maabuu/posebusters

Symmetry-corrected RMSD

Closed this issue · 5 comments

eunos-1128 commented

Hello,

I have a question on posebuster's RMSD specifications.

Recently, an RMSD called spyrmsd(repo, paper) that takes into account the symmetry of molecules has been devised, but is there a reason why you used the RDKit RMSD calculation implementation?

maabuu commented

The RDKit's documentation states that the RMSD functions do take symmetry into account, even for conjugated terminal functional groups. https://rdkit.org/docs/source/rdkit.Chem.rdMolAlign.html

Do you maybe have an example in mind for when RDKit yields an RMSD that is larger than the RMSD spyrmsd gives? That would be a good reason to use spyrmsd.

eunos-1128 commented

Do you maybe have an example in mind for when RDKit yields an RMSD that is larger than the RMSD spyrmsd gives? That would be a good reason to use spyrmsd.

Yes, I meant to mention such cases.

The RDKit's documentation states that the RMSD functions do take symmetry into account, even for conjugated terminal functional groups. https://rdkit.org/docs/source/rdkit.Chem.rdMolAlign.html

I didn't know that. Thank you for telling :)

Do you have any plan to incorporate spyrmsd into Posebusters?

maabuu commented

Do you maybe have an example in mind for when RDKit yields an RMSD that is larger than the RMSD spyrmsd gives? That would be a good reason to use spyrmsd.

Yes, I meant to mention such cases.

Nice, please share. I am not aware of any.

The RDKit's documentation states that the RMSD functions do take symmetry into account, even for conjugated terminal functional groups. https://rdkit.org/docs/source/rdkit.Chem.rdMolAlign.html

I didn't know that. Thank you for telling :)

Do you have any plan to incorporate spyrmsd into Posebusters?

Only if there is functionality that RDKit does not cover.

eunos-1128 commented

I supposed some cases that RDKit's RMSD have lower RMSDs than spyrmsd's exist, but I haven't find out such cases actually.

I created this issue to ask you that you had designed this tool with in mind for such cases and Posebusters will deal with them in the future.

If I find them, I'll make report in new issue.

Thank you for answering politely.

maabuu commented

Thank you! I will close the issue for now.

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