Integer-based representation for amino acids
This module implements an amino acid alphabet, which is a specific instance of the `Alphabet.S_int` module. It represents the set of 20 standard amino acids.
The alphabet is represented as an integer alphabet, where each amino acid is assigned a unique integer index.
Conversion functions are provided to convert between the integer index and the corresponding character representation of an amino acid.
Note: The integer indices of amino acids start from 0 and go up to 19.
include Alphabet.S_intinclude Alphabet.S
with type t = private int
and type vector = private Linear_algebra.vec
and type matrix = private Linear_algebra.mat
and type 'a table = private 'a arraytype vector = private Linear_algebra.vectype matrix = private Linear_algebra.matval all : t listval to_int : t -> intval counts : t Core.Sequence.t -> int tablemodule Table : sig ... endmodule Vector : sig ... endval flat_profile : unit -> vectorval random_profile : Gsl.Rng.t -> float -> vectormodule Matrix : sig ... endval of_int : int -> t optionval of_int_exn : int -> tval yojson_of_vector : vector -> Yojson.Safe.tyojson_of_vector vec converts a vector representing the values of amino acids into a Yojson.Safe.t JSON object.
let amino_acid_values = [|1.2; 3.4; 2.1|] (* Vector representing amino acid values *)
let json_repr = yojson_of_vector amino_acid_values (* Conversion to JSON object *)In this example, if amino_acid_values represents the values of three amino acids in the order "Alanine", "Aspartic Acid", and "Cysteine", then json_repr will be a JSON object with the following structure:
{
"A": 1.2,
"D": 3.4,
"C": 2.1
}Each amino acid is represented as a key-value pair in the JSON object, where the key is the character representation and the value is the corresponding value in the vector.
This function is useful when you need to serialize amino acid values in a JSON format for storage or communication purposes.
val vector_of_yojson : Yojson.Safe.t -> vectorvector_of_yojson aa_list converts a JSON object of type `Yojson.Safe.t` into a vector of amino acid values. The JSON object should contain key-value pairs, where the key is the character representation of an amino acid and the value is the corresponding value. The order of the key-value pairs should follow the alphabetical order. If any amino acid is missing or the order is not correct, an exception is raised.
val to_char : t -> charto_char aa converts the integer index of an amino acid aa to its character representation.
val of_char : char -> t optionof_char c converts a character representation c of an amino acid to its corresponding integer index, returning an option. If the character is not a valid amino acid, None is returned.