I have a molecule containing a thiazole ring which has been generated by a
reaction in Rdkit.
Sanitising the molecule gives kekulization error...
Traceback (most recent call last):
File "", line 1, in
To troubleshoot your sanitization problems, I think it would be helpful if
you could share your SMARTS reaction string and the rdkit version you are
I just simulated the Hantzsch thiazole synthesis shown on Wikipedia, and
everythink worked normally for me. Admittedly, my reaction
PBF = 0 <=> 2D & PBF >0 <=> 3D.
I forget that point.
Dr. Guillaume GODIN
Chemoinformatic & Datamining
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Looks like I'm late to the game. I don't know about the PMI descriptors
per-se, but if a planar molecule is in it's inertial frame, one of the axes
should be zero (whether it is x, y or z) which means that the one of the
M1x, M1y or M1z should be zero.
We had some good experimentation with
I think we agree here. Here I was talking about the raw Moment (M1z) not
the moment of interia (MI1), I should have made the disctinction more
explicit. Moments are not necessarily Moments of inertia. The terminology
After a brief discussion with Greg, the Moments.py does the
In the inertial frame this is trivial, however, with the current RDKit
can't you just use the plane of best fit here for the planar/3D? For a
linear molecule, you can use the PMI descriptors.
See PBF in RDKit
On Tue, Jan 17, 2017 at
The dimensions along one of the axes of a planar molecule in its inertial
frame will be zero, but the principal moments of inertia will all be
non-zero. The moment of inertia about an axis can only be zero if all the
atoms in the molecule are precisely aligned on that axis. That's only
Great! I also notice confusing usage of moment of Inertia in those descriptors.
For exemple in WHIM case, we need to know if the molecule is linear, planar or
3D in order to compute the descriptors.
I did not find a easy way to determine this yet.
Dr. Guillaume GODIN
The new version looks good to me as far as I can test it. PMI and NPR are
still fine, the radius of gyration is right (for an extremely artificial
test system) and the asphericity index also seems right (despite my best
efforts to confuse things further - sorry about that!). Also highlights
I don't have anything to add to this other than to agree with Curt: I think
that the existing code should work fine with thiazoles.
@Curt: thanks for providing this detailed and thought-through answer!
On Tue, Jan 17, 2017 at 7:01 PM, Curt Fischer
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