I just solve it, Just in case someone also needs it.
You can compute the inertia tensor after aligning with the principal axes with CanonicalizeConformer(). This tensor is now therefore diagonal, and the symbol of the ii components tell you the direction they are pointing out. Just rotate in those directions so the principal moment of inertia components coincide. Best regards, Pablo Ramos Ph.D. at Covestro Deutschland AG [cid:image001.png@01D73C2E.E0FB5990] covestro.com<http://www.covestro.com/> Telephone +49 214 6009 7356 Covestro Deutschland AG COVDEAG-Chief Commer-PUR-R&D-EMEA-PMD B103, R164 51365 Leverkusen, Germany pablo.ra...@covestro.com<mailto:pablo.ra...@covestro.com> From: Pablo Ramos Sent: Wednesday, 28 April 2021 13:11 To: rdkit-discuss@lists.sourceforge.net Subject: Problems when aligning the moment of inertia with the principal axes Dear community, There is the function CanonicalizeConformer() that allows you to align molecules based in the moment of inertia. I want to use it to align molecules that are exactly the same, but whose atom indices are different. rdkit.Chem.rdMolAlign module contains functions that take symmetry into account, so atoms are indistinguishable and end up just creating the same molecule with the same atom indices, which is not what I want to get. Using CanonicalizeConformer() I get the left picture. What I want to get is the right one. Right one can be obtained by performing a 180° rotation along the X and Y axes. I was wondering if there is a way to get right picture directly, without habving to perform the rotation. [cid:image002.png@01D73C34.CFEC6120][cid:image003.png@01D73C34.CFEC6120] Best regards, Pablo Ramos Ph.D. at Covestro Deutschland AG [cid:image001.png@01D73C2E.E0FB5990] covestro.com<http://www.covestro.com/> Telephone +49 214 6009 7356 Covestro Deutschland AG COVDEAG-Chief Commer-PUR-R&D-EMEA-PMD B103, R164 51365 Leverkusen, Germany pablo.ra...@covestro.com<mailto:pablo.ra...@covestro.com>
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