MolVS: Molecule Validation and Standardization

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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/