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https://github.com/domdfcoding/chemistry_tools

Python tools for analysis of chemical compounds.
https://github.com/domdfcoding/chemistry_tools

chemistry python python3 utility

Last synced: 21 days ago
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Python tools for analysis of chemical compounds.

Host: GitHub
URL: https://github.com/domdfcoding/chemistry_tools
Owner: domdfcoding
License: lgpl-3.0
Created: 2019-06-12T20:03:45.000Z (over 5 years ago)
Default Branch: master
Last Pushed: 2024-04-26T08:27:58.000Z (6 months ago)
Last Synced: 2024-05-02T05:16:42.216Z (6 months ago)
Topics: chemistry, python, python3, utility
Language: Python
Homepage: https://chemistry_tools.readthedocs.io/en/latest
Size: 1.07 MB
Stars: 0
Watchers: 3
Forks: 1
Open Issues: 1
Metadata Files:
- Readme: README.rst
- Contributing: CONTRIBUTING.rst
- License: LICENSE

Awesome Lists containing this project

README

        =====================

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

|

Copyright 2017 Matt Swain 

https://github.com/mcs07/PubChemPy

Available under the MIT License

SpectrumSimilarity

======================================

Perform mass spectrum similarity calculations

|

Adapted from SpectrumSimilarity.R

Part of OrgMassSpecR

Copyright 2011-2017 Nathan Dodder 

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.

|

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

Copyright (c) 2015-2018, Björn Dahlgren

All rights reserved.

|

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

|

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

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

Licensed under the Apache License