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 inspection 
after alignment. I attach one example of 2 conformers of a molecule, that are 
GetConformerRMS() returns an RMS value of 1.32 (with Hydrogens) and 0.70 
(disregarding Hydrogens).
GetBestRMS() returns an RMS value of 0.03 (with Hydrogens) and 0.02 
(disregarding Hydrogens).

Clearly, the GetBestRMS() result is the one I´d expect (I am interested in the 
all-atom RMSDs with Hydrogens). I guess GetConformerRMS() cannot align the two 
conformers properly hence the high RMS value. My question is why not? The atom 
ordering and all bonds are exactly the same in both conformers. Why do I need 
the GetBestRMS() alignment of all possible permutations of matching atom orders 
in both conformers to get the alignment correct? I would like to avoid using 
GetBestRMS()as it is far too slow for my purposes (processing many molecules 
with many conformers).

Many thanks for any hints,

Attachment: confs.sdf
Description: confs.sdf

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