kate-fie / syndirella

Generates and scores synthetically practical elaborations from fragment screens
https://syndirella.readthedocs.io/en/latest/
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Add more specific check for chirality in SMARTS #3

Closed kate-fie closed 8 months ago

kate-fie commented 9 months ago

I've noticed that some reactant catalog data is not stereochemistry specific. A more strict check on making sure that the chirality of all queried reactants is correct should be done.

Example of the problem for an epoxide + amine coupling: Epoxide:

image

Amine:

image

Product:

image

But the reactants in the epoxide metadata look like this: {'catalogName': 'enamine_bb', 'catalogId': 'EN300-44840', 'smiles': 'c1cc2c(cc1C1CO1)OCO2', 'link': 'https://www.enaminestore.com/catalog/EN300-44840', 'purchaseInfo': {'isBuildingBlock': True, 'isScreening': False, 'bbLeadTimeWeeks': 1.0, 'bbPriceRange': '< $100 / g'}}, {'catalogName': 'enamine_made', 'catalogId': 'BBV-49121744', 'smiles': 'c1cc2c(cc1[C@H]1CO1)OCO2', 'purchaseInfo': {'isBuildingBlock': True, 'isScreening': False, 'bbLeadTimeWeeks': 6.0, 'bbPriceRange': '$500-1k / g'}}

Clearly the first reactant and its catalog info should be removed since it does not define chirality information.

kate-fie commented 9 months ago

To be more specific, I need to make sure that all stereocenters of compound are sampled when placing

kate-fie commented 8 months ago

This is done.