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
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
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
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