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MolVS: Molecule Validation and Standardization

.. sectionauthor:: Matt Swain <m.swain@me.com>

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'

Each standardization module is also available separately, allowing the development of custom standardization processes.

Features

  • Normalization of functional groups to a consistent format.
  • Recombination of separated charges.
  • Breaking of bonds to metal atoms.
  • Competitive reionization to ensure strongest acids ionize first in partially ionize molecules.
  • Tautomer enumeration and canonicalization.
  • Neutralization of charges.
  • Standardization or removal of stereochemistry information.
  • Filtering of salt and solvent fragments.
  • Generation of fragment, isotope, charge, tautomer or stereochemistry insensitive parent structures.
  • Validations to identify molecules with unusual and potentially troublesome characteristics.

User guide

A step-by-step guide to getting started with MolVS.

.. toctree::
   :maxdepth: 1

   guide/intro
   guide/install
   guide/gettingstarted
   guide/validate
   guide/standardize
   guide/tautomer
   guide/fragment
   guide/charge
   guide/cli
   guide/contributing

API documentation

Comprehensive API documentation with information on every function, class and method. This is automatically generated from the MolVS source code and comments.

.. toctree::
   :maxdepth: 2

   api


Useful links