Re: [Rdkit-discuss] PMI API

No problem Greg, reading carefully the Todeschini article, them said that Ic,Ib,Ia are determine as max & min values of I other all 3D axis passing throught the center of mass! The "global PM" is never zero (sum of mi*ri*ri) idem for PMi even for planar molecule. But When you have a planar

Re: [Rdkit-discuss] PMI API

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...

Re: [Rdkit-discuss] PMI API

On Sun, Jan 15, 2017 at 5:15 PM, Chris Earnshaw wrote: > > I've built a version of RDKit with fixes from https://github.com/ > greglandrum/rdkit/tree/fix/github1262 and can confirm that it gives > exactly the same values of PMI and NPR that I got with the RDKit fork by >

Re: [Rdkit-discuss] PMI API

Thanks Greg I've built a version of RDKit with fixes from https://github.com/ greglandrum/rdkit/tree/fix/github1262 and can confirm that it gives exactly the same values of PMI and NPR that I got with the RDKit fork by 'hahnda6'. I can't say for certain that the PMI values are correct in absolute

Re: [Rdkit-discuss] PMI API

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 DIVISION DIRECT

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,

Re: [Rdkit-discuss] PMI API

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

Re: [Rdkit-discuss] PMI API

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 getSVD(MatrixXd A) { JacobiSVD mysvd(A,

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 wrote: > 4) The big one! The returned results look very odd. They