SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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seqan3::dssp9 Class Reference

The protein structure alphabet of the characters "HGIEBTSCX". More...

#include <seqan3/alphabet/structure/dssp9.hpp>

+ Inheritance diagram for seqan3::dssp9:

Public Member Functions

Constructors, destructor and assignment
constexpr dssp9 () noexcept=default
constexpr dssp9 (dssp9 const &) noexcept=default
constexpr dssp9 (dssp9 &&) noexcept=default
constexpr dssp9operator= (dssp9 const &) noexcept=default
constexpr dssp9operator= (dssp9 &&) noexcept=default
 ~dssp9 () noexcept=default
- Public Member Functions inherited from seqan3::alphabet_base< dssp9, 9 >
constexpr alphabet_base () noexcept=default
constexpr alphabet_base (alphabet_base const &) noexcept=default
constexpr alphabet_base (alphabet_base &&) noexcept=default
constexpr alphabet_baseoperator= (alphabet_base const &) noexcept=default
constexpr alphabet_baseoperator= (alphabet_base &&) noexcept=default
 ~alphabet_base () noexcept=default
constexpr char_type to_char () const noexcept
 Return the letter as a character of char_type.
constexpr rank_type to_rank () const noexcept
 Return the letter's numeric value (rank in the alphabet).
constexpr dssp9assign_char (char_type const chr) noexcept
 Assign from a character, implicitly converts invalid characters.
constexpr dssp9assign_rank (rank_type const c) noexcept
 Assign from a numeric value.

Additional Inherited Members

- Static Public Attributes inherited from seqan3::alphabet_base< dssp9, 9 >
static constexpr detail::min_viable_uint_t< size > alphabet_size
 The size of the alphabet, i.e. the number of different values it can take.
- Protected Types inherited from seqan3::alphabet_base< dssp9, 9 >
using char_type = std::conditional_t< std::same_as< char, void >, char, char >
 The char representation; conditional needed to make semi alphabet definitions legal.
using rank_type = detail::min_viable_uint_t< size - 1 >
 The type of the alphabet when represented as a number (e.g. via to_rank()).

Detailed Description

The protein structure alphabet of the characters "HGIEBTSCX".

The DSSP annotation links structure elements to protein sequences. Originally created with 7 letters as a file format for the DSSP program (, it is also used in the stockholm file format for structure alignments, extended by the characters C and X (

The letter abbreviations are as follows:

H = alpha helix B = beta bridge E = strand G = helix-3 I = helix-5 T = turn S = bend C = coil/loop X = unknown


// 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
int main()
using namespace seqan3::literals;
seqan3::dssp9 letter{'H'_dssp9};
seqan3::debug_stream << letter << '\n'; // prints "B"
letter.assign_char('F'); // Unknown characters are implicitly converted to 'X'.
seqan3::debug_stream << letter << '\n'; // prints "X"
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition alphabet_base.hpp:160
The protein structure alphabet of the characters "HGIEBTSCX".
Definition dssp9.hpp:59
Provides seqan3::debug_stream and related types.
Provides the dssp format for protein structure.
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition debug_stream.hpp:37
The SeqAn namespace for literals.

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

The documentation for this class was generated from the following file:
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