Advancing Open Source and Open Science for Chemistry

The Open Chemistry project is a collection of open source, cross platform libraries and applications for the exploration, analysis and generation of chemical data. The organization is an umbrella of projects developed by long-time collaborators and innovators in open chemistry such as the Avogadro, cclib, Open Babel, 3DMol.js, and RDKit projects. The first three alone have been downloaded over 900,000 times and cited in over 2,000 academic papers. Our goal is to improve the state of the art, and facilitate the open exchange of chemical data and ideas while utilizing the best technologies from quantum chemistry codes, molecular dynamics, informatics, analytics, and visualization.

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Technologies

  • python
  • c++
  • javascript
  • java
  • opengl

Topics

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Open Chemistry 2018 Projects

  • Adarsh Balasubramanian
    Avogadro 2: Molecular Dynamics
    This project aims to implement support for Molecular Dynamics in Avogadro. Molecular dynamics (MD) is a computer simulation method for studying the...
  • Boran Adas
    Create a generalized fingerprinting API
    Chemical fingerprints are very important for both querying chemical data (using similarity in fingerprint space) and the use of molecular entities in...
  • Naruki Yoshikawa
    Fast, Efficient Fragment-Based Coordinate Generation
    Chemical information is provided in various formats. Open Babel is a tool to convert file formats. When we translate a format which does not include...
  • Skand Vishwanath Peri
    Imaging Tools
    DeepChem has been great library for the application of deep learning for drug/chemical discovery. As of now there is no imaging models implemented in...
  • Kunal Sharma
    Implementing new parsers
    In this project I aim to implement new parsers for MOLCAS and TURBOMOLE. They will be a part of the cclib.parser module and will be implemented along...
  • Evgeny Sorokin
    MS/MS identification module for MZmine.
    The goal is to implement a wrapper (common interface) for the identification algorithms’ logic in MSDK (that will allow to invoke tools like SIRIUS...
  • Susan Leung
    RDKit-MolVS Integration Project - GSoC 2018
    MolVS (https://molvs.readthedocs.io/en/latest/) provides very useful functionality for molecular validation and standardization. MolVS is built using...
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2018