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molvs

Molecule Validation and Standardization

https://github.com/mcs07/molvs

Science Score: 10.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.4%) to scientific vocabulary

Keywords

cheminformatics chemistry python rdkit standardization validation
Last synced: 6 months ago · JSON representation

Repository

Molecule Validation and Standardization

Basic Info
Statistics
  • Stars: 174
  • Watchers: 18
  • Forks: 56
  • Open Issues: 23
  • Releases: 0
Topics
cheminformatics chemistry python rdkit standardization validation
Created over 11 years ago · Last pushed almost 6 years ago
Metadata Files
Readme Changelog Contributing License

README.rst 

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/

Owner

  • Name: Matt Swain
  • Login: mcs07
  • Kind: user
  • Location: New York, NY
  • Company: @DEShawResearch

Developing software for drug discovery

GitHub Events

Total
  • Watch event: 18
  • Issue comment event: 1
  • Fork event: 4
Last Year
  • Watch event: 18
  • Issue comment event: 1
  • Fork event: 4

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 145
  • Total Committers: 3
  • Avg Commits per committer: 48.333
  • Development Distribution Score (DDS): 0.021
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Matt Swain m****n@m****m 142
Brian Cole c****b@d****m 2
JoshuaMeyers j****s@r****m 1
Committer Domains (Top 20 + Academic)
rocketmail.com: 1 deshawresearch.com: 1 me.com: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 29
  • Total pull requests: 12
  • Average time to close issues: about 1 month
  • Average time to close pull requests: about 16 hours
  • Total issue authors: 23
  • Total pull request authors: 7
  • Average comments per issue: 1.79
  • Average comments per pull request: 0.42
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • UnixJunkie (3)
  • jose-manuel (3)
  • benbowen (2)
  • jw-feng (2)
  • mainguyenanhvu (1)
  • chupvl (1)
  • alexisparenty (1)
  • thesketh (1)
  • khoivan88 (1)
  • aparamon (1)
  • jvansan (1)
  • adlvdl (1)
  • ghost (1)
  • mmagithub (1)
  • sergsb (1)
Pull Request Authors
  • mcs07 (5)
  • gjgetzinger (2)
  • gitter-badger (1)
  • UnixJunkie (1)
  • coleb (1)
  • fossabot (1)
  • JoshuaMeyers (1)
Top Labels
Issue Labels
bug (7) enhancement (2) question (1) wontfix (1) documentation (1)
Pull Request Labels
bug (5) enhancement (2)

Packages

  • Total packages: 4
  • Total downloads:
    • pypi 13,443 last-month
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 13
    (may contain duplicates)
  • Total versions: 32
  • Total maintainers: 1
pypi.org: molvs

Molecule Validation and Standardization

  • Versions: 11
  • Dependent Packages: 1
  • Dependent Repositories: 8
  • Downloads: 13,443 Last month
Rankings
Downloads: 4.7%
Dependent packages count: 4.8%
Dependent repos count: 5.2%
Average: 5.3%
Forks count: 5.9%
Stargazers count: 6.0%
Maintainers (1)
mcs07
Last synced: 6 months ago
proxy.golang.org: github.com/mcs07/MolVS
  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 9.0%
Average: 9.6%
Dependent repos count: 10.2%
Last synced: 6 months ago
proxy.golang.org: github.com/mcs07/molvs
  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 9.0%
Average: 9.6%
Dependent repos count: 10.2%
Last synced: 6 months ago
conda-forge.org: molvs
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 5
Rankings
Dependent repos count: 14.8%
Forks count: 25.9%
Average: 30.9%
Stargazers count: 31.4%
Dependent packages count: 51.6%
Last synced: 6 months ago

Dependencies

environment.yml conda
  • pip 19.0.3.*
  • pytest 4.3.1.*
  • rdkit 2018.09.1.*
  • six 1.12.0.*
  • twine 1.13.0.*
setup.py pypi
  • six *