It seems the shape alignment is in a wrong 3D reference frame - how to fix
this?
Here a code snippet looping over all conformations, then finding the one
with the lowest score.
I was under the assumption "query3d" should be at the end in the same
reference frame as "references3d", but it is not? Has anyone a working 3D
shape alignment, ensuring things are truly aligned in the same reference
frame? Thanks /.Joerg
pyO3A=rdMolAlign.GetO3A(query3d_conf, references3d)
rmsd=pyO3A.Align()
score = pyO3A.Score()
rmsd, trans_matrix = pyO3A.Trans()
if highestConfId!=-1:
rdkit.Chem.AllChem.TransformMol(query3d, trans_matrix,
confId=highestConfId, keepConfs=True)
--
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