The reduced Murphy amino acid alphabet.. More...

#include <bio/alphabet/aminoacid/aa10murphy.hpp>

Inheritance diagram for bio::alphabet::aa10murphy:

Public Member Functions
Constructors, destructor and assignment
constexpr	aa10murphy () noexcept=default
	Defaulted.

constexpr	aa10murphy (aa10murphy const &) noexcept=default
	Defaulted.

constexpr	aa10murphy (aa10murphy &&) noexcept=default
	Defaulted.

constexpr aa10murphy &	operator= (aa10murphy const &) noexcept=default
	Defaulted.

constexpr aa10murphy &	operator= (aa10murphy &&) noexcept=default
	Defaulted.

	~aa10murphy () noexcept=default
	Defaulted.

Read functions
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).

Write functions
constexpr derived_type &	assign_char (char_type const c) noexcept
	Assign from a character, implicitly converts invalid characters.

constexpr derived_type &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value.

Static Public Member Functions
static constexpr bool	char_is_valid (char_type const c) noexcept
	Validate whether a character value has a one-to-one mapping to an alphabet value.

Static Public Attributes
static constexpr size_t	alphabet_size = 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_t, void >, char, char_t >
	The char representation; conditional needed to make semi alphabet definitions legal.

using	rank_type = meta::detail::min_viable_uint_t< size - 1 >
	The type of the alphabet when represented as a number (e.g. via to_rank()).

Static Protected Attributes
static constexpr std::array< rank_type, 256 >	char_to_rank
	Char to value conversion table.

static constexpr std::array< char_type, alphabet_size >	rank_to_char
	Value to char conversion table.

Related Functions
(Note that these are not member functions.)
Literals
consteval aa10murphy	operator""_aa10murphy (char const c)
	The bio::alphabet::aa10murphy char literal.

template<meta::detail::literal_buffer_string str>
constexpr std::vector< aa10murphy >	operator""_aa10murphy ()
	The bio::alphabet::aa10murphy string literal.

Detailed Description

The reduced Murphy amino acid alphabet.

.

The alphabet consists of letters A, B, C, F, G, H, I, K, P, S B represents charged/polar residues (E,D,N,Q). C represents cystein and the species-specific amino acid Selenocysteine. F represents amino acids with large and mainly hydrophobic aromatic side chains (F,W,Y). I represents large hydrophobes (L,V,I,M). K represents long-chain positively charged residues (K,R) and the species-specific amino acid Pyrrolysine. S represents alcohols (S,T) and unknown. A, G, H and P do not represent any other amino acids other than themselves.

This alphabet allows to reduce the aminoacid alphabet size to 10 but is still able to recognize and represent folding of all proteins. Amino acids are grouped together based on similar physical and chemical properties.

Note: Letters which belong in the extended alphabet will be automatically converted. Terminator characters are converted to F, because the most commonly occurring stop codon in higher eukaryotes is UGA ². This is most similar to a Tryptophan which in this alphabet gets converted to Phenylalanine. Anything unknown is converted to S.

Input Letter	Converts to
D	B¹
E	B¹
J	I¹
L	I¹
M	I¹
N	B¹
O	K¹
Q	B¹
R	K¹
T	S¹
U	C¹
V	I¹
W	F¹
Y	F¹
Z	B¹
X (Unknown)	S¹
* (Terminator)	F^1,2

¹L. R. Murphy, A. Wallqvist, and R. M. Levy. Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein Eng., 13(3):149–152, Mar 2000.
²Trotta, E. (2016). Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage. BMC Genomics, 17, 366. https://doi.org/10.1186/s12864-016-2692-4

#include <bio/alphabet/aminoacid/aa10murphy.hpp>
#include <bio/alphabet/aminoacid/aa27.hpp>
#include <bio/alphabet/fmt.hpp>
#include <bio/ranges/views/convert.hpp>
 
using namespace bio::alphabet::literals;
 
int main()
{
    // Construction of aa10murphy amino acids from character
    bio::alphabet::aa10murphy my_letter{'A'_aa10murphy};
 
    my_letter.assign_char('C');
    my_letter.assign_char('?'); // all unknown characters are converted to 'S'_aa10murphy implicitly
 
    if (my_letter.to_char() == 'S')
        fmt::print("{}", "yeah\n"); // "yeah";
 
