Dear Jörg,
I have just tried this and it seems to work for me.
I have created a gist here which shows an example usage on multiple
conformations:
https://gist.github.com/ptosco/b9b7341251457fe26441dc17609ae34a
As the notebook contains 3Dmol.js renderings that won't show up in the
gist, I have also created an HTML version which may be more convenient
for you to browse here:
http://htmlpreview.github.io/?https://gist.githubusercontent.com/ptosco/2bc42766a1672f61135d7d7dcce72223/raw/302e459d98c9f4e2fd0f1f2b23221d54c7bd2d8a/o3a.html
I think the problem in your case might originate from the fact that when
you call pyO3A.Align() the transformation is directly applied to the
query molecule, and the RMSD is returned.
If you call pyO3A.Trans() after calling pyO3A.Align() the transformation
will actually be an identity transformation, as the query has already
been aligned when Align() was called, so no further transformation is
required. So if you try to apply the transformation to the original
coordinates instead, that will result in no change to the coordinates,
being an identity.
If you only need the transformation to apply it at a later stage, you
should not call Align first.
I hope the above is clear; feel free to contact me if not (also off-list).
Cheers,
Paolo
On 16/06/2019 17:56, Jörg Kurt Wegner wrote:
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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