The reduced Murphy amino acid alphabet. More...

#include <seqan3/alphabet/aminoacid/aa10murphy.hpp>

Inheritance diagram for seqan3::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.

Public Member Functions inherited from seqan3::aminoacid_base< aa10murphy, 10 >
constexpr	aminoacid_base (other_aa_type const other) noexcept
	Allow explicit construction from any other aminoacid type and convert via the character representation. More...

Public Member Functions inherited from seqan3::alphabet_base< derived_type, size, char_t >
constexpr	alphabet_base () noexcept=default
	Defaulted.

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

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

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

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

	~alphabet_base () noexcept=default
	Defaulted.

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...

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

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

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

static constexpr char_type	rank_to_char [alphabet_size]
	Value to char conversion table. More...

Related Functions
(Note that these are not member functions.)
using	aa10murphy_vector = std::vector< aa10murphy >
	Alias for an std::vector of seqan3::aa10murphy. More...

Literals
constexpr aa10murphy	operator""_aa10murphy (char const c) noexcept
	The seqan3::aa10murphy char literal. More...

aa10murphy_vector	operator""_aa10murphy (char const *const s, size_t const n)
	The seqan3::aa10murphy string literal. More...

Additional Inherited Members
Static Public Member Functions inherited from seqan3::aminoacid_base< aa10murphy, 10 >
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. More...

Static Public Attributes inherited from seqan3::alphabet_base< derived_type, size, char_t >
static constexpr detail::min_viable_uint_t< size >	alphabet_size = size
	The size of the alphabet, i.e. the number of different values it can take. More...

Protected Types inherited from seqan3::alphabet_base< derived_type, size, char_t >
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. 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...

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 <seqan3/alphabet/aminoacid/aa10murphy.hpp>
#include <seqan3/alphabet/aminoacid/aa27.hpp>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/range/views/convert.hpp>
 
using seqan3::operator""_aa10murphy;
using seqan3::operator""_aa27;
 
int main()
{
    // Construction of aa10murphy amino acids from character
    seqan3::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')
        seqan3::debug_stream << "yeah\n"; // "yeah";
 
    // Convert aa27 alphabet to aa10_murphy
    seqan3::aa27_vector v1{"AVRSTXOUB"_aa27};
    auto v2 = v1 | seqan3::views::convert<seqan3::aa10murphy>; // AIKSSSKCB
 
    seqan3::debug_stream << v2 << "\n";
 
    return 0;
}

This entity is stable. Since version 3.1.

Friends And Related Function Documentation

◆ aa10murphy_vector

using aa10murphy_vector = std::vector<aa10murphy>

This entity is stable. Since version 3.1.

◆ operator""_aa10murphy() [1/2]

aa10murphy_vector operator""_aa10murphy	(	char const *const	s,
		size_t const	n
	)

Parameters

[in]	s	A pointer to the character string to assign.
[in]	n	The size of the character string to assign.

Returns: seqan3::aa10murphy_vector

You can use this string literal to easily assign to aa10murphy_vector:

Attention: All seqan3 literals are in the namespace seqan3!

This entity is stable. Since version 3.1.

◆ operator""_aa10murphy() [2/2]

constexpr aa10murphy operator""_aa10murphy ( char const c )

Parameters

[in] c The character to assign.

Returns: seqan3::aa10murphy

This entity is stable. Since version 3.1.

Member Data Documentation

◆ rank_to_char

constexpr char_type seqan3::aa10murphy::rank_to_char[alphabet_size]

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:

seqan3/alphabet/aminoacid/aa10murphy.hpp

Public Member Functions

Static Protected Attributes

Related Functions

Additional Inherited Members

Detailed Description

Friends And Related Function Documentation

◆ aa10murphy_vector

◆ operator""_aa10murphy() [1/2]

◆ operator""_aa10murphy() [2/2]

Member Data Documentation

◆ rank_to_char