Get surface area

import molsysmt as msm

molecular_system = msm.convert(msm.systems['T4 lysozyme L99A']['181l.h5msm'],
                               selection='molecule_type=="protein"')

sa_groups = msm.physchem.get_surface_area(molecular_system, element='group', definition='collantes')

view = msm.view(molecular_system)
msm.thirds.nglview.set_color_by_value(view, values=sa_groups, min_value=0.0, cmap="Purples")

view