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Chemistry Tools

.. start short_desc

Python tools for analysis of chemical compounds.

.. end short_desc

.. start shields

.. list-table:: :stub-columns: 1 :widths: 10 90

* - Docs
  - |docs| |docs_check|
* - Tests
  - |actions_linux| |actions_windows| |actions_macos| |coveralls|
* - PyPI
  - |pypi-version| |supported-versions| |supported-implementations| |wheel|
* - Anaconda
  - |conda-version| |conda-platform|
* - Activity
  - |commits-latest| |commits-since| |maintained| |pypi-downloads|
* - QA
  - |codefactor| |actions_flake8| |actions_mypy|
* - Other
  - |license| |language| |requires|

.. |docs| image:: https://img.shields.io/readthedocs/chemistry-tools/latest?logo=read-the-docs :target: https://chemistry-tools.readthedocs.io/en/latest :alt: Documentation Build Status

.. |docs_check| image:: https://github.com/domdfcoding/chemistry_tools/workflows/Docs%20Check/badge.svg :target: https://github.com/domdfcoding/chemistry_tools/actions?query=workflow%3A%22Docs+Check%22 :alt: Docs Check Status

.. |actions_linux| image:: https://github.com/domdfcoding/chemistry_tools/workflows/Linux/badge.svg :target: https://github.com/domdfcoding/chemistry_tools/actions?query=workflow%3A%22Linux%22 :alt: Linux Test Status

.. |actions_windows| image:: https://github.com/domdfcoding/chemistry_tools/workflows/Windows/badge.svg :target: https://github.com/domdfcoding/chemistry_tools/actions?query=workflow%3A%22Windows%22 :alt: Windows Test Status

.. |actions_macos| image:: https://github.com/domdfcoding/chemistry_tools/workflows/macOS/badge.svg :target: https://github.com/domdfcoding/chemistry_tools/actions?query=workflow%3A%22macOS%22 :alt: macOS Test Status

.. |actions_flake8| image:: https://github.com/domdfcoding/chemistry_tools/workflows/Flake8/badge.svg :target: https://github.com/domdfcoding/chemistry_tools/actions?query=workflow%3A%22Flake8%22 :alt: Flake8 Status

.. |actions_mypy| image:: https://github.com/domdfcoding/chemistry_tools/workflows/mypy/badge.svg :target: https://github.com/domdfcoding/chemistry_tools/actions?query=workflow%3A%22mypy%22 :alt: mypy status

.. |requires| image:: https://dependency-dash.repo-helper.uk/github/domdfcoding/chemistry_tools/badge.svg :target: https://dependency-dash.repo-helper.uk/github/domdfcoding/chemistry_tools/ :alt: Requirements Status

.. |coveralls| image:: https://img.shields.io/coveralls/github/domdfcoding/chemistry_tools/master?logo=coveralls :target: https://coveralls.io/github/domdfcoding/chemistry_tools?branch=master :alt: Coverage

.. |codefactor| image:: https://img.shields.io/codefactor/grade/github/domdfcoding/chemistry_tools?logo=codefactor :target: https://www.codefactor.io/repository/github/domdfcoding/chemistry_tools :alt: CodeFactor Grade

.. |pypi-version| image:: https://img.shields.io/pypi/v/chemistry_tools :target: https://pypi.org/project/chemistry_tools/ :alt: PyPI - Package Version

.. |supported-versions| image:: https://img.shields.io/pypi/pyversions/chemistry_tools?logo=python&logoColor=white :target: https://pypi.org/project/chemistry_tools/ :alt: PyPI - Supported Python Versions

.. |supported-implementations| image:: https://img.shields.io/pypi/implementation/chemistry_tools :target: https://pypi.org/project/chemistry_tools/ :alt: PyPI - Supported Implementations

.. |wheel| image:: https://img.shields.io/pypi/wheel/chemistry_tools :target: https://pypi.org/project/chemistry_tools/ :alt: PyPI - Wheel

.. |conda-version| image:: https://img.shields.io/conda/v/domdfcoding/chemistry_tools?logo=anaconda :target: https://anaconda.org/domdfcoding/chemistry_tools :alt: Conda - Package Version

.. |conda-platform| image:: https://img.shields.io/conda/pn/domdfcoding/chemistry_tools?label=conda%7Cplatform :target: https://anaconda.org/domdfcoding/chemistry_tools :alt: Conda - Platform

.. |license| image:: https://img.shields.io/github/license/domdfcoding/chemistry_tools :target: https://github.com/domdfcoding/chemistry_tools/blob/master/LICENSE :alt: License

.. |language| image:: https://img.shields.io/github/languages/top/domdfcoding/chemistry_tools :alt: GitHub top language

.. |commits-since| image:: https://img.shields.io/github/commits-since/domdfcoding/chemistry_tools/v1.1.1 :target: https://github.com/domdfcoding/chemistry_tools/pulse :alt: GitHub commits since tagged version

.. |commits-latest| image:: https://img.shields.io/github/last-commit/domdfcoding/chemistry_tools :target: https://github.com/domdfcoding/chemistry_tools/commit/master :alt: GitHub last commit

.. |maintained| image:: https://img.shields.io/maintenance/yes/2024 :alt: Maintenance

.. |pypi-downloads| image:: https://img.shields.io/pypi/dm/chemistry_tools :target: https://pypi.org/project/chemistry_tools/ :alt: PyPI - Downloads

.. end shields

Installation

.. start installation

chemistry_tools can be installed from PyPI or Anaconda.

To install with pip:

.. code-block:: bash

$ python -m pip install chemistry_tools

To install with conda:

* First add the required channels

.. code-block:: bash

	$ conda config --add channels https://conda.anaconda.org/conda-forge
	$ conda config --add channels https://conda.anaconda.org/domdfcoding

* Then install

.. code-block:: bash

	$ conda install chemistry_tools

.. end installation

lookup and pubchem adapted from PubChemPy

Python interface to the PubChem REST API

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Copyright 2017 Matt Swain [email protected]

https://github.com/mcs07/PubChemPy

Available under the MIT License

SpectrumSimilarity

Perform mass spectrum similarity calculations

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Adapted from SpectrumSimilarity.R

Part of OrgMassSpecR

Copyright 2011-2017 Nathan Dodder [email protected]

https://cran.r-project.org/web/packages/OrgMassSpecR/index.html

Available under the BSD 2-Clause License

elements and formulae

Provides properties for the elements in the periodic table, and functions for parsing formulae and calculating isotope distributions.

Calculations are based on the isotopic composition of the elements. Mass deficiency due to chemical bonding is not taken into account.

Examples of valid formulae are H2O, [2H]2O, CH3COOH, EtOH, CuSO4.5H2O, and (COOH)2. Formulae are case sensitive.

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Based on ChemPy (https://github.com/bjodah/chempy)

Copyright (c) 2015-2018, Björn Dahlgren

All rights reserved.

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Also based on molmass (https://github.com/cgohlke/molmass)

Copyright (c) 1990-2020, Christoph Gohlke

All rights reserved.

Licensed under the BSD 3-Clause License

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Also based on Pyteomics (https://github.com/levitsky/pyteomics)

Copyright (c) 2011-2015, Anton Goloborodko & Lev Levitsky

Licensed under the Apache License