Thanks Guillaume!
On Sun, Jan 15, 2017 at 5:01 PM, Guillaume GODIN <
guillaume.go...@firmenich.com> wrote:
> Here, Dragon results for the 3 molecules: I've included both Whim and 3D
> descriptors but I don't have access to PMi!
>
>
> I found the second document in agreement with Peter answer...
>
>
> BR,
>
> *Dr. Guillaume GODIN*
> Principal Scientist
> Chemoinformatic & Datamining
> Innovation
> CORPORATE R&D DIVISION
> DIRECT LINE +41 (0)22 780 3645 <+41%2022%20780%2036%2045>
> MOBILE +41 (0)79 536 1039 <+41%2079%20536%2010%2039>
> Firmenich SA
> RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>
> ------------------------------
> *De :* Peter Gedeck <peter.ged...@gmail.com>
> *Envoyé :* dimanche 15 janvier 2017 15:07
> *À :* Greg Landrum; RDKit Discuss; Guillaume GODIN
>
> *Objet :* Re: [Rdkit-discuss] PMI API
>
> According to this:
> https://en.wikipedia.org/wiki/List_of_moments_of_inertia
> The moments of inertia of a disk (something like benzene) are:
>
> Iz = mr^2/2
> Ix = Iy = mr^2/4
>
> None of them is zero. The smallest moment of inertia of a rod-like
> molecule (e.g. C#C) is zero.
>
> Best,
>
> Peter
>
>
>
> On Sun, Jan 15, 2017 at 8:15 AM Greg Landrum <greg.land...@gmail.com>
> wrote:
>
>> Hi Guillaume,
>>
>> I think it this case it's something else. According to the Todeschini
>> article the smallest moment of inertia of a planar molecule like benzene
>> should be zero. The eigenvalues of the inertia matrix for benzene, however,
>> are definitely not zero (and not close enough that it's likely to be
>> round-off error).
>> It would be very nice if you could run the three files I mention through
>> Dragon and let me know what it calculates for those descriptors.
>>
>> -greg
>>
>>
>> _____________________________
>> From: Guillaume GODIN <guillaume.go...@firmenich.com>
>> Sent: Sunday, January 15, 2017 1:11 PM
>> Subject: RE: [Rdkit-discuss] PMI API
>> To: Greg Landrum <greg.land...@gmail.com>, RDKit Discuss <
>> rdkit-discuss@lists.sourceforge.net>, Chris Earnshaw <
>> cgearns...@gmail.com>
>>
>>
>>
>> Dear Greg,
>>
>>
>> I suspect that it's a precision error or eigen algorithm shift between
>> rdkit c++ & dragon.
>>
>>
>> To obtain good value, I suggest to try to implement a test on the eigen
>> values like i did in gateway.cpp implementation.
>>
>>
>>
>> JacobiSVD<MatrixXd> getSVD(MatrixXd A) {
>>
>> JacobiSVD<MatrixXd> mysvd(A, ComputeThinU | ComputeThinV);
>>
>> return mysvd;
>>
>> }
>>
>>
>> // get the A-1 matrix using
>>
>> MatrixXd GetPinv(MatrixXd A){
>>
>> JacobiSVD<MatrixXd> svd = getSVD(A);
>>
>> double pinvtoler=1.e-2;// choose your tolerance wisely!
>>
>> VectorXd vs=svd.singularValues();
>>
>> VectorXd vsinv=svd.singularValues();
>>
>>
>> for (unsignedint i=0; i<A.cols(); ++i) {
>>
>> if ( vs(i) > pinvtoler )
>>
>> vsinv(i)=1.0/vs(i);
>>
>> else vsinv(i)=0.0;
>>
>> }
>>
>>
>> MatrixXd S = vsinv.asDiagonal();
>>
>> MatrixXd Ap = svd.matrixV() * S * svd.matrixU().transpose();
>>
>> return Ap;
>>
>> }
>>
>>
>> If it's not solve the problem, I would like to test it in Matlab. can you
>> provide me the 3 (3d xyz matrix) of your example please ?
