jspaaks / matchms-spec2vec

spec2vec

Word2Vec based similarity measure of mass spectrometry data.

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Documentation for users

Installation

Install spec2vec from Anaconda Cloud with

conda install --channel nlesc --channel bioconda --channel conda-forge spec2vec

Glossary of terms

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
GNPS	Knowledge base for sharing of mass spectrometry data (link).
InChI / 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 / INCHIKEY	An indentifier for molecules. For example, the InChI key for carbon dioxide is InChIKey=CURLTUGMZLYLDI-UHFFFAOYSA-N (yes, it includes the substring InChIKey=).
MGF File / Mascot Generic Format	A plan ASCII file format to store peak list data from a mass spectrometry experiment. Links: matrixscience.com, fiehnlab.ucdavis.edu.
parent mass / 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 / 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 O[H]O, carbon dioxide is encoded as O=C=O, etc. SMILES-encoded species may be converted to InChIKey using a resolver like this one. The Wikipedia entry for SMILES is here.

Documentation for developers

Installation

To install spec2vec, do:

git clone https://github.com/iomega/spec2vec.git
cd spec2vec
conda env create --file conda/environment-dev.yml
conda activate spec2vec-dev
pip install --editable .

Run the linter with:

prospector

Run tests (including coverage) with:

pytest

Conda package

To build anaconda package locally, do:

conda deactivate
conda env create --file conda/environment-build.yml
conda activate spec2vec-build
BUILD_FOLDER=/tmp/spec2vec/_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 spec2vec conda package as spec2vec-<version>*.tar.bz2 in $BUILD_FOLDER/noarch/. You can test if installation of this conda package works with:

# make a clean environment
conda deactivate
cd $(mktemp -d)
conda env create --name test python=3.7
conda activate test

conda install \
  --channel bioconda \
  --channel conda-forge \
  --channel file://${CONDA_PREFIX}/noarch/ \
  spec2vec

To publish the package on anaconda cloud, do:

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 spec2vec package from the active environment:

conda remove spec2vec

To remove spec2vec environment:

conda env remove --name spec2vec

Contributing

If you want to contribute to the development of spec2vec, have a look at the contribution guidelines.

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 and the NLeSC/python-template.