Re: [Rdkit-discuss] GetConformerRMS() vs GetBestRMS()

2017-09-11 Thread Udvarhelyi, Aniko
Thanks Greg for this detailed answer. Yes, indeed this helps. From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: Freitag, 8. September 2017 12:10 To: Udvarhelyi, Aniko Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] GetConformerRMS() vs GetBestRMS() Hi Anikó, Both

Re: [Rdkit-discuss] GetConformerRMS() vs GetBestRMS()

2017-09-08 Thread Greg Landrum
Hi Anikó, Both functions do an alignment. The big difference here is coming because GetBestRMS() looks at all 2D-identical alignments of the molecules to each other while GetConformerRMS() only does the alignment once: using the atom numbers. Practically speaking what does that mean for your

[Rdkit-discuss] GetConformerRMS() vs GetBestRMS()

2017-09-08 Thread Udvarhelyi, Aniko
Dear All, I would like to compute RMS values between conformers of the same molecule that are not aligned. Unfortunately, I can´t get along very well with the GetConformerRMS() function, it gives far too high RMS values even for conformers that are clearly (near-)identical as judged by visual