Structure

Provides types to represent single elements of RNA and protein structures. More...

Collaboration diagram for Structure:

Classes
class	seqan3::dot_bracket3
	The three letter RNA structure alphabet of the characters ".()". More...
class	seqan3::dssp9
	The protein structure alphabet of the characters "HGIEBTSCX". More...
interface	rna_structure_alphabet
	A concept that indicates whether an alphabet represents RNA structure. More...
class	seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >
	A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet. More...
class	seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >
	A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet. More...
class	seqan3::wuss< SIZE >
	The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd... More...

Variables
constexpr auto	seqan3::is_pair_close = detail::adl_only::is_pair_close_cpo{}
	Check whether the given character represents a leftward interaction in an RNA structure.
constexpr auto	seqan3::is_pair_open = detail::adl_only::is_pair_open_cpo{}
	Check whether the given character represents a rightward interaction in an RNA structure.
constexpr auto	seqan3::is_unpaired = detail::adl_only::is_unpaired_cpo{}
	Check whether the given character represents an unpaired nucleotide in an RNA structure.
template<typename alph_t >
constexpr auto	seqan3::max_pseudoknot_depth = detail::adl_only::max_pseudoknot_depth_cpo<alph_t>{}()
	A type trait that holds the ability of the structure alphabet to represent pseudoknots, i.e. crossing interactions, up to a certain depth.
constexpr auto	seqan3::pseudoknot_id = detail::adl_only::pseudoknot_id_cpo{}
	Retrieve an id for the level of a pseudoknotted interaction (also known as 'page number').

Detailed Description

Provides types to represent single elements of RNA and protein structures.

See also

Alphabet

The following alphabets are currently supported in SeqAn. Please see the format's page for more details.

Name	Chars	Description
Dot Bracket	().	Simple annotation that defines base pairs. No pseudoknots allowed.
WUSS	.<>:,-_~;()[]{}AaBb...	Annotation that provides further markups and pseudoknots.
DSSP	HBEGITSCX	Structure encoding for proteins.

Variable Documentation

is_pair_close

constexpr auto seqan3::is_pair_close = detail::adl_only::is_pair_close_cpo{}

inlineconstexpr

Check whether the given character represents a leftward interaction in an RNA structure.

Template Parameters

your_type

Type of the argument.

Parameters

chr	The RNA structure character whose property is checked.

Returns

True if the character represents a leftward interaction, False otherwise.

This is a function object. Invoke it with the parameter(s) specified above.

It acts as a wrapper and looks for three possible implementations (in this order):

1. A static member function is_pair_close(your_type const a) of the class seqan3::custom::alphabet<your_type>.
2. A free function is_pair_close(your_type const a) in the namespace of your type (or as friend).
3. A member function called is_pair_close().

Functions are only considered for one of the above cases if they are marked noexcept (constexpr is not required, but recommended) and if the returned type is bool.

Every RNA structure alphabet type must provide one of the above.

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <iostream>
 
#include <seqan3/alphabet/structure/wuss.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    bool is_closing_char_member = '}'_wuss51.is_pair_close();
    bool is_closing_char_free = seqan3::is_pair_close('.'_wuss51);
 
    std::cout << std::boolalpha << is_closing_char_member << '\n'; // true
    std::cout << std::boolalpha << is_closing_char_free << '\n';   // false
}

Customisation point

This is a customisation point (see Customisation). To specify the behaviour for your own alphabet type, simply provide one of the three functions specified above.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

is_pair_open

constexpr auto seqan3::is_pair_open = detail::adl_only::is_pair_open_cpo{}

inlineconstexpr

Check whether the given character represents a rightward interaction in an RNA structure.

Template Parameters

your_type

Type of the argument.

Parameters

chr	The RNA structure character whose property is checked.

Returns

True if the character represents a rightward interaction, False otherwise.

This is a function object. Invoke it with the parameter(s) specified above.

It acts as a wrapper and looks for three possible implementations (in this order):

1. A static member function is_pair_open(your_type const a) of the class seqan3::custom::alphabet<your_type>.
2. A free function is_pair_open(your_type const a) in the namespace of your type (or as friend).
3. A member function called is_pair_open().

Functions are only considered for one of the above cases if they are marked noexcept (constexpr is not required, but recommended) and if the returned type is bool.

Every RNA structure alphabet type must provide one of the above.

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <iostream>
 
#include <seqan3/alphabet/structure/wuss.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    bool is_opening_char_member = '{'_wuss51.is_pair_open();
    bool is_opening_char_free = seqan3::is_pair_open('.'_wuss51);
 
    std::cout << std::boolalpha << is_opening_char_member << '\n'; // true
    std::cout << std::boolalpha << is_opening_char_free << '\n';   // false
}

Customisation point

This is a customisation point (see Customisation). To specify the behaviour for your own alphabet type, simply provide one of the three functions specified above.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

is_unpaired

constexpr auto seqan3::is_unpaired = detail::adl_only::is_unpaired_cpo{}

inlineconstexpr

Check whether the given character represents an unpaired nucleotide in an RNA structure.

