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maxhodak / keras-molecules

Autoencoder network for learning a continuous representation of molecular structures.
MIT License
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add smilesparser.py for parsing SMILES strings. #41

Closed dakoner closed 7 years ago

dakoner commented 7 years ago

This will be useful if people want to train with charsets that are element names like 'Br'

dakoner commented 7 years ago

I've decided to put this in my own repo, as it's not strictly required for reproducing the paper's results.

pechersky commented 7 years ago

How do you envision utilizing the parser? Is there a set of termination symbols the parses implicitly encodes that you can use to generate a "charset"?

dakoner commented 7 years ago

I explicitly encoded a few terminals (see OrganicSymbol, AromaticSymbol, and ElementSymbol), but it really should use the explicit list of all elements: http://opensmiles.org/opensmiles.html spec explicitly lists all the terminals, so I think (using your SMILESDataGenerator as an example) you could use the list of terminals as your charset.

On Tue, Nov 22, 2016 at 9:36 AM, Yakov Pechersky notifications@github.com wrote:

How do you envision utilizing the parser? Is there a set of termination symbols the parses implicitly encodes that you can use to generate a "charset"?

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