GithubHelp home page GithubHelp logo

Add universal identifier about cmiles HOT 3 OPEN

openforcefield avatar openforcefield commented on August 17, 2024
Add universal identifier

from cmiles.

Comments (3)

ChayaSt avatar ChayaSt commented on August 17, 2024

I added more extensive testing (#9 ) of the new OpenEye unique protomer and found that there are some tautomers and mesomers it does not capture.
Here is a Jupyter notebook that looks at some tautomer classes.
https://github.com/openforcefield/cmiles/blob/id/examples/Tautomers.ipynb

In addition, you need the OpenEye license to use this so I was wondering if we can use the InChI for this purpose.

The structure of InChI:

  1. The first layer is the chemical formula - so this will be the same for all tautomers
  2. The second layer is the connectivity. This can have up to 3 sublayers.
    1. All bonds to non-bridging hydrogens atoms (same for most tautomers)
    2. Bonds of immobile H-atoms (This will be different for keto-enol tautomers)
    3. H-atoms that can be found in more than one location. This should technically be the same for all tautomers but that is not always the case.

If we use the chemical formula and the first sublayer of the connectivity, we should be able to capture more tautomers. It would be nice if we'd be able to use the first 14 characters of the InChI key, but that uses the entire connectivity layer for hashing so they differ for some tautomers.

We might be able to use the new Mixture InhChI, however, the problem will be enumerating all tautomers a priori.

from cmiles.

ChayaSt avatar ChayaSt commented on August 17, 2024

I'm looking into the FiCuS identifier which can be accessed here.
Some slides I found on this identifier:

from cmiles.

ChayaSt avatar ChayaSt commented on August 17, 2024

Partially addressed by #9

from cmiles.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.