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
	Defaulted.
constexpr	dssp9 (dssp9 const &) noexcept=default
	Defaulted.
constexpr	dssp9 (dssp9 &&) noexcept=default
	Defaulted.
constexpr dssp9 &	operator= (dssp9 const &) noexcept=default
	Defaulted.
constexpr dssp9 &	operator= (dssp9 &&) noexcept=default
	Defaulted.
	~dssp9 () noexcept=default
Read functions
constexpr char_type	to_char () const noexcept
	Return the letter as a character of char_type. More...
constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet). More...
Write functions
constexpr dssp9 &	assign_char (char_type const c) noexcept
	Assign from a character, implicitly converts invalid characters. More...
constexpr dssp9 &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value. More...

Static Public Attributes
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. More...

Protected Types
Member types
using	char_type = std::conditional_t< std::same_as< char, void >, char, char >
	The char representation; conditional needed to make semi alphabet definitions legal. More...
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()). More...

Related Functions
(Note that these are not member functions.)
Literals
std::vector< dssp9 >	operator""_dssp9 (const char *str, std::size_t len)
	The seqan3::dssp9 string literal. More...
constexpr dssp9	operator""_dssp9 (char const ch) noexcept
	The seqan3::dssp9 char literal. More...

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 (http://www.cmbi.ru.nl/dssp.html), it is also used in the stockholm file format for structure alignments, extended by the characters C and X (https://en.wikipedia.org/wiki/Stockholm_format).

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

Usage

The following code example creates a dssp9 vector, modifies it, and prints the result to stderr.

#include <vector>
 
#include <seqan3/alphabet/structure/dssp9.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_dssp9;
 
    // create vector
    std::vector<seqan3::dssp9> vec{'E'_dssp9, 'H'_dssp9, 'H'_dssp9, 'H'_dssp9, 'T'_dssp9, 'G'_dssp9};
 
    // modify and print
    vec[1] = 'C'_dssp9;
 
    for (seqan3::dssp9 chr : vec)
        seqan3::debug_stream << seqan3::to_char(chr);  // ECHHTG
        
    seqan3::debug_stream << "\n";
}

Member Typedef Documentation

char_type

using seqan3::alphabet_base< dssp9 , size, char >::char_type = std::conditional_t<std::same_as<char , void>, char, char >

protectedinherited

The char representation; conditional needed to make semi alphabet definitions legal.

We need a return type for seqan3::alphabet_base::to_char and seqan3::alphabet_base::assign_char other than void to make these in-class definitions valid when char_t is void.

This entity is stable. Since version 3.1.

rank_type

using seqan3::alphabet_base< dssp9 , size, char >::rank_type = detail::min_viable_uint_t<size - 1>

protectedinherited

The type of the alphabet when represented as a number (e.g. via to_rank()).

This entity is stable. Since version 3.1.

Constructor & Destructor Documentation

~dssp9()

seqan3::dssp9::~dssp9 ( )

defaultnoexcept

Defaulted.

Member Function Documentation

assign_char()

constexpr dssp9 & seqan3::alphabet_base< dssp9 , size, char >::assign_char ( char_type const  c )

inlineconstexprnoexceptinherited

Assign from a character, implicitly converts invalid characters.

Parameters

c	The character to be assigned.

Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

assign_rank()

constexpr dssp9 & seqan3::alphabet_base< dssp9 , size, char >::assign_rank ( rank_type const  c )

inlineconstexprnoexceptinherited

Assign from a numeric value.

Parameters

c	The rank to be assigned.

Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

to_char()

constexpr char_type seqan3::alphabet_base< dssp9 , size, char >::to_char ( ) const

inlineconstexprnoexceptinherited

Return the letter as a character of char_type.

Provides an implementation for seqan3::to_char, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

to_rank()

constexpr rank_type seqan3::alphabet_base< dssp9 , size, char >::to_rank ( ) const

inlineconstexprnoexceptinherited

Return the letter's numeric value (rank in the alphabet).

Provides an implementation for seqan3::to_rank, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

Friends And Related Function Documentation

operator""_dssp9() [1/2]

constexpr dssp9 operator""_dssp9 ( char const  ch )

related

The seqan3::dssp9 char literal.

Parameters

[in]

ch

The character to represent as dssp.

Returns

seqan3::dssp9

You can use this string literal to assign a seqan3::dssp9 character:

#include <seqan3/alphabet/structure/dssp9.hpp>
 
int main()
{
    using seqan3::operator""_dssp9;
 
    // Using the char literal to assign a single DSSP annotation:
    seqan3::dssp9 my_letter{'I'_dssp9};
    
    my_letter.assign_char('G');      // <- assigns the char explicitly
}

operator""_dssp9() [2/2]

std::vector< dssp9 > operator""_dssp9 ( const char *  str, std::size_t  len  )

related

The seqan3::dssp9 string literal.

Parameters

[in]	str	A pointer to the character string to assign.
[in]	len	The size of the character string to assign.

Returns

std::vector<seqan3::dssp9>

You can use this string literal to easily assign to a vector of seqan3::dssp9 characters:

#include <vector>
 
#include <seqan3/alphabet/structure/dssp9.hpp>
 
int main()
{
    using seqan3::operator""_dssp9;
 
    // Using the string literal to assign a vector of DSSP annotations:
    std::vector<seqan3::dssp9> foo{"EHHHHT"_dssp9};
    std::vector<seqan3::dssp9> bar = "EHHHHT"_dssp9;
    auto bax = "EHHHHT"_dssp9;
}

Member Data Documentation

alphabet_size

constexpr detail::min_viable_uint_t<size> seqan3::alphabet_base< dssp9 , size, char >::alphabet_size

staticconstexprinherited

The size of the alphabet, i.e. the number of different values it can take.

This entity is stable. Since version 3.1.

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

• seqan3/alphabet/structure/dssp9.hpp