Recently been having a play around with the new 3D structural nodes which is a great and welcome addition. (And incidently I like the new categorisation of the nodes in the node repository).
However, I am finding the Add Conformers node somewhat odd. I dont understand what process it is using to derive these 3D cooridinates, some kind of Molecular Mechanics?
The reason I ask is the output has with alarming regularity, bent aromatic rings, especially prevalent in bicyclics like benzoxazoles. Why are calculations providing such an output. Note I am adding the generate 3D coordinates node as a starting point first, prior to this node.
I have noticed that the optimise geometry node will repair these errors, but shouldnt this be automatically part of the process, I am not sure why the output from the Add Conformers node would be useful in its own right.
The conformations that come straight from the Add Conformers node have not been cleaned up by a force field at all, that's why they are so ugly.
Our thought was to provide the unprocessed conformers in case people want to perform other processing on them before cleaning them up with a force field.
It would be pretty easy for us to make the default behavior to do a bit of cleanup with UFF and allow this to be toggled off via an advanced setting.
I think adding some kind of force field cleanup would be useful, as an option, or to make it clear in the node description that it is recommended to follow this node with the Optimisation node.
I just uploaded a new RDKit Nodes version to the Nightly Build that has now the "Cleanup with UFF" option in the Add Conformers node. As Greg suggested it is switched on by default to do a bit of cleanup with UFF and we allow the user to toggle it off via an advanced setting.
Please have look and let me know if this it is working for you. Thanks!