Closed alejandrovr closed 2 years ago
True. But I'm a bit scared of changing this default :grimacing:
Also because it might not be wrong. I think fixHs (aka AddHs) doesn't remove the existing ones (at least it doesn't call the function) so it could lead to different behaviour if you do removeHs=True & fixHs=True
vs removeHs=False & fixHs=True
.
I'll need to test this a bit
I see... take your time! ;)
Finally we agreed to add logging instead of changing the defaults which makes it clear to the user what modifications have been done to the molecule https://github.com/Acellera/moleculekit/commit/0957519de75bd7d2043591b35c874f80e74375af
This returns a smallmol object with Hydrogens
SmallMolLib(reflig_sdf, removeHs=True)[0]
This returns a smallmol object without hydrogens:
SmallMolLib(reflig_sdf, removeHs=True, fixHs=False)[0]
fixHs is by default set to True, so hydrogens are "re-added" after removing then, which leads to unexpected behavior.