Distance measures between Secondary Structures

Functions

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

SWIG Wrapper Notes:: This function is available as an overloaded method bp_distance(). See, e.g. RNA.bp_distance() in the Python API.

See also

vrna_bp_distance()

Parameters:

pt1 – First structure in dot-bracket notation
pt2 – Second structure in dot-bracket notation

Returns:

The base pair distance between pt1 and pt2

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

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). See, e.g. RNA.bp_distance() in the Python API.