching brackets will be used during conversion, the optional argument options can be used. See also the description of vrna_ptable_from_string() for available options. (default: VRNA_BRACKETS_RND).