Dear CDK Community,
I am using the CDK node for RMSD calculation. Now there are two Methods available as stated in the node description:
“At the moment two types of RMSD calculations are possible. One based on the alignment using the Kabsch algorithm and the other based on the isomorphic alignment of the molecular structure and using the global geometry.”
Now I found a lot, including a code example for the Kabsch calculation, but I could not figure out how the second method is working.
As far as I have understood the Kabsch algorithm requires the same molecule (i.e same number of atoms), whereas the isomorphic alignment is based on the most common substructure, is that correct?
Is there any documentation or page I overlooked to read a bit more about the methods?
Thanks in advance!