Protein-ligand examples should use ilrmsdmatrix-based clustering

## **Desired feature/enhancement**

The various protein-ligand docking examples should use ilrmsd-based clustering instead of the current clustering method which defined a fixed number of clusters.

## **Motivation**

Mimics the haddock2.5 clustering

## **Description**

Update the various toml files in the docking-protein-ligand and docking-protein-ligand-shape

