Removing Dummy/Unknown Atoms From a Molecule


I have the results from a docking run I have done, however the structures come with dummy atoms represented by * in the molecule image. I was wondering is there a node that can remove all these dummy atoms without altering the charge of the atoms they are attached to as these represented lone pairs in the docking output and are not needed.

I can’t upload .sdf files, so I have included a workflow with the SDF reader node with just my compounds imported.

Dummy.knwf (1.5 MB)