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
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________________________________
De : Brian Kelley <fustiga...@gmail.com>
Envoyé : mardi 17 janvier 2017 13:44
À : Chris Earnshaw
Cc : Rdkit-discuss@lists.sourceforge.net; 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
<cgearns...@gmail.com<mailto:cgearns...@gmail.com>> 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
<fustiga...@gmail.com<mailto:fustiga...@gmail.com>> 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
<cgearns...@gmail.com<mailto:cgearns...@gmail.com>> 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
<greg.land...@gmail.com<mailto:greg.land...@gmail.com>> wrote:
On Mon, Jan 16, 2017 at 10:22 AM, Chris Earnshaw
<ch...@cge-compchem.co.uk<mailto:ch...@cge-compchem.co.uk>> 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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