If you are dealing with a molecule from a crystal structure then you can invert molecules in it using the symmetric_molecule method (API reference). Here is an example:
inverted_mol = my_crystal.symmetric_molecule('-x,-y,-z', (0, 0, 0), force=True)
By default the method only allows you to apply operations compatible with that crystal's space-group symmetry (as in the GUI tool) but you can force inversion with the force=True option.
If you only have a molecule, with no crystal information, this method can't be used. However, if comparing molecules using the overlay method you can allow for inversion. Alternatively, you can create an empty default crystal and put the molecule into it and then apply the operations as above.