Hi James,
What you've done seems correct to me; I have prepared an example gist here:
https://gist.github.com/ptosco/40c2530c67d9c0930b8efbc8c92da0be
which indeed shows correct matches.
One observation here is that Open3DALIGN was conceived to generate
alignments for 3D-QSAR; it really doesn't a great job at computing a 3D
similarity score, as it was not made for that purpose. So the attempts
to score an existing overlay "in place" might be disappointing.
Cheers,
p.
On 26/11/2019 17:00, James Davidson wrote:
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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