The protein structure alphabet of the characters "HGIEBTSCX". More...
#include <seqan3/alphabet/structure/dssp9.hpp>
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. | |
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()). | |
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... | |
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
The following code example creates a dssp9 vector, modifies it, and prints the result to stderr.
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defaultnoexcept |
Defaulted.
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inlineconstexprnoexceptinherited |
Assign from a character, implicitly converts invalid characters.
c | The character to be assigned. |
Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.
Constant.
Guaranteed not to throw.
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inlineconstexprnoexceptinherited |
Assign from a numeric value.
c | The rank to be assigned. |
Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.
Constant.
Guaranteed not to throw.
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inlineconstexprnoexceptinherited |
Return the letter as a character of char_type.
Provides an implementation for seqan3::to_char, required to model seqan3::alphabet.
Constant.
Guaranteed not to throw.
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inlineconstexprnoexceptinherited |
Return the letter's numeric value (rank in the alphabet).
Provides an implementation for seqan3::to_rank, required to model seqan3::semialphabet.
Constant.
Guaranteed not to throw.
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related |
The seqan3::dssp9 char literal.
[in] | ch | The character to represent as dssp. |
You can use this string literal to assign a seqan3::dssp9 character:
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related |
The seqan3::dssp9 string literal.
[in] | str | A pointer to the character string to assign. |
[in] | len | The size of the character string to assign. |
You can use this string literal to easily assign to a vector of seqan3::dssp9 characters: