%load_ext autoreload
%autoreload 2

import molsysmt as msm

Get entity index

AAA

molsys = msm.convert(msm.systems['chicken villin HP35']['chicken_villin_HP35_solvated.h5msm'])

indices = msm.element.entity.get_entity_index(molsys, element='entity', selection='all',
                                              redefine_molecules=False, redefine_indices=False)

indices

[0, 1, 2]

indices = msm.element.entity.get_entity_index(molsys, element='entity', selection='all',
                                              redefine_molecules=False, redefine_indices=True)

indices

[0, 1, 2]