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moleculemaker / somn-frontend

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Somn: Warning Messages for Stereochemistry and Heavy Atoms #25

Open David-Bianchi opened 1 week ago

David-Bianchi commented 1 week ago

Warning messages upon Somn SMILES input validation for molecules containing stereochemistry (dashes etc.) or heavy atoms (more than 150 atoms etc.)

  1. Stereochemistry

See the following Slack link for David's initial pybel code for this: https://moleculemakerlabinst.slack.com/archives/C064A6PR01M/p1724949118827219

Link for Figma designs: https://www.figma.com/design/XMOJNiIiIK7Q8zdRIWBFE5?node-id=1956-26304#930837523

Image

  1. Heavy atoms (greater than 150 atoms)

See the following Slack link for David's initial pybel code for this: https://moleculemakerlabinst.slack.com/archives/C064A6PR01M/p1727891243631019

Link for Figma designs: https://www.figma.com/design/XMOJNiIiIK7Q8zdRIWBFE5?node-id=2000-26785#959605189

Image

ckouder commented 1 week ago

Hi David, thank you for creating this issue! Will take a look next week or Friday if have time

David-Bianchi commented 1 week ago

Sounds good, thanks Bingji! Let me know here or in Slack if you have any questions on it.

ckouder commented 1 day ago

Hi David, please let me know if this issue still persists with openbabel parsing cdxml? This might be covered before but i'd like to double check to make sure if I use the right tool

David-Bianchi commented 1 day ago

@ckouder, this is a good point! The openbabel code should work for this, we just have to double check that it doesn't leave any "open valences" (which would show up as two extraneous dots over an atom in the image), and that the Hs get properly added with .addHs() and the pull request mentioned in the issue that you shared above.