>>
>>
>> I also have Dragon 6
>>
>>
>> best regards,
>>
>> *Dr. Guillaume GODIN*
>> Principal Scientist
>> Chemoinformatic & Datamining
>> Innovation
>> CORPORATE R&D DIVISION
>> DIRECT LINE +41 (0)22 780 3645 <022%20780%2036%2045>
>> MOBILE +41 (0)79 536 1039 <079%20536%2010%2039>
>> Firmenich SA
>> RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>>
>> ------------------------------
>> *De :* Greg Landrum <greg.land...@gmail.com>
>> *Envoyé :* dimanche 15 janvier 2017 11:50
>> *À :* Chris Earnshaw; RDKit Discuss
>> *Objet :* Re: [Rdkit-discuss] PMI API
>>
>> I managed to make some time to look into this this weekend and I've found
>> a bug and something I don't understand. Hopefully the community can help
>> out here.
>> On Sun, Jan 8, 2017 at 11:17 AM, Chris Earnshaw <cgearns...@gmail.com>
>> wrote:
>>
>> 4) The big one! The returned results look very odd. They appear to relate
>> more to the dimensions of the molecule than the moments of inertia. For a
>> rod-like molecule (dimethylacetylene) I'd expect two large and one small
>> PMI (e.g. PMI1: 6.61651 PMI2: 150.434 PMI3: 150.434 NPR1: 0.0439828
>> NPR2: 0.999998) but actually get PMI1: 0.061647 PMI2: 0.061652 PMI3:
>> 25.3699 NPR1: 0.002430 NPR2: 0.002430.
>> For disk-like (benzene) the result should be one large and two medium
>> (e.g. PMI1: 89.1448 PMI2: 89.1495 PMI3: 178.294 NPR1: 0.499987 NPR2:
>> 0.500013) but get PMI1: 2.37457e-10 PMI2: 11.0844 PMI3: 11.0851 NPR1:
>> 2.14213e-11 NPR2: 0.999933.
>> Finally for a roughly spherical molecule (neopentane) the NPR values look
>> reasonable (no great surprise) but the absolute PMI values may be too
>> small: old program - PMI1: 114.795 PMI2: 114.797 PMI3: 114.799
>> NPR1: 0.999966 NPR2: 0.999988, new program - PMI1: 6.59466 PMI2:
>> 6.59488 PMI3: 6.59531 NPR1: 0.999902 NPR2: 0.999935
>>
>>
>> Your expectations are correct: the current RDKit implementation is wrong.
>> The corresponding github entry is here: https://github.com/
>> rdkit/rdkit/issues/1262
>> This is due to a mistake in the way the principal moments are calculated
>> (which is due to the fact that I don't spend a lot of time working
>> with/thinking about 3D descriptors). Instead of using the
>> eigenvectors/eigenvalues of the inertia matrix (the tensor of inertia) the
>> RDKit is currently using the covariance matrix. There's some more on the
>> relationship between these two here: http://number-none.com/
>> blow/inertia/deriving_i.html
>>
>> The problem is easy to fix (and I have something working here:
>> https://github.com/greglandrum/rdkit/tree/fix/github1262), but it screws
>> up the values of the descriptors that are derived from here:
>> Todeschini and Consoni "Descriptors from Molecular Geometry" Handbook of
>> Chemoinformaticshttp://dx.doi.org/10.1002/9783527618279.ch37
>> These include the radius of gyration, inertial shape factor, etc.
>> Within that article they state that Ic = 0 for planar molecules. Ignoring
>> the inequality on page 1010, which says that Ic is the largest moment and
>> is contradicted by the rest of the text (particularly the inequalities on
>> page 1011), Ic corresponds to the smallest principal moment : PMI1.
>>
>> So now I'm confused, but I'm hoping this is obvious to someone versed in
>> the field: I'd like to reproduce the descriptors described in the
>> Todeschini article, but I clearly can't do that using the actual moments of
>> inertia. I could keep using the eigenvalues of the covariance matrix there,
>> but that doesn't match what's described in the text.
>>
>> Two things that would be extremely helpful:
>> 1) an explanation of the disconnect here from someone who knows this
>> stuff, I would guess that it's pretty simple
>> 2) The results of running the files github1262_1.mol, github1262_2.mol,
>> and github1262_3.mol from here: https://github.com/
>> greglandrum/rdkit/tree/fix/github1262/Code/GraphMol/
>> MolTransforms/test_data through Dragon and calculating the radius of
>> gyration, inertial shape factor, eccentricity, molecular asphericity, and
>> spherocity index.
>>
>> Best,
>> -greg
>>
>>
>>
>>
>>
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