rna_folding.hh File Reference

RNA folding algorithm implementation. More...

#include <algorithm>
#include <iostream>
#include <vector>
#include <fstream>
#include "herrlog.hh"

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Functions
std::vector< std::vector< int > >	create_matrix (const std::string &rna_sequence, const int &minimal_loop_length=0)
	Function to create the DP matrix for RNA folding. More...
int	rna_score (const std::string &rna_sequence, const int &minimal_loop_length=0)
	Function to calculate number of bonds (theoretical) in the RNA. More...
void	traceback (const std::vector< std::vector< int >> &nm, const std::string &rna, std::vector< std::pair< int, int >> &fold, int i, int j)
	Function to traceback DP and get the bonds structure. More...
std::string	dot_write (const std::string &rna, const std::vector< std::pair< int, int >> &fold)
	Function to create the dot-bracket notation from the bonds. More...
void	dot_bracket_to_dot (const std::string &sequence, const std::string &structure)
	Creates a DOT script from the RNA sequence and structure and calls graphviz. More...

Detailed Description

RNA folding algorithm implementation.

Author

Adarsh Das (saphereye.github.io)

Copyright

Copyright (c) 2024

Definition in file rna_folding.hh.

Function Documentation

create_matrix()

std::vector<std::vector<int> > create_matrix	(	const std::string &	rna_sequence,
		const int &	minimal_loop_length = 0
	)

Function to create the DP matrix for RNA folding.

Parameters

rna_sequence

Returns

int

Definition at line 22 of file rna_folding.hh.

dot_bracket_to_dot()

void dot_bracket_to_dot	(	const std::string &	sequence,
		const std::string &	structure
	)

Creates a DOT script from the RNA sequence and structure and calls graphviz.

Parameters

sequence
structure

Definition at line 129 of file rna_folding.hh.

dot_write()

std::string dot_write	(	const std::string &	rna,
		const std::vector< std::pair< int, int >> &	fold
	)

Function to create the dot-bracket notation from the bonds.

Parameters

rna
fold

Returns

std::string

Definition at line 111 of file rna_folding.hh.

rna_score()

int rna_score	(	const std::string &	rna_sequence,
		const int &	minimal_loop_length = 0
	)

Function to calculate number of bonds (theoretical) in the RNA.

Parameters

rna_sequence
minimal_loop_length

Returns

int

Definition at line 61 of file rna_folding.hh.

traceback()

void traceback	(	const std::vector< std::vector< int >> &	nm,
		const std::string &	rna,
		std::vector< std::pair< int, int >> &	fold,
		int	i,
		int	j
	)

Function to traceback DP and get the bonds structure.

Parameters

nm
rna
fold
i
j

Definition at line 77 of file rna_folding.hh.