When using MolDarting on a protein-ligand system, it's necessary to first account for the overall rotation and translational changes for the protein-ligand complex in regards to the reference darts. To account for those rotational and translational changes, heavy atoms of the residues around the binding site are chosen. When checking if the current configuration is within the rotational and translational regions, the chosen binding site residues of the selected dart are superposed to the same binding site residues of the current pose, then the rotational and translational distances are calculated.