SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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seqan3::aa10murphy Class Reference

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 aa10murphyoperator= (aa10murphy const &) noexcept=default
 Defaulted.
 
constexpr aa10murphyoperator= (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.
 
- 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_baseoperator= (alphabet_base const &) noexcept=default
 Defaulted.
 
constexpr alphabet_baseoperator= (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.
 
constexpr rank_type to_rank () const noexcept
 Return the letter's numeric value (rank in the alphabet).
 
constexpr derived_type & assign_char (char_type const chr) noexcept
 Assign from a character, implicitly converts invalid characters.
 
constexpr derived_type & assign_rank (rank_type const c) noexcept
 Assign from a numeric value.
 

Related Symbols

(Note that these are not member symbols.)

using aa10murphy_vector = std::vector< aa10murphy >
 Alias for a std::vector of seqan3::aa10murphy.
 

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.
 
- 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.
 
- 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.
 
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()).
 

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) F1,2

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

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
int main()
{
using namespace seqan3::literals;
seqan3::aa10murphy letter{'A'_aa10murphy};
letter.assign_char('C');
seqan3::debug_stream << letter << '\n'; // prints "C"
letter.assign_char('?'); // Unknown characters are implicitly converted to S.
seqan3::debug_stream << letter << '\n'; // prints "S"
}
Provides seqan3::aa10murphy, container aliases and string literals.
The reduced Murphy amino acid alphabet.
Definition aa10murphy.hpp:79
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition alphabet_base.hpp:160
Provides seqan3::debug_stream and related types.
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition debug_stream.hpp:37
The SeqAn namespace for literals.

This entity is stable. Since version 3.1.

Friends And Related Symbol Documentation

◆ aa10murphy_vector

Alias for a std::vector of seqan3::aa10murphy.

This entity is stable. Since version 3.1.


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