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>
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> 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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>>
>
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