jsdir / MolVS

Molecule Validation and Standardization

MolVS: Molecule Validation and Standardization

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, simply run:

pip install molvs

Alternatively, try one of the other installation options.

Documentation

Full documentation is available at http://molvs.readthedocs.org.

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