[Rdkit-discuss] Kekulizing thiazoles

Dear all I have a molecule containing a thiazole ring which has been generated by a reaction in Rdkit. Sanitising the molecule gives kekulization error... Chem.SanitizeMol(forwardProduct_) Traceback (most recent call last): File "", line 1, in Chem.SanitizeMol(forwardProduct_)

Re: [Rdkit-discuss] Kekulizing thiazoles

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 using. I just simulated the Hantzsch thiazole synthesis shown on Wikipedia, and everythink worked normally for me. Admittedly, my reaction

Re: [Rdkit-discuss] PMI API

Thanks Brian, PBF = 0 <=> 2D & PBF >0 <=> 3D. I forget that point. BR, Dr. Guillaume GODIN Principal Scientist Chemoinformatic & Datamining Innovation CORPORATE R DIVISION DIRECT LINE +41 (0)22 780 3645 MOBILE +41 (0)79 536 1039 Firmenich SA RUE DES JEUNES 1 | CASE

Re: [Rdkit-discuss] PMI API

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

Re: [Rdkit-discuss] PMI API

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 gets confusing. After a brief discussion with Greg, the Moments.py does the

Re: [Rdkit-discuss] PMI API

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 http://pubs.acs.org/doi/abs/10.1021/ci300293f Cheers, Brian On Tue, Jan 17, 2017 at

Re: [Rdkit-discuss] PMI API

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 possible

Re: [Rdkit-discuss] PMI API

​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. BR,​ Dr. Guillaume GODIN Principal

Re: [Rdkit-discuss] PMI API

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 even

Re: [Rdkit-discuss] Kekulizing thiazoles

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! -greg On Tue, Jan 17, 2017 at 7:01 PM, Curt Fischer wrote: > To