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> 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>
> 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> wrote:
>>
>>>
>>>
>>> On Mon, Jan 16, 2017 at 10:22 AM, Chris Earnshaw <
>>> 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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