Hi Charmaine,
can you provide a reproducible example of your workflow? Please reply to
me directly.
Thanks, cheers
p.
On 14/01/2020 11:40, Chu, Charmaine wrote:
Dear Rdkit community,
I’ve been trying to align some small molecules to a defined
substructure using GetO3A but it doesn’t seem to work properly.
For example, I would be aligning some small molecules containing a
piperidine ring within the structure to a reference piperidine ring
but it wouldn’t align properly.
I’ve tried striping the atoms apart from the piperidine substructure
of the small molecules to do the alignment (which would then follow by
transformation of the original small molecule using the transformation
matrix) but by inspecting the alignment the N within the piperidine
ring does not always align to the same position as the reference
piperidine ring.
If I try adding a constrain map to it then the chair conformation does
not always face the same way (like how it would reflect by the plane
of best fit)
The work is being done using the python node within KNIME as a part of
the workflow.
What would be the fix for this?
Regards,
Charmaine Chu
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