Struct RnaSecondaryStructure 

pub struct RnaSecondaryStructure {
    pub pairs: Vec<Option<usize>>,
    pub length: usize,
}

An RNA secondary structure as a pair table.

Each position i in the sequence is either paired to some position j (pairs[i] = Some(j)) or unpaired (pairs[i] = None). Pairs are non-crossing: if i pairs with j, no pair (p, q) exists with i < p < j < q.

Fields

pairs: Vec<Option<usize>>

Pair table: pairs[i] = Some(j) if position i is paired with j.

length: usize

Length of the sequence.

Implementations

impl RnaSecondaryStructure

pub fn from_dot_bracket(s: &str) -> Result<Self>

Parse a dot-bracket string into a secondary structure.

( and ) denote paired bases; . denotes unpaired bases.

Errors

Returns an error if parentheses are unbalanced or the string contains characters other than (, ), and ..

Example

use cyanea_seq::rna_structure::RnaSecondaryStructure;

let s = RnaSecondaryStructure::from_dot_bracket("(((...)))").unwrap();
assert_eq!(s.num_pairs(), 3);

pub fn to_dot_bracket(&self) -> String

Convert this structure to dot-bracket notation.

Example

use cyanea_seq::rna_structure::RnaSecondaryStructure;

let s = RnaSecondaryStructure::from_dot_bracket("..((..))..").unwrap();
assert_eq!(s.to_dot_bracket(), "..((..))..");

pub fn base_pairs(&self) -> Vec<(usize, usize)>

Return sorted list of base pairs (i, j) where i < j.

pub fn is_paired(&self, i: usize) -> bool

Check whether position i is paired.

pub fn partner(&self, i: usize) -> Option<usize>

Return the pairing partner of position i, if any.

pub fn num_pairs(&self) -> usize

Number of base pairs in the structure.

Trait Implementations

impl Clone for RnaSecondaryStructure

fn clone(&self) -> RnaSecondaryStructure

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for RnaSecondaryStructure

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl PartialEq for RnaSecondaryStructure

fn eq(&self, other: &RnaSecondaryStructure) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl Eq for RnaSecondaryStructure

impl StructuralPartialEq for RnaSecondaryStructure