Reference Molecules

The reference molecules module provides lookups for mzPAF reference molecules.

class tacular.refmol.RefMolID(*values)

Bases: StrEnum

Enum of reference molecule IDs

ADENINE = 'Adenine'

CYTOSINE = 'Cytosine'

GUANINE = 'Guanine'

ITRAQ113 = 'iTRAQ113'

ITRAQ114 = 'iTRAQ114'

ITRAQ115 = 'iTRAQ115'

ITRAQ116 = 'iTRAQ116'

ITRAQ117 = 'iTRAQ117'

ITRAQ118 = 'iTRAQ118'

ITRAQ119 = 'iTRAQ119'

ITRAQ121 = 'iTRAQ121'

ITRAQ4PLEX = 'iTRAQ4plex'

ITRAQ8PLEX = 'iTRAQ8plex'

SIDECHAIN_A = 'sidechain_A'

SIDECHAIN_C = 'sidechain_C'

SIDECHAIN_D = 'sidechain_D'

SIDECHAIN_E = 'sidechain_E'

SIDECHAIN_F = 'sidechain_F'

SIDECHAIN_G = 'sidechain_G'

SIDECHAIN_H = 'sidechain_H'

SIDECHAIN_I = 'sidechain_I'

SIDECHAIN_J = 'sidechain_J'

SIDECHAIN_K = 'sidechain_K'

SIDECHAIN_L = 'sidechain_L'

SIDECHAIN_M = 'sidechain_M'

SIDECHAIN_N = 'sidechain_N'

SIDECHAIN_O = 'sidechain_O'

SIDECHAIN_Q = 'sidechain_Q'

SIDECHAIN_R = 'sidechain_R'

SIDECHAIN_S = 'sidechain_S'

SIDECHAIN_T = 'sidechain_T'

SIDECHAIN_U = 'sidechain_U'

SIDECHAIN_V = 'sidechain_V'

SIDECHAIN_W = 'sidechain_W'

SIDECHAIN_Y = 'sidechain_Y'

THYMINE = 'Thymine'

TMT126 = 'TMT126'

TMT126_ETD = 'TMT126-ETD'

TMT127C = 'TMT127C'

TMT127C_ETD = 'TMT127C-ETD'

TMT127N = 'TMT127N'

TMT127N_ETD = 'TMT127N-ETD'

TMT128C = 'TMT128C'

TMT128C_ETD = 'TMT128C-ETD'

TMT128N = 'TMT128N'

TMT128N_ETD = 'TMT128N-ETD'

TMT129C = 'TMT129C'

TMT129C_ETD = 'TMT129C-ETD'

TMT129N = 'TMT129N'

TMT129N_ETD = 'TMT129N-ETD'

TMT130C = 'TMT130C'

TMT130C_ETD = 'TMT130C-ETD'

TMT130N = 'TMT130N'

TMT130N_ETD = 'TMT130N-ETD'

TMT131C = 'TMT131C'

TMT131C_ETD = 'TMT131C-ETD'

TMT131N = 'TMT131N'

TMT131N_ETD = 'TMT131N-ETD'

TMT132C = 'TMT132C'

TMT132N = 'TMT132N'

TMT133C = 'TMT133C'

TMT133N = 'TMT133N'

TMT134C = 'TMT134C'

TMT134N = 'TMT134N'

TMT135N = 'TMT135N'

TMT2PLEX = 'TMT2plex'

TMT6PLEX = 'TMT6plex'

TMTPRO = 'TMTpro'

TMTPRO_ZERO = 'TMTpro_zero'

TMTZERO = 'TMTzero'

URACIL = 'Uracil'

class tacular.refmol.RefMolInfo(name, label_type, molecule_type, chemical_formula, monoisotopic_mass, average_mass, dict_composition)

Bases: object

Information about a reference molecule

Parameters:

• name (str)

• label_type (str)

• molecule_type (str)

• chemical_formula (str)

• monoisotopic_mass (float)

• average_mass (float)

• dict_composition (dict[str, int])

average_mass: float

chemical_formula: str

property composition: Counter[ElementInfo]

Get the composition as a Counter

dict_composition: dict[str, int]

get_mass(monoisotopic=True)

Get the mass of the molecule

Return type:

float

Parameters:

monoisotopic (bool)

label_type: str

molecule_type: str

monoisotopic_mass: float

name: str

to_dict(float_precision=6)

Convert the RefMolInfo to a dictionary

Return type:

dict[str, object]

Parameters:

float_precision (int)

class tacular.refmol.RefMolLookup(refmol_data)

Bases: object

Parameters:

refmol_data (dict[RefMolID, RefMolInfo])

get(key)

Get reference molecule or None if not found

Return type:

RefMolInfo | None

Parameters:

key (str | RefMolID)

query_id(refmol_id)

Query by RefMolID enum

Return type:

RefMolInfo | None

Parameters:

refmol_id (RefMolID)

query_label_type(label_type)

Query all molecules by label type (e.g., ‘TMT’, ‘iTRAQ’)

Return type:

list[RefMolInfo]

Parameters:

label_type (str)

query_molecule_type(molecule_type)

Query all molecules by molecule type (e.g., ‘reporter’, ‘sidechain’, ‘nucleobase’)

Return type:

list[RefMolInfo]

Parameters:

molecule_type (str)

query_name(name)

Query by reference molecule name (e.g., ‘TMT126’, ‘sidechain_A’)

Return type:

RefMolInfo | None

Parameters:

name (str)