Not directly, I'm afraid. The code is in there - this exact functionality
is used by Confab and so it should not be too hard to expose, but it's not
available at the moment. Do you want to file a feature request at the issue
tracker (https://github.com/openbabel/openbabel/issues)?
In its absence, you can of course write a Python script to do by looping
over the conformers and doing the pairwise comparison. We have an OBAlign
object which you can use for this purpose, and it can return the heavy-atom
symmetry-corrected RMSD. It assumes that the atoms are in the same order in
each conformer though.
- Noel
On 7 November 2017 at 15:58, MD Simulation <mdsimulationgr...@gmail.com>
wrote:
> Hello,
>
> I have about 100 conformers. Some of those are similar based on RMSD when
> looked at in VMD. I would like to eliminate redundant conformers based on
> RMSD. Is there a way to do that within Open Babel?
>
> Thanks
> Carrie
>
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