The protein structure alphabet of the characters "HGIEBTSCX". More...
#include <seqan3/alphabet/structure/dssp9.hpp>
Public Types | |
Member types | |
using | char_type = char |
The type of the alphabet when converted to char (e.g. via to_char()). | |
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()). | |
Public Member Functions | |
Constructors, destructor and assignment | |
constexpr | dssp9 () |
constexpr | dssp9 (dssp9 const &)=default |
constexpr | dssp9 (dssp9 &&)=default |
constexpr dssp9 & | operator= (dssp9 const &)=default |
constexpr dssp9 & | operator= (dssp9 &&)=default |
~dssp9 ()=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 (std::conditional_t< std::Same< char_type, void >, char, char_type > const c) noexcept |
Assign from a character. More... | |
constexpr dssp9 & | assign_rank (rank_type const c) noexcept |
Assign from a numeric value. More... | |
Static Public Attributes | |
static detail::min_viable_uint_t< size > constexpr | value_size |
The size of the alphabet, i.e. the number of different values it can take. | |
Letter values | |
Static member "letters" that can be assigned to the alphabet or used in aggregate initialization. Similar to an Enum interface. Don't worry about the | |
static const dssp9 | H = dssp9{}.assign_char('H') |
static const dssp9 | B = dssp9{}.assign_char('B') |
static const dssp9 | E = dssp9{}.assign_char('E') |
static const dssp9 | G = dssp9{}.assign_char('G') |
static const dssp9 | I = dssp9{}.assign_char('I') |
static const dssp9 | T = dssp9{}.assign_char('T') |
static const dssp9 | S = dssp9{}.assign_char('S') |
static const dssp9 | C = dssp9{}.assign_char('C') |
static const dssp9 | X = dssp9{}.assign_char('X') |
Related Functions | |
(Note that these are not member functions.) | |
std::vector< dssp9 > | operator""_dssp9 (const char *str, std::size_t len) |
dssp9 literal More... | |
Requirements for seqan3::alphabet_concept | |
You can expect these functions on all types that implement seqan3::alphabet_concept. | |
template<typename alphabet_type > | |
using | underlying_char_t = typename underlying_char< alphabet_type >::type |
The char_type of the alphabet. [type metafunction shortcut]. More... | |
char_type | to_char (alphabet_concept const alph) |
Returns the alphabet letter's value in character representation. More... | |
alphabet_concept && | assign_char (alphabet_concept &&alph, char_type const chr) |
Returns the alphabet letter's value in character representation. More... | |
Requirements for seqan3::semi_alphabet_concept | |
You can expect these functions on all types that implement seqan3::semi_alphabet_concept. | |
template<typename semi_alphabet_type > | |
using | underlying_rank_t = typename underlying_rank< semi_alphabet_type >::type |
The rank_type of the semi_alphabet. [type metafunction shortcut]. More... | |
template<typename alphabet_type > | |
constexpr auto | alphabet_size_v = alphabet_size<alphabet_type>::value |
The size of the alphabet. [value metafunction shortcut]. More... | |
rank_type | to_rank (semi_alphabet_concept const alph) |
Returns the alphabet letter's value in rank representation. More... | |
semi_alphabet_concept && | assign_rank (semi_alphabet_concept &&alph, rank_type const rank) |
Returns the alphabet letter's value in rank representation. More... | |
Requirements for std::Swappable | |
You can expect these functions on all types that implement std::Swappable. | |
void | swap (t &lhs, t &rhs) |
Swaps the contents of two objects. More... | |
Requirements for std::EqualityComparable | |
You can expect these functions on all types that implement std::Equality_comparable. | |
bool | operator== (type const &lhs, type const &rhs) |
(In-)Equality comparison. More... | |
bool | operator!= (type const &lhs, type const &rhs) |
(In-)Equality comparison. More... | |
Requirements for std::StrictTotallyOrdered | |
You can expect these functions on all types that implement std::StrictTotallyOrdered. | |
bool | operator< (type const &lhs, type const &rhs) |
Less-than, greater-than and -or-equal comparisons. More... | |
bool | operator<= (type const &lhs, type const &rhs) |
Less-than, greater-than and -or-equal comparisons. More... | |
bool | operator> (type const &lhs, type const &rhs) |
Less-than, greater-than and -or-equal comparisons. More... | |
bool | operator>= (type const &lhs, type const &rhs) |
Less-than, greater-than and -or-equal comparisons. 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
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inlinenoexceptinherited |
Assign from a character.
Satisfies the seqan3::alphabet_concept::assign_char() requirement via the seqan3::assign_char() wrapper.
Constant.
Guaranteed not to throw.
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inlinenoexceptinherited |
Assign from a numeric value.
Satisfies the seqan3::semi_alphabet_concept::assign_rank() requirement via the seqan3::assign_rank() wrapper.
Constant.
Guaranteed not to throw.
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inlinenoexceptinherited |
Return the letter as a character of char_type.
Satisfies the seqan3::alphabet_concept::to_char() requirement via the seqan3::to_char() wrapper.
Constant.
Guaranteed not to throw.
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inlinenoexceptinherited |
Return the letter's numeric value (rank in the alphabet).
Satisfies the seqan3::semi_alphabet_concept::to_rank() requirement via the to_rank() wrapper.
Constant.
Guaranteed not to throw.
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related |