best way to calculate spyrmsd for ligands with different number of atoms? #141
Description
what is the best way to calculate spyrmsd when the ligands don't have the same number of atoms?
For example, if I have a pdb with certain ligand that has some missing atoms in the structure, and I need to calculate the rmsd between this ground truth ligand and the output of a docked ligand (which is the same ligand but has no missing atoms).
In this case spyrmsd will give an error: coords1.shape == coords2.shape
Is there a way for spyrmsd to only calculate the rmsd on the overlapping atoms between these two ligands?