RDKit add conformers

Community Extensions
1

Hi,
I was using the add conformers node, no issues there, but I was wondering is it using the “old” distance geometry method? The node description reads like it is but does not explicitly say so.
If so is any node or option planned for the ETKDG Method?

Thanks a lot!
Jennifer

2

Hi Jennifer,

this node was written a few years ago, so at that time this method was “new”, but I am sure from today’s perspective you would refer to it as the “old” method. I just looked up what methods are called from the Java API of RDKit:

  • DistanceGeom.EmbedMultipleConfs(molTemp, iNumberOfConformers,
    iMaxIterations, iRandomSeed,
    true /* clearConfs /, bUseRandomCoordinates, dBoxSizeMultiplier,
    true /     randNegEig /, 1 / numZeroFail /, dPruneRmsThreshold,
    null /     coordMap /, 1e-3 / optmizerForceTol /,
    false /     ignoreSmoothingFailures */,
    bEnforceChirality,bUseExpTorsionAngles,bUseBasicKnowldge)

  • ForceField.UFFOptimizeMolecule

There are currently no plans to implemented changes from my side. Maybe Greg can comment on what it would take to make an option available to support the ETKDG method in addition. If it is not too much work, chances increase that this could be done soon.

Kind regards,
Manuel

3

Hi Manuel,

thank you for the clarification.
It would be great to have this as the ETKDG seems to be a very good alternative to licensed software.

Best regards,
Jennifer

4

Apologies that I’ve been in “stealth mode” recently.

This is there already.
If you look in the Advanced tab of the node you’ll find this:

image
image1565×1290 297 KB

I’ve shown the defaults, which is to use ETKDG. The ET part is “experimental torsion angle terms”, and “K” is “use basic knowledge terms”.

I hope this helps

5

Thank you very much!
Good to know I already used it :slight_smile:

6

This topic was automatically closed 90 days after the last reply. New replies are no longer allowed.