On 07/09/2009 03:44 PM, Javier Ángel Velázquez Muriel wrote: > I agree with Dina, and still don't see why rmsd has to assume anything. > What you do before computing rmsd is your business. It is like sqrt(), > or cos(), or whatever. Provided the arguments are correct, the way you > interpret the result of the function is your business again.
Yes, Dina's interface looks like a good one to me (except that it should return double, and go in a separate header, as Daniel said). But it should definitely be stated in the function description that the size of the two XYZs need to be the same (as, presumably, they do), that a 1:1 correspondence is used, and (just to make it absolutely clear) that no kind of fitting is done before calculating the RMSD. I agree with Javi - calculating the RMSD, performing a superposition, and making an alignment are three separate things - but we should clarify it just to be sure.
Whenever I've seen RMSD used, it means coordinate RMSD. We routinely also use DRMSD in Modeller, of course.
Ben