matchms.exporting package

Functions for exporting mass spectral data

Individual Spectrum(), or lists of Spectrum() can be exported to json, mgf, or msp files.

matchms.exporting.save_as_json(spectrums: List[Spectrum], filename: str, export_style: str = 'matchms')[source]

Save spectrum(s) as json file.

losses of spectrum will not be saved.

Example:

import numpy as np
from matchms import Spectrum
from matchms.exporting import save_as_json

# Create dummy spectrum
spectrum = Spectrum(mz=np.array([100, 200, 300], dtype="float"),
                    intensities=np.array([10, 10, 500], dtype="float"),
                    metadata={"charge": -1,
                              "inchi": '"InChI=1S/C6H12"',
                              "precursor_mz": 222.2})

# Write spectrum to test file
save_as_json(spectrum, "test.json")
Parameters:

  • spectrums – Expected input is a list of Spectrum objects.

  • filename – Provide filename to save spectrum(s).

  • export_style – Converts the keys to the required export style. One of [“matchms”, “massbank”, “nist”, “riken”, “gnps”]. Default is “matchms”

matchms.exporting.save_as_mgf(spectrums: List[Spectrum] | Spectrum, filename: str, export_style: str = 'matchms')[source]

Save spectrum(s) as mgf file.

losses of spectrum will not be saved.

Example:

import numpy as np
from matchms import Spectrum
from matchms.exporting import save_as_mgf

# Create dummy spectrum
spectrum = Spectrum(mz=np.array([100, 200, 300], dtype="float"),
                    intensities=np.array([10, 10, 500], dtype="float"),
                    metadata={"charge": -1,
                              "inchi": '"InChI=1S/C6H12"',
                              "precursor_mz": 222.2})

# Write spectrum to test file
save_as_mgf(spectrum, "test.mgf")
Parameters:

  • spectrums – Expected input are match.Spectrum.Spectrum() objects.

  • filename – Provide filename to save spectrum(s).

  • export_style – Converts the keys to the required export style. One of [“matchms”, “massbank”, “nist”, “riken”, “gnps”]. Default is “matchms”

matchms.exporting.save_as_msp(spectrums: List[Spectrum], filename: str, write_peak_comments: bool = True, mode: str = 'a', style: str = 'matchms')[source]

Save spectrum(s) as msp file.

losses of spectrum will not be saved.

Example:

import numpy as np
from matchms import Spectrum
from matchms.exporting import save_as_msp

# Create dummy spectrum
spectrum = Spectrum(mz=np.array([100, 200, 300], dtype="float"),
                    intensities=np.array([10, 10, 500], dtype="float"),
                    metadata={"charge": -1,
                              "inchi": '"InChI=1S/C6H12"',
                              "precursor_mz": 222.2})

# Write spectrum to test file
save_as_msp(spectrum, "test.msp")
Parameters:

  • spectrums – Expected input are match.Spectrum.Spectrum() objects.

  • filename – Provide filename to save spectrum(s).

  • write_peak_comments – Writes peak comments to individual peaks after the respective mz/intensity pair when set to True. Default is True.

  • mode – Mode on how to write to file. One of [“w”, “a”] (write/append). Default is append.

  • style – Converts the keys to required Export style. One of [“massbank”, “nist”, “riken”, “gnps”]. Default is “matchms”

matchms.exporting.save_spectra(spectrums: List[Spectrum], file: str, export_style: str = 'matchms') → None[source]

Saves spectra as the file type specified.

The following file extensions can be used: “json”, “mgf”, “msp”

Args:

spectrums:

The spectra that are saved.

file:

Path to file containing spectra, with file extension “json”, “mgf”, “msp”

ftype:

Optional. Filetype

export_style:

Converts the keys to the required export style. One of [“matchms”, “massbank”, “nist”, “riken”, “gnps”]. Default is “matchms”

Submodules