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?
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?