SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
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

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 dssp9assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr dssp9assign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 
Constructors, destructor and assignment
constexpr dssp9 () noexcept=default
 Defaulted.
 
constexpr dssp9 (dssp9 const &) noexcept=default
 Defaulted.
 
constexpr dssp9 (dssp9 &&) noexcept=default
 Defaulted.
 
constexpr dssp9operator= (dssp9 const &) noexcept=default
 Defaulted.
 
constexpr dssp9operator= (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 dssp9assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr dssp9assign_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.
 

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.
 
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()).
 
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.
 
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()).
 

Related Functions

(Note that these are not member functions.)

Literals
std::vector< dssp9operator""_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>
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)
}

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
cThe character to be assigned.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ assign_rank()

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

Assign from a numeric value.

Parameters
cThe rank to be assigned.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ to_char()

constexpr char_type seqan3::alphabet_base< dssp9 , size, char >::to_char
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.

◆ to_rank()

constexpr rank_type seqan3::alphabet_base< dssp9 , size, char >::to_rank
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.

Friends And Related Function Documentation

◆ operator""_dssp9() [1/2]

constexpr dssp9 operator""_dssp9 ( char const  ch)
related

The seqan3::dssp9 char literal.

Parameters
[in]chThe character to represent as dssp.
Returns
seqan3::dssp9

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

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]strA pointer to the character string to assign.
[in]lenThe 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>
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;
}

The documentation for this class was generated from the following file:
debug_stream.hpp
Provides seqan3::debug_stream and related types.
seqan3::dssp9
The protein structure alphabet of the characters "HGIEBTSCX".
Definition: dssp9.hpp:60
vector
seqan3::to_char
constexpr auto to_char
Return the char representation of an alphabet object.
Definition: concept.hpp:321
seqan3::alphabet_base::assign_char
constexpr derived_type & assign_char(char_type const c) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:142
dssp9.hpp
Provides the dssp format for protein structure.
seqan3::debug_stream
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:42