    // Convert aa27 alphabet to aa10_murphy
    std::vector<bio::alphabet::aa27> v1{"AVRSTXOUB"_aa27};
    auto v2 = v1 | bio::views::convert<bio::alphabet::aa10murphy>; // AIKSSSKCB
 
    fmt::print("{}\n", v2);
 
    return 0;
}

Member Function Documentation

◆ assign_char()

template<typename derived_type , size_t size, typename char_t = char>

constexpr derived_type & bio::alphabet::base< derived_type, size, char_t >::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 bio::alphabet::assign_char_to, required to model bio::alphabet::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ assign_rank()

template<typename derived_type , size_t size, typename char_t = char>

constexpr derived_type & bio::alphabet::base< derived_type, size, char_t >::assign_rank ( rank_type const c )

inlineconstexprnoexceptinherited

Assign from a numeric value.

Parameters

c	The rank to be assigned.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ char_is_valid()

static constexpr bool bio::alphabet::aminoacid_base< aa10murphy , size >::char_is_valid ( char_type const c )

inlinestaticconstexprnoexceptinherited

Validate whether a character value has a one-to-one mapping to an alphabet value.

Models the bio::alphabet::semialphabet::char_is_valid_for() requirement via the bio::alphabet::char_is_valid_for() wrapper.

Behaviour specific to amino acids: True also for lower case letters that silently convert to their upper case.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ to_char()

template<typename derived_type , size_t size, typename char_t = char>

constexpr char_type bio::alphabet::base< derived_type, size, char_t >::to_char ( ) const

inlineconstexprnoexceptinherited

Return the letter as a character of char_type.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ to_rank()

template<typename derived_type , size_t size, typename char_t = char>

constexpr rank_type bio::alphabet::base< derived_type, size, char_t >::to_rank ( ) const

inlineconstexprnoexceptinherited

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

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

Friends And Related Function Documentation

◆ operator""_aa10murphy() [1/2]

template<meta::detail::literal_buffer_string str>

constexpr std::vector< aa10murphy > operator""_aa10murphy ( )

Returns: std::vector<bio::alphabet::aa10murphy>

You can use this string literal to easily create a std::vector<bio::alphabet::aa10murphy>:

#include <bio/alphabet/aminoacid/aa10murphy.hpp>
#include <bio/alphabet/aminoacid/aa27.hpp>
#include <bio/alphabet/fmt.hpp>
#include <bio/ranges/views/convert.hpp>
 
using namespace bio::alphabet::literals;
 
int main()
{
    // Construction of aa10murphy amino acids from character
    bio::alphabet::aa10murphy my_letter{'A'_aa10murphy};
 
    my_letter.assign_char('C');
    my_letter.assign_char('?'); // all unknown characters are converted to 'S'_aa10murphy implicitly
 
    if (my_letter.to_char() == 'S')
        fmt::print("{}", "yeah\n"); // "yeah";
 
    // Convert aa27 alphabet to aa10_murphy
    std::vector<bio::alphabet::aa27> v1{"AVRSTXOUB"_aa27};
    auto v2 = v1 | bio::views::convert<bio::alphabet::aa10murphy>; // AIKSSSKCB
 
    fmt::print("{}\n", v2);
 
    return 0;
}

◆ operator""_aa10murphy() [2/2]

consteval aa10murphy operator""_aa10murphy ( char const c )

Returns: bio::alphabet::aa10murphy

Member Data Documentation

◆ rank_to_char

constexpr std::array<char_type, alphabet_size> bio::alphabet::aa10murphy::rank_to_char

staticconstexprprotected

Initial value:

{
      'A',
      'B',
      'C',
      'F',
      'G',
      'H',
      'I',
      'K',
      'P',
      'S',
    }

Value to char conversion table.

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

bio/alphabet/aminoacid/aa10murphy.hpp

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Types

Static Protected Attributes

Related Functions

Detailed Description

Member Function Documentation

◆ assign_char()

Complexity

Exceptions

◆ assign_rank()

Complexity

Exceptions

◆ char_is_valid()

Complexity

Exceptions

◆ to_char()

Complexity

Exceptions

◆ to_rank()

Complexity

Exceptions

Friends And Related Function Documentation

◆ operator""_aa10murphy() [1/2]

◆ operator""_aa10murphy() [2/2]

Member Data Documentation

◆ rank_to_char