Neutral Deltas

The neutral deltas module provides lookups for neutral losses and gains.

class tacular.neutral_deltas.NeutralDelta(*values)[source]

Bases: StrEnum

Neutral loss deltas for fragment ions

AMMONIA = 'NH3'

CARBON_DIOXIDE = 'CO2'

CARBON_MONOXIDE = 'CO'

FORMAMIDE = 'HCONH2'

FORMIC_ACID = 'HCOOH'

HYDROGEN = 'H'

MERCAPTOACETAMIDE = 'C2H5NOS'

MERCAPTOACETIC_ACID = 'C2H4O2S'

METAPHOSPHORIC_ACID = 'HPO3'

METHANESULFENIC_ACID = 'CH4OS'

PHOSPHORIC_ACID = 'H3PO4'

SULFUR_TRIOXIDE = 'SO3'

WATER = 'H2O'

class tacular.neutral_deltas.NeutralDeltaInfo(formula, name, description, amino_acids, monoisotopic_mass, average_mass, dict_composition)[source]

Bases: object

Parameters:

formula (str)
name (str)
description (str)
amino_acids (frozenset[str])
monoisotopic_mass (float)
average_mass (float)
dict_composition (dict[str, int])

amino_acids: frozenset[str]

average_mass: float

calculate_loss_sites(sequence)[source]

Calculate the number of possible loss sites in a sequence

Return type:: int
Parameters:: sequence (str)

property composition: Counter[ElementInfo][source]: Get the composition as a Counter

description: str

dict_composition: dict[str, int]

formula: str

get_mass(monoisotopic=True)[source]

Get the mass of the fragment ion

Return type:: float
Parameters:: monoisotopic (bool)

monoisotopic_mass: float

name: str

to_dict(float_precision=6)[source]

Convert to dictionary representation

Return type:: dict[str, object]
Parameters:: float_precision (int)

class tacular.neutral_deltas.NeutralDeltaLookup(neutral_delta_data)[source]

Bases: object

Parameters:: neutral_delta_data (dict[NeutralDelta, NeutralDeltaInfo])

query_delta(delta)[source]

Query by NeutralDelta enum

Return type:: NeutralDeltaInfo | None
Parameters:: delta (NeutralDelta)

query_formula(formula)[source]

Query by chemical formula (e.g., ‘H2O’, ‘NH3’)

Return type:: NeutralDeltaInfo | None
Parameters:: formula (str)

query_name(name)[source]

Query by neutral delta name (e.g., ‘Water’, ‘Ammonia’)

Return type:: NeutralDeltaInfo | None
Parameters:: name (str)