matchms.exporting.save_as_json module

class matchms.exporting.save_as_json.SpectrumJSONEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]

Bases: json.encoder.JSONEncoder

__init__(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)

Constructor for JSONEncoder, with sensible defaults.

If skipkeys is false, then it is a TypeError to attempt encoding of keys that are not str, int, float or None. If skipkeys is True, such items are simply skipped.

If ensure_ascii is true, the output is guaranteed to be str objects with all incoming non-ASCII characters escaped. If ensure_ascii is false, the output can contain non-ASCII characters.

If check_circular is true, then lists, dicts, and custom encoded objects will be checked for circular references during encoding to prevent an infinite recursion (which would cause an OverflowError). Otherwise, no such check takes place.

If allow_nan is true, then NaN, Infinity, and -Infinity will be encoded as such. This behavior is not JSON specification compliant, but is consistent with most JavaScript based encoders and decoders. Otherwise, it will be a ValueError to encode such floats.

If sort_keys is true, then the output of dictionaries will be sorted by key; this is useful for regression tests to ensure that JSON serializations can be compared on a day-to-day basis.

If indent is a non-negative integer, then JSON array elements and object members will be pretty-printed with that indent level. An indent level of 0 will only insert newlines. None is the most compact representation.

If specified, separators should be an (item_separator, key_separator) tuple. The default is (’, ‘, ‘: ‘) if indent is None and (‘,’, ‘: ‘) otherwise. To get the most compact JSON representation, you should specify (‘,’, ‘:’) to eliminate whitespace.

If specified, default is a function that gets called for objects that can’t otherwise be serialized. It should return a JSON encodable version of the object or raise a TypeError.

default(o)[source]

JSON Encoder which can encode a Spectrum object

encode(o)

Return a JSON string representation of a Python data structure.

>>> from json.encoder import JSONEncoder
>>> JSONEncoder().encode({"foo": ["bar", "baz"]})
'{"foo": ["bar", "baz"]}'
iterencode(o, _one_shot=False)

Encode the given object and yield each string representation as available.

For example:

for chunk in JSONEncoder().iterencode(bigobject):
    mysocket.write(chunk)
matchms.exporting.save_as_json.save_as_json(spectrums: List[matchms.Spectrum.Spectrum], filename: str)[source]

Save spectrum(s) as json file.

losses of spectrum will not be saved.

Example:

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

# Create dummy spectrum
spectrum = Spectrum(mz=numpy.array([100, 200, 300], dtype="float"),
                    intensities=numpy.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).