Compound

Overview

class modifinder.classes.Compound(spectrum: List[Tuple[float, float]], precursor_mz: float, precursor_charge: int, adduct: str, smiles: str | None = None, **kwargs)[source]

A class to represent a compound

The compound always has spectrum data. If the compound structure is known, it also has a structure property.

id(str)

Type:: The id of the compound

spectrum(Spectrum)

Type:: Spectrum Tuple representing mz, intensity, Precursor mass and Charge for mass spectrumetry data

structure(Chem.Mol)

Type:: The structure of the compound

is_known(bool)

Type:: A boolean indicating whether the compound is known, derived from the structure

name(str)

Type:: The name of the compound

accession(str)

Type:: The accession of the compound

library_membership(str)

Type:: The GNPS library membership of the compound

Examples

Create a compound by providing the necessary information:

>>> compound = Compound(id="CCMSLIB00005435812", peaks=[[110.066925,38499.089844],[138.060638,412152.093750],[195.079575,6894530.000000],[195.200180,480874.812500],[196.082092,43027.628906]], precursor_mz=195.087, precursor_charge=1, adduct="[M+H]+", smiles="CN1C=NC2=C1C(=O)N(C(=O)N2C)C")

Alternatively, you can create a compound by providing a dictionary of data:

>>> data = {
...     "id": "CCMSLIB00005435812",
...     "peaks": [[110.066925,38499.089844],[138.060638,412152.093750],[195.079575,6894530.000000],[195.200180,480874.812500],[196.082092,43027.628906]],
...     "precursor_mz": 195.087,
...     "charge": 1,
...     "adduct": "[M+H]+",
...     "smiles": "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
... }
>>> compound = Compound(data)

__init__(spectrum: List[Tuple[float, float]], precursor_mz: float, precursor_charge: int, adduct: str, smiles: str | None = None, **kwargs)[source]

Initialize the Compound class

The compound class can be initialized in three different ways: 1. By providing a dictionary of data to the data parameter that contains all the necessary information 2. By providing the necessary information as parameter

If both the data and the parameters are provided, the parameters will override the data.

If of the incoming data and kwargs are provided, an empty instance of the class will be created.

Parameters:

incoming_data (input data (optional, default: None)) – The data to initialize the class with, can be a dictionary of data or a compound object. If not provided, the class will be initialized with the provided keyword arguments. If provided, the keyword arguments will still override the data.
kwargs (keyword arguments (optional, default: No attributes)) – Attributes to initialize the class with, if provided, they will override the attributes from the data

`clear`()	Clear the compound data and reset all the attributes to None
`copy`()	Return a copy of the compound
`get_meta_data`()	Get the meta data of the compound