Template Parameters

your_type

Type of the argument.

Parameters

chr	The RNA structure character whose property is checked.

Returns

True if the character represents an unpaired site, False otherwise.

This is a function object. Invoke it with the parameter(s) specified above.

It acts as a wrapper and looks for three possible implementations (in this order):

1. A static member function is_unpaired(your_type const a) of the class seqan3::custom::alphabet<your_type>.
2. A free function is_unpaired(your_type const a) in the namespace of your type (or as friend).
3. A member function called is_unpaired().

Functions are only considered for one of the above cases if they are marked noexcept (constexpr is not required, but recommended) and if the returned type is bool.

Every RNA structure alphabet type must provide one of the above.

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <iostream>
 
#include <seqan3/alphabet/structure/wuss.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    bool is_unpaired_char_member = '.'_wuss51.is_unpaired();
    bool is_unpaired_char_free = seqan3::is_unpaired('{'_wuss51);
 
    std::cout << std::boolalpha << is_unpaired_char_member << '\n'; // true
    std::cout << std::boolalpha << is_unpaired_char_free << '\n';   // false
}

Customisation point

This is a customisation point (see Customisation). To specify the behaviour for your own alphabet type, simply provide one of the three functions specified above.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

max_pseudoknot_depth

template<typename alph_t >

constexpr auto seqan3::max_pseudoknot_depth = detail::adl_only::max_pseudoknot_depth_cpo<alph_t>{}()

inlineconstexpr

A type trait that holds the ability of the structure alphabet to represent pseudoknots, i.e. crossing interactions, up to a certain depth.

Template Parameters

your_type

Type of the argument.

Parameters

chr	The RNA structure character whose property is checked.

Returns

The maximum supported nestedness, or 1 if the alphabet cannot support pseudoknots.

The value is the maximum allowed depth of pseudoknots. A value of 1 denotes no pseudoknots ((....)), while higher values denote the maximum allowed complexity of crossing interactions, e.g. depth 2 (({....))} or depth 3 ({[....)}].

This is a function object. Invoke it with the parameter(s) specified above.

It acts as a wrapper and looks for three possible implementations (in this order):

1. A static member variable max_pseudoknot_depth of the class seqan3::custom::alphabet<your_type>.
2. A free function max_pseudoknot_depth(your_type const) in the namespace of your type (or as friend).
3. A static member variable max_pseudoknot_depth of the class your_type.

Functions/variables are only considered for one of the above cases if they are marked noexcept and constexpr and if the returned type is convertible to size_t. For 2. the value of the argument to the function shall be ignored, the argument is only used to select the function via argument-dependent lookup.

Every RNA structure alphabet type must provide one of the above.

Example

These are the expressions to retrieve the value:

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <iostream>
 
#include <seqan3/alphabet/structure/wuss.hpp>
 
int main()
{
    uint8_t max_depth_member = seqan3::wuss51::max_pseudoknot_depth;
    uint8_t max_depth_meta = seqan3::max_pseudoknot_depth<seqan3::wuss51>;
    std::cout << static_cast<uint16_t>(max_depth_member) << '\n'; // 22
    std::cout << static_cast<uint16_t>(max_depth_meta) << '\n';   // 22
}

Customisation point

This is a customisation point (see Customisation). To specify the behaviour for your own alphabet type, simply provide one of the three functions specified above.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

pseudoknot_id

constexpr auto seqan3::pseudoknot_id = detail::adl_only::pseudoknot_id_cpo{}

inlineconstexpr

Retrieve an id for the level of a pseudoknotted interaction (also known as 'page number').

Template Parameters

your_type

Type of the argument.

Parameters

chr	The RNA structure character whose property is checked.

Returns

A std::optional containing the pseudoknot identifier if alph represents an interaction. The returned value is std::nullopt for unpaired sites. For non-nested interactions the identifier is always 0. It is guaranteed to be smaller than seqan3::max_pseudoknot_depth.

This is a function object. Invoke it with the parameter(s) specified above.

It acts as a wrapper and looks for three possible implementations (in this order):

1. A static member function pseudoknot_id(your_type const a) of the class seqan3::custom::alphabet<your_type>.
2. A free function pseudoknot_id(your_type const a) in the namespace of your type (or as friend).
3. A member function of your_type called pseudoknot_id().

Functions are only considered for one of the above cases if they are marked noexcept (constexpr is not required, but recommended) and the return type is convertible to size_t.

Every RNA structure alphabet type must provide one of the above.

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/structure/wuss.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    auto pk_opt = '.'_wuss51.pseudoknot_id();   // std::optional -> false
    pk_opt = seqan3::pseudoknot_id('{'_wuss51); // std::optional -> true: 3
 
    if (pk_opt)
        seqan3::debug_stream << *pk_opt << '\n'; // 3
}

Customisation point

This is a customisation point (see Customisation). To specify the behaviour for your own alphabet type, simply provide one of the three functions specified above.

This entity is experimental and subject to change in the future. Experimental since version 3.1.