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 <
guillaume.go...@firmenich.com> 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
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> RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>
> ------------------------------
> *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>
> 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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