Re: [Rdkit-discuss] PMI API

[Guillaume G. <Gui...@fi...>]

Thanks Brian,


PBF = 0 <=> 2D & PBF >0 <=> 3D.


I forget that point.


BR,

Dr. Guillaume GODIN
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________________________________
De : Brian Kelley <fus...@gm...>
Envoyé : mardi 17 janvier 2017 14:06
À : Guillaume GODIN
Cc : cge...@gm...; Rdk...@li...; Greg Landrum
Objet : 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 7:58 AM, Guillaume GODIN <Gui...@fi...<mailto:Gui...@fi...>> wrote:

​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 Scientist
Chemoinformatic & Datamining
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645<tel:+41%2022%20780%2036%2045>
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________________________________
De : Brian Kelley <fus...@gm...<mailto:fus...@gm...>>
Envoyé : mardi 17 janvier 2017 13:44
À : Chris Earnshaw
Cc : Rdk...@li...<mailto:Rdk...@li...>; Greg Landrum
Objet : 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 correct calculation which indirectly verifies MOE and the newer RDKit implementation.

Cheers,
 Brian

On Tue, Jan 17, 2017 at 7:39 AM, Chris Earnshaw <cge...@gm...<mailto:cge...@gm...>> wrote:
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 for linear molecules. There's no way to draw a straight line axis through all the atoms in a non-linear molecule, which would be a requirement for the corresponding moment of inertia to be zero.

Chris

On 17 January 2017 at 12:29, Brian Kelley <fus...@gm...<mailto:fus...@gm...>> wrote:
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 multipole expansion of moments (essentially based on the description of electrostatic multipoles) that might be nice to add to the PMI framework.

Greg, I'm assuming that the Moments.py we opensourced a while back is similarly broken?  I'm attaching it here for posterity but it does appear to match the moe PMI's.



On Tue, Jan 17, 2017 at 4:55 AM, Chris Earnshaw <cge...@gm...<mailto:cge...@gm...>> wrote:
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 more confusion in the Todeschini article - the approximate asphericity values for prolate and oblate molecules are reversed.

The only (very trivial) thing I've spotted is the comment in the inertialShapeFactor function. 'planar or no coordinates' should be 'linear or no coordinates' to avoid confusion.

Chris

On 16 January 2017 at 09:30, Greg Landrum <gre...@gm...<mailto:gre...@gm...>> wrote:


On Mon, Jan 16, 2017 at 10:22 AM, Chris Earnshaw <ch...@cg...<mailto:ch...@cg...>> wrote:

Either way, it makes it rather hard to trust their derivations generally - especially as there appear to be other errors (e.g. the denominator in eq. 16 should be the square root of the given sum of squares, according to their reference).

Indeed. Given the problems encountered, I went back and checked some additional references to find definitions of the descriptors. The results are in this PR, which I'd love feedback on if you have time to take a look:
https://github.com/rdkit/rdkit/pull/1265

I didn't manage to find any information about "inertial shape factor" and don't have access to the references cited in the Todeschini paper, but I think the others are now reasonably reliable.

-greg




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