https://github.com/mcs07/mongodb-chemistry

Ideas for chemical similarity searches in MongoDB.
https://github.com/mcs07/mongodb-chemistry

cheminformatics chemistry mongodb python search similarity

Last synced: 8 days ago
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Ideas for chemical similarity searches in MongoDB.

• Host: GitHub
• URL: https://github.com/mcs07/mongodb-chemistry
• Owner: mcs07
• License: mit
• Created: 2014-06-03T16:04:37.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2015-02-08T18:42:04.000Z (almost 10 years ago)
• Last Synced: 2024-04-19T05:44:05.501Z (7 months ago)
• Topics: cheminformatics, chemistry, mongodb, python, search, similarity
• Language: Python
• Homepage: http://blog.matt-swain.com/post/87093745652/chemical-similarity-search-in-mongodb
• Size: 957 KB
• Stars: 24
• Watchers: 7
• Forks: 9
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# MongoDB Chemistry

Chemical similarity search implementation in MongoDB, with performance analysis.

See [this blog post](http://blog.matt-swain.com/post/87093745652/chemical-similarity-search-in-mongodb) for more information.

See also:

- [Presentation slides](https://speakerdeck.com/mcs07/chemical-structure-handling-in-mongodb)

- [Blog post by Rajarshi Guha](http://blog.rguha.net/?p=1261)

- [Blog post by Davy Suvee](http://datablend.be/?p=254) ([part 2](http://datablend.be/?p=256), [part 3](http://datablend.be/?p=265))

## Installation

### Mac OS X

    brew install rdkit mongodb

    pip install git+https://github.com/mcs07/mongodb-chemistry.git

    

### Ubuntu

See [scripts/bootstrap.sh](https://github.com/mcs07/mongodb-chemistry/blob/master/scripts/bootstrap.sh).

## Usage

A simple example:

    mchem load mymols.sdf

    mchem addfp

    mchem countfp

    mchem similar O=C(Oc1ccccc1C(=O)O)C

See [scripts/chembl.sh](https://github.com/mcs07/mongodb-chemistry/blob/master/scripts/chembl.sh) for a more detailed example.