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CDK-R / cdkr

Integrating R and the CDK
https://cdk-r.github.io/cdkr/
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Parsing SMILES with heavy atoms #118

Open joannawolthuis opened 3 years ago

joannawolthuis commented 3 years ago

Hi there,

First of all, thanks for your work on this package! I make heavy use of it in my mass spectrometry database parser package. I recently was asked if I could also allow users to provide SMILES structures of heavy labeled (13C) compounds as input. However, i notice that upon parsing SMILES with 13Cs, the string either fails to parse (rarely) or changes the heavy C back to a regular C (mol2formula does not have any heavy atoms included). Is there any functionality to work with heavy labeled atoms?

Kind regards, Joanna

zachcp commented 3 years ago

Hi @joannawolthuis ,

Thanks for your issue. Can you post a small bit of code showing what you are seeing and I'll see what if we can address it.

zach cp