Amino Acids

The amino acids module provides lookups for standard and non-standard amino acids.

class tacular.amino_acids.AALookup(data)

Bases: object

Parameters:

data (dict[AminoAcid, AminoAcidInfo])

property ambiguous_amino_acids: tuple[AminoAcidInfo, ...]

Get ambiguous amino acids (B, J, X, Z)

composition(key)

Get the elemental composition of the amino acid identified by key

Return type:

dict[ElementInfo, int]

Parameters:

key (str)

get(key, default=None)

Get amino acid info or None if not found

Return type:

AminoAcidInfo | None

Parameters:

• key (str)

• default (AminoAcidInfo | None)

is_ambiguous(key)

Check if the amino acid identified by key is ambiguous

Return type:

bool

Parameters:

key (str)

is_mass_ambiguous(key)

Check if the amino acid identified by key has mass ambiguity

Return type:

bool

Parameters:

key (str)

is_mass_unambiguous(key)

Check if the amino acid identified by key has no mass ambiguity

Return type:

bool

Parameters:

key (str)

is_unambiguous(key)

Check if the amino acid identified by key is unambiguous

Return type:

bool

Parameters:

key (str)

mass(key, monoisotopic=True)

Get the mass of the amino acid identified by key

Return type:

float

Parameters:

• key (str)

• monoisotopic (bool)

property mass_amino_acids: tuple[AminoAcidInfo, ...]

Get amino acids that have defined masses

property mass_unambiguous_amino_acids: tuple[AminoAcidInfo, ...]

Get unambiguous amino acids that have defined masses

name(name)

Return type:

AminoAcidInfo

Parameters:

name (str)

one_letter(code)

Return type:

AminoAcidInfo

Parameters:

code (str)

property ordered_amino_acids: tuple[AminoAcidInfo, ...]

Get amino acids in order of one-letter codes A-Z

three_letter(code)

Return type:

AminoAcidInfo

Parameters:

code (str)

property unambiguous_amino_acids: tuple[AminoAcidInfo, ...]

Get unambiguous amino acids (all except B, J, X, Z)

class tacular.amino_acids.AminoAcid(*values)

Bases: StrEnum

Enumeration of amino acid single-letter codes.

A = 'A'

B = 'B'

C = 'C'

D = 'D'

E = 'E'

F = 'F'

G = 'G'

H = 'H'

I = 'I'

J = 'J'

K = 'K'

L = 'L'

M = 'M'

N = 'N'

O = 'O'

P = 'P'

Q = 'Q'

R = 'R'

S = 'S'

T = 'T'

U = 'U'

V = 'V'

W = 'W'

X = 'X'

Y = 'Y'

Z = 'Z'

classmethod from_str(aa)

Get AminoAcid enum from string

Return type:

AminoAcid

Parameters:

aa (str)

class tacular.amino_acids.AminoAcidInfo(id, name, three_letter_code, formula, monoisotopic_mass, average_mass, dict_composition, is_mass_ambiguous=False, is_ambiguous=False)

Bases: object

Information about an amino acid

Parameters:

• id (str)

• name (str)

• three_letter_code (str)

• formula (str | None)

• monoisotopic_mass (float | None)

• average_mass (float | None)

• dict_composition (dict[str, int] | None)

• is_mass_ambiguous (bool)

• is_ambiguous (bool)

average_mass: float | None

property composition: Counter[ElementInfo] | None

Get the composition as a Counter

dict_composition: dict[str, int] | None

formula: str | None

get_mass(monoisotopic=True)

Get the mass of the amino acid

Return type:

float | None

Parameters:

monoisotopic (bool)

id: str

is_ambiguous: bool = False

is_mass_ambiguous: bool = False

monoisotopic_mass: float | None

name: str

property one_letter_code: str

three_letter_code: str

to_dict(float_precision=6)

Convert the AminoAcidInfo to a dictionary

Return type:

dict[str, object]

Parameters:

float_precision (int)