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 >> >> >> > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
Moments.py
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