ConstrainedEmbed should be what you need. If it's saying that your molecule
doesn't match the core then that's where you need to look. Maybe the core
is not an exact substructure?
If you still have difficulties you could generate the MCS between the
structures and use that as the core.
Greg's blog
Hello
I'm having a hard time trying to build a 3D structure for a new molecule
(new) based on a reference molecule (ref).
In this case, ref is a substructure of new, and I want the coordinates of
their matching atoms to be exactly the same.
I have tried using:
Chem.rdDepictor.GenerateDepictionMat
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