suppress rdkit reaction atom map warning in residue padder #198
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rwxayheee
approved these changes
Oct 15, 2024
rwxayheee
reviewed
Oct 15, 2024
| rdkit_logger = logging.getLogger("rdkit") | ||
| rdkit_logger.handlers[0].setLevel("WARNING") | ||
| rdkit_logger.handlers[0].setFormatter( | ||
| logging.Formatter('[RDKit] %(levelname)s:%(message)s'), |
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Because it's in init, it will change the format of RDKit logging messages (severity >= warning) once meeko is imported. Do you want to enforce this?
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Just leaving a record of what we discussed: I don't know. It may be useful to know which messages come from RDKit.
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For the reaction run by ResiduePadders, it suppresses the following rdkit warnings:
these arise because the product has atom labels that the reactants don't, but those labels are added on purpose. The filter is removed immediately after the reaction. Since the logger is a singleton, it is not guaranteed that the same warning won't be suppressed when multiprocessing from some other reaction that happens to be running, but I think that's OK.