Depends on what you need this data for - if you are comparing to actual wet-lab data, you would calculate molecular weight and other properties you can calculate from the sequence alone on the actual sequence you are expressing, including parts that are not visible in your model such as disordered regions, affinity tags and so on.

Hi, the exclusion or inclusion of amino acids in model depends upon your research objectives. All mentioned parameters are concern with amino acid composition. Elimination of amino acids responsible for change in parameter. So, u think on what is the criteria of amino acid elimination and why u can eliminate it from target.