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kate-fie / syndirella

Generates and scores synthetically practical elaborations from fragment screens
https://syndirella.readthedocs.io/en/latest/
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Better handling for unsuccessful base minimisation #38

Closed kate-fie closed 3 months ago

kate-fie commented 4 months ago

Sometimes the base compound does not successfully minimise, I need to handle these cases better and output errors. Need to add the following implementation:

  1. Place base compound first, attempt to place. If it does not minimise, replace up to 4 more times until it successfully does. Record as flag if it had to be replaced, and what errors were output.
  2. After a successful minimisation, run through intramolecular validity checks similar to PoseBusters. If it does not pass, replace up to 4 more times.

This results in 5 attempts to place + run intermolecular checks for the base compound since it is pivotal to make sure the base compound is valid before performing elaborations from it.

kate-fie commented 3 months ago

Implemented this but only replacing up to 2 times. Although there are cases I noticed that the base compound could be placed (for one of the stereoisomers) but then at the end of elaboration none of the stereoisomers could be successfully minimised... An edge case to be aware of