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chembl / ChEMBL_Structure_Pipeline

ChEMBL database structure pipelines
MIT License
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Status output being written to stdout instead of stderr #36

Closed gpatbrady closed 2 years ago

gpatbrady commented 2 years ago

Thank you for this pipeline; very helpful! I am writing a python command line wrapper to some of this functionality and it appears to me that some of the "runtime" info that ought to be sent to stderr is being sent to stdout. I'm using the standardize() and get_parent_mol() functions in particular, and my output (to stdout) is being polluted with e.g. stuff like

[21:22:44] Initializing Normalizer [21:22:44] Running Uncharger [21:22:44] Running Uncharger [21:22:44] Running Normalizer [21:22:44] Running Uncharger [21:22:44] Running Uncharger [21:22:44] Running Uncharger

Cheers, pat

gpatbrady commented 2 years ago

Or a way to suppress this output altogether would be great.

greglandrum commented 2 years ago

@gpatbrady, those messages are coming from the RDKit core. The incantation to disable the RDKit info log is:

from rdkit import RDLogger
RDLogger.DisableLog("rdApp.info")
gpatbrady commented 2 years ago

Oh sweet; I'll give that a shot! Thanks! Pat

On Mon, Feb 21, 2022, 1:01 AM Greg Landrum @.***> wrote:

@gpatbrady https://github.com/gpatbrady, those messages are coming from the RDKit core. The incantation to disable the RDKit info log is:

from rdkit import RDLogger RDLogger.DisableLog("rdApp.info")

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