This modulates the effect of residue_span_range; if True, the disulfide bridges are taken into account when calculating the residue index difference between two atoms (i.e., disulfides make some atom pairs closer in sequence). energy_data.covalent_cys = True is slow and only has an effect when certain statistical non-bonded potentials are used (i.e., energy_data.dynamic_modeller is True and the non-bonded library has been derived considering the disulfide effect). Thus, it should generally be set to False.