https://github.com/mcs07/molvs
Molecule Validation and Standardization
https://github.com/mcs07/molvs
cheminformatics chemistry python rdkit standardization validation
Last synced: 6 months ago
JSON representation
Molecule Validation and Standardization
- Host: GitHub
- URL: https://github.com/mcs07/molvs
- Owner: mcs07
- License: mit
- Created: 2014-06-30T13:37:47.000Z (over 11 years ago)
- Default Branch: master
- Last Pushed: 2020-04-16T18:15:23.000Z (over 5 years ago)
- Last Synced: 2025-03-30T00:05:40.742Z (6 months ago)
- Topics: cheminformatics, chemistry, python, rdkit, standardization, validation
- Language: Python
- Homepage: https://molvs.readthedocs.io/
- Size: 266 KB
- Stars: 170
- Watchers: 18
- Forks: 55
- Open Issues: 22
-
Metadata Files:
- Readme: README.rst
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.rst
- License: LICENSE
Awesome Lists containing this project
README
MolVS: Molecule Validation and Standardization
==============================================
.. image:: https://img.shields.io/pypi/v/MolVS.svg?style=flat-square
:alt: PyPI package
:target: https://pypi.python.org/pypi/MolVS
.. image:: https://img.shields.io/conda/vn/conda-forge/molvs.svg?style=flat-square
:alt: Conda package
:target: https://anaconda.org/conda-forge/molvs
.. image:: https://img.shields.io/github/license/mcs07/MolVS.svg?style=flat-square
:alt: MIT license
:target: https://github.com/mcs07/MolVS/blob/master/LICENSE
.. image:: https://img.shields.io/azure-devops/build/mcs07/MolVS/1.svg?style=flat-square
:alt: Azure DevOps tests
:target: https://dev.azure.com/mcs07/MolVS/_build?definitionId=1
**MolVS** is a molecule validation and standardization tool, written in Python using the `RDKit chemistry framework`_.
Building a collection of chemical structures from different sources can be difficult due to differing representations,
drawing conventions and mistakes. MolVS can standardize chemical structures to improve data quality, help with
de-duplication and identify relationships between molecules.
There are sensible defaults that make it easy to get started::
>>> from molvs import standardize_smiles
>>> standardize_smiles('[Na]OC(=O)c1ccc(C[S+2]([O-])([O-]))cc1')
'[Na+].O=C([O-])c1ccc(CS(=O)=O)cc1'
Installation
------------
To install MolVS with Anaconda Python, simply run::
conda install -c conda-forge molvs
Alternatively, try one of the other `installation options`_.
Documentation
-------------
Full documentation is available at https://molvs.readthedocs.io.
Contribute
----------
- Feature ideas and bug reports are welcome on the `Issue Tracker`_.
- Fork the `source code`_ on GitHub, make changes and send a pull request.
License
-------
MolVS is licensed under the `MIT license`_.
Similar projects
----------------
There are a number of projects with similar goals that take differing approaches:
- `Francis Atkinson's Standardiser`_
- `RSC Chemistry Validation and Standardization Platform (CVSP)`_
- `PubChem Standardization Service`_
- `Tripod Structure standardizer`_
- `FDA Substance Registration System Standard Operating Procedure`_
- `ChemAxon Structure Standardizer`_
.. _`RDKit chemistry framework`: http://www.rdkit.org
.. _`installation options`: http://molvs.readthedocs.io/en/latest/guide/install.html
.. _`source code`: https://github.com/mcs07/MolVS
.. _`Issue Tracker`: https://github.com/mcs07/MolVS/issues
.. _`MIT license`: https://github.com/mcs07/MolVS/blob/master/LICENSE
.. _`Francis Atkinson's Standardiser`: https://wwwdev.ebi.ac.uk/chembl/extra/francis/standardiser/
.. _`RSC Chemistry Validation and Standardization Platform (CVSP)`: http://cvsp.chemspider.com
.. _`PubChem Standardization Service`: https://pubchem.ncbi.nlm.nih.gov/standardize/standardize.cgi
.. _`Tripod Structure standardizer`: https://tripod.nih.gov/?p=61
.. _`FDA Substance Registration System Standard Operating Procedure`: http://www.fda.gov/downloads/ForIndustry/DataStandards/SubstanceRegistrationSystem-UniqueIngredientIdentifierUNII/ucm127743.pdf
.. _`ChemAxon Structure Standardizer`: http://www.chemaxon.com/products/standardizer/