esmraldi.theoreticalspectrum¶
Module Contents¶
Classes¶
This class aims at generating a theoretical spectrum from a list of species |
- class esmraldi.theoreticalspectrum.TheoreticalSpectrum(molecules, adducts, modifications=[])¶
This class aims at generating a theoretical spectrum from a list of species
- mix_species(species, optional=False)¶
Mix species of different families.
All possible combinations are extracted.
- Parameters
- species: list
SpeciesRule list
- optional: bool
whether this species if optional or not
- Returns
- np.ndarray
mix of SpeciesRule
- merge_dicts_mz(dict1, dict2)¶
Merges two dictionaries, where keys=values and values=mz by summing their keys and values.
- Parameters
- dict1: dict
first dictionary
- dict2: dict
second dictionary
- Returns
- dict
merged dictionary
- expand_mix(mix)¶
Generates the full list of species from all species rules contained in the mix.
Maps the masses to all possible names.
- Parameters
- mix: np.ndarray
mix of SpeciesRule
- Returns
- dict
mapping of all species (name to mz)
- molecules_regexp(adduct, molecules)¶
Extracts all molecules with fit the regexp in adduct.
- Parameters
- adduct: SpeciesRule
adduct or modification
- molecules: dict
all molecules
- Returns
- dict
molecules which match the adduct or modification
- mix_molecules_regexp(mix, molecules)¶
All molecules matching regexp from species in a mix.
- Parameters
- mix: list
list of SpeciesRule
- molecules: dict
all molecules
- Returns
- dict
molecules matching every modification add functions
- add_all_adducts_to_molecules(molecules, adducts)¶
Add adducts and modifications, and every permutation of them to molecules.
- Parameters
- molecules: dict
molecule mapping names to mz
- adducts: list
adduct species rule list
- Returns
- dict
theoretical spectrum
- add_adduct_to_molecules(molecules, adduct, rules_max={})¶
Add one adduct to all molecules.
- Parameters
- molecules: list
molecule molecule names to mz
- adduct: SpeciesRule
adduct or modification
- rules_max: dict
rules constraining number of adduct per molecule
- Returns
- dict
molecules with every combination of adduct
- add_adducts_to_molecules_regexp(adduct)¶
Add adducts based on regexp.
- Parameters
- adduct: SpeciesRule
adduct or modification
- Returns
- dict
molecules matching regexp of adduct