I guess I was thinkng required arg.
On Mar 16, 2014 3:53 AM, "Robert McGibbon" <notifications@github.com> wrote:

> In MDTraj/rmsd/_lprmsd.pyx:
>
> > +    Parameters
> > +    ----------
> > +    target : md.Trajectory
> > +        For each conformation in this trajectory, compute the RMSD to
> > +        a particular 'reference' conformation in another trajectory
> > +        object.
> > +    reference : md.Trajectory
> > +        The object containing the reference conformation to measure distances
> > +        to.
> > +    frame : int
> > +        The index of the conformation in `reference` to measure
> > +        distances to.
> > +    atom_indices : array_like, or None
> > +        The indices of the atoms to use in the RMSD calculation. If not
> > +        supplied, all atoms will be used.
> > +    permute_groups : list of array_like, or None
>
> I agree that the use case for None is pretty weak, but I can't think of a
> better default argument. This seems better than not providing a default
> argument at all. (?)
>
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>