[DNM] Refactor rmsd.py #75
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Note: DNM since this will break analysis in openfe protocols
Renamed
ligand_wandertoligand_COM_driftligand_rmsdandligand_COM_driftare now more nested, storing information for multiple ligands if presentExpose selection indices for protein and ligands
Enable ligand RMSD and wander calculation for files containing more than one ligands (e.g. SepTop). Ligands can be selected based on a MDAnalysis selection string. This assumes ligands are in separate residues.