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
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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'
To install MolVS with Anaconda Python, simply run::
conda install -c conda-forge molvs
Alternatively, try one of the other installation options
_.
Full documentation is available at https://molvs.readthedocs.io.
Issue Tracker
_.source code
_ on GitHub, make changes and send a pull request.MolVS is licensed under the MIT license
_.
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/