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In search experiments, it can be observed that MEGAN sometimes produces odd molecules containing
C+
atoms, which violate valence despite being accepted as valid byrdkit
. These molecules fail sanitization through MEGAN'sfix_explicit_hs
utility, and so far our wrapper has been ignoring this and passing the molecule through to the model to propose reactions (likely pushing the problematicC+
atom to reactants). In this PR, the underlying model is not called on inputs which failfix_explicit_hs
, and rather an empty list of reactions is returned in this case. Relatedly, I also silenced some of the other internal warnings produced by the MEGAN model by applying a (now improved)suppress_outputs
context manager.