agreed. It looks fine to me. Have you run the tests on your machine? Travis
will skip Assign.py since it uses RMSD. Maybe we should add a cluster and
assign test that doesn't use rmsd...


On Wed, Feb 27, 2013 at 9:05 PM, Robert McGibbon
<notifications@github.com>wrote:

> In src/python/assigning.py:
>
> >
> >      n_trajs, max_traj_length = project.n_trajs, np.max(project.traj_lengths)
> >      assignments = -1 * np.ones((n_trajs, max_traj_length), dtype='int')
> >      distances = -1 * np.ones((n_trajs, max_traj_length), dtype='float32')
> >
> > -    # if we're using an RMSD metric, get the relevant indices from the generators
> > -    # then inject a blank array into RMSD
> > -    # TODO clean this up
> > -    if isinstance(metric, metrics.RMSD):
> > -        atom_indices = metric.atomindices
> > -        metric.atomindices = None # probably bad...
> > -        logger.info('RMSD metric - loading only the atom indices required')
> > -    else:
> > -        atom_indices = None
> > -
> >      pgens = metric.prepare_trajectory(generators)
> >
> >      for i in xrange(n_trajs):
>
> yeah. we can do that lated though.
>
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>