Dear All (especially Paolo!),
I have a strong suspicion I have already asked this at some point in the past -
so apologies in advance (but I can't seem to find the answer)...
I am interested in taking an existing overlay of two RDKit molecules in 3D and
scoring the overlay using Open3DAlign scoring scheme (eg with MMFF atom-types),
but *without* trying to optimise the alignment or score.
I thought setting maxIters=0 in the call to AllChem.GetO3A() would do the trick
(I even tried setting options=3 to "trigger local optimization"). Eg
o3a = AllChem.GetO3A(prb_mol, ref_mol, maxIters=0, options=3)
o3a.Matches() # Show the matches
But while the options setting certainly changes the matching atoms (and the
score), the matches don't seem to correspond well to my starting alignment...
Any advice is greatly appreciated (including, of course, simply pointing me to
the old answer that I am likely missing!)
Kind regards
James
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