The elemental analysis plug-in is inconsistent regarding isotopes. I drew a structure C12H19D2NO4, and it told me the formula was C12H21NO4, but it calculated the mass correctly (245). The formula should be displayed with the isotopes explicitly indicated.
The Elemental Analysis plugin supports both approaches. The "formula" function returnes the elemental formula without separating the isotopes. The "iformula" function however separates the isotopes. You can test them with the command line cxcalc tool:
$ cxcalc "[2H]OCCC" formula
$ cxcalc "[2H]OCCC" iformula
id Isotope formula
Not all functions of the Elemental Analysis plugin is available through the Marvin GUI, but you can access them via the API an the cxcalc command line tool. If you need it in the GUI as well we can add it.
The iformula option should be the default in the Marvin GUI. If someone goes to the trouble of specifying isotopes in their drawing, they are doing so for a reason.
We will display both the isotope formula and the isotope composition functions on the Elemental Analysis plugin dialog, additionally to the current ones.