.. image:: readthedocs/_static/matchms.png :width: 600 :alt: matchms logo

################################################################################ matchms ################################################################################ Vector representation and similarity measure for mass spectrometry data.

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Documentation for users

Installation

Install matchms from Anaconda Cloud with

.. code-block:: console

conda install --channel nlesc --channel bioconda --channel conda-forge matchms

Glossary of terms

.. list-table:: :header-rows: 1

• • Term
    • Description
• • adduct / addition product
    • During ionization in a mass spectrometer, the molecules of the injected compound break apart into fragments. When fragments combine into a new compound, this is known as an addition product, or adduct. Wikipedia <https://en.wikipedia.org/wiki/Adduct>__
• • GNPS
    • Knowledge base for sharing of mass spectrometry data (link <https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp>__).
• • InChI / :code:INCHI
    • InChI is short for International Chemical Identifier. InChIs are useful in retrieving information associated with a certain molecule from a database.
• • InChIKey / InChI key / :code:INCHIKEY
    • An indentifier for molecules. For example, the InChI key for carbon dioxide is :code:InChIKey=CURLTUGMZLYLDI-UHFFFAOYSA-N (yes, it includes the substring :code:InChIKey=).
• • MGF File / Mascot Generic Format
    • A plan ASCII file format to store peak list data from a mass spectrometry experiment. Links: matrixscience.com <http://www.matrixscience.com/help/data_file_help.html#GEN>, fiehnlab.ucdavis.edu <https://fiehnlab.ucdavis.edu/projects/lipidblast/mgf-files>.
• • parent mass / :code:parent_mass
    • Actual mass (in Dalton) of the original compound prior to fragmentation. It can be recalculated from the precursor m/z by taking into account the charge state and proton/electron masses.
• • precursor m/z / :code:precursor_mz
    • Mass-to-charge ratio of the compound targeted for fragmentation.
• • SMILES
    • A line notation for describing the structure of chemical species using short ASCII strings. For example, water is encoded as :code:O[H]O, carbon dioxide is encoded as :code:O=C=O, etc. SMILES-encoded species may be converted to InChIKey using a resolver like this one <https://cactus.nci.nih.gov/chemical/structure>__. The Wikipedia entry for SMILES is here <https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system>__.

Documentation for developers

Installation

To install matchms, do:

.. code-block:: console

git clone https://github.com/matchms/matchms.git cd matchms conda env create --file conda/environment-dev.yml conda activate matchms-dev pip install --editable .

Run the linter with:

.. code-block:: console

prospector

Run tests (including coverage) with:

.. code-block:: console

pytest

Conda package

To build anaconda package locally, do:

.. code-block:: console

conda deactivate conda env create --file conda/environment-build.yml conda activate matchms-build BUILD_FOLDER=/tmp/matchms/_build rm -rfv $BUILD_FOLDER;mkdir -p $BUILD_FOLDER conda build --numpy 1.18.1 --no-include-recipe -c bioconda -c conda-forge \ --croot $BUILD_FOLDER ./conda

If successful, this will yield the built matchms conda package as matchms-<version>*.tar.bz2 in $BUILD_FOLDER/noarch/. You can test if installation of this conda package works with:

.. code-block:: console

conda install \ --channel bioconda \ --channel conda-forge \ --channel file://${CONDA_PREFIX}/output/noarch/ \ matchms

To publish the package on anaconda cloud, do:

.. code-block:: console

anaconda --token ${{ secrets.ANACONDA_TOKEN }} upload --user nlesc --force $BUILD_FOLDER/noarch/*.tar.bz2

where secrets.ANACONDA_TOKEN is a token to be generated on the Anaconda Cloud website. This secret should be added to GitHub repository.

To remove matchms package:

.. code-block:: console

conda remove matchms

To remove matchms-build environment:

.. code-block:: console

conda env remove --name matchms-build

Flowchart

.. image:: flowchart.svg.png :width: 400 :alt: Flowchart

Contributing

If you want to contribute to the development of matchms, have a look at the contribution guidelines <CONTRIBUTING.md>_.

License

Copyright (c) 2020, Netherlands eScience Center

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Credits

This package was created with Cookiecutter <https://github.com/audreyr/cookiecutter> and the NLeSC/python-template <https://github.com/NLeSC/python-template>.