SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
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.
 
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 aa10murphyassign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr aa10murphyassign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 

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. More...
 

Static Public Attributes

static detail::min_viable_uint_t< size > constexpr alphabet_size
 The size of the alphabet, i.e. the number of different values it can take.
 

Protected 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 = 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 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 (const char *s, std::size_t n)
 The seqan3::aa10murphy string literal. More...
 
Requirements for std::totally_ordered

You can expect these functions on all types that implement std::totally_ordered.

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...
 
Requirements for std::equality_comparable

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::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...
 

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

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;
}

Member Function Documentation

◆ assign_char()

constexpr aa10murphy & seqan3::alphabet_base< aa10murphy , size, char >::assign_char ( char_type const  c)
inlinenoexceptinherited

Assign from a character, implicitly converts invalid characters.

Parameters
cThe character to be assigned.

Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ assign_rank()

constexpr aa10murphy & seqan3::alphabet_base< aa10murphy , size, char >::assign_rank ( rank_type const  c)
inlinenoexceptinherited

Assign from a numeric value.

Parameters
cThe rank to be assigned.

Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ char_is_valid()

static constexpr bool seqan3::aminoacid_base< aa10murphy , size >::char_is_valid ( char_type const  c)
inlinestaticnoexceptinherited

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

Models the seqan3::semialphabet::char_is_valid_for() requirement via the seqan3::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()

constexpr char_type seqan3::alphabet_base< aa10murphy , size, char >::to_char ( ) const
inlinenoexceptinherited

Return the letter as a character of char_type.

Provides an implementation for seqan3::to_char, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ to_rank()

constexpr rank_type seqan3::alphabet_base< aa10murphy , size, char >::to_rank ( ) const
inlinenoexceptinherited

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

Provides an implementation for seqan3::to_rank, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

Friends And Related Function Documentation

◆ aa10murphy_vector

◆ operator""_aa10murphy() [1/2]

constexpr aa10murphy operator""_aa10murphy ( char const  c)
related

The seqan3::aa10murphy char literal.

Parameters
[in]cThe character to assign.
Returns
seqan3::aa10murphy

◆ operator""_aa10murphy() [2/2]

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

The seqan3::aa10murphy string literal.

Parameters
[in]sA pointer to the character string to assign.
[in]nThe 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!

Member Data Documentation

◆ rank_to_char

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