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choderalab / openmoltools

An open set of tools for automating tasks relating to small molecules
MIT License
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openeye.get_charges() emits warning #276

Open jchodera opened 5 years ago

jchodera commented 5 years ago

When YANK calls openeye.get_charges(), a Warning: title line exceeds 80 characters is frequently emitted. In some of our experiments, we get over 3000 of these warnings. It would be nice to silently eat this warning, since it has little consequence.

Lnaden commented 5 years ago

I think on some much older systems, some SQL databases, and some punch cards, it might be an issue, but I don't see a reason it would be any more.

andrrizzi commented 5 years ago

To be clearer, the warning may be issued when we write out the molecule as a mol2 file rather than in openeye.get_charges().

What happens in get_charges() is that we call openeye.normalize_molecule(), which assign its IUPAC name as the title of the molecule. For complex compounds, the IUPAC name exceeds the 80 characters limit.