Jan,
Do you want to do a supervised alignment (i.e. you specify which atoms in
the fragment map to which atoms in the molecule) or unsupervised alignment
(where the algorithm needs to figure this out)/
It sounds like you're interested in the first; this blog post may be useful
Is there a way to rigidly align a 3D molecule to a fragment?
I want to compare several conformations by aligning a rigid part of the molecule
Best regards, Jan
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