2009/7/9 Javier Ãngel VelÃzquez Muriel <>:
> It does not matter. rmsd is going to give you a number no matter if the
> molecules are aligned or not. The thing is how you interpret the number, so
> discussing about alignment does not apply for implementation, only for
> interpretation. Correspondence does apply. If not addressed, fine with me :)
Sure. But for the API, all we really care about is interpretation :-)
I think the name had better make clear which interpretation is
correct.