dynotx / liminal-orm

ORM and toolkit to help keep your Benchling schemas and downstream dependencies in sync.
https://dynotx.github.io/liminal-orm/
Apache License 2.0
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add molecule entity type #52

Open jorge-computedfield opened 1 week ago

jorge-computedfield commented 1 week ago

There's an entity type that's not included in the current version: molecules. They are part of the normal registry but are only available if a separate licence is bought for "chemistry" (not sure what name Benchling gives to this). My understanding is that this would have to be added here: https://github.com/dynotx/liminal-orm/blob/main/liminal/enums/__init__.py#L2 and all the references to these enums updated.

ndamania00 commented 18 hours ago

The default fields are id, source_id, name, canonical_smiles. The rest is exactly the same as say custom_entities (i.e: you can add the same field types as far as I can tell, choose between registry IDs / names, naming template, etc). In case you are not familiar with SMILES: https://openbabel.org/docs/FileFormats/Canonical_SMILES_format.html