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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