There isn't currently any easy way to do this. One workaround that could
make the manual stuff a bit less painful would be find those Hs, convert
them into Ds, call RemoveHs(), and then convert the Ds back into Hs.
It seems like it does make sense to modify the RemoveHs() function:
Is there a recommended way in RDKit to preserve hydrogens necessary for
representing cis/trans stereochemistry of imines?
For example, given the attached SDF I need to maintain explicit hydrogens
in the output SMILES string to maintain the imine cis/trans
stereo-chemistry.
mol =
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