pt.compute does not take lists of trajectories

[pindakaas42]

Most pytraj functions take a Trajectory-like or a list of Trajectory. Would it be possible to implement this behaviour for compute?
Thank you very much.

[hainm]

Most pytraj functions take a Trajectory-like or a list of Trajectory.

can you post an example about taking list of trajectory here? I don't recall I implemented it.

Would it be possible to implement this behaviour for compute?

Work around is join the trajectories (in memory) to a single one; or using iterload(list_of_filenames, ...)

pt.iterload([fn0, fn1, ...], top=...)

[hainm]

otherwise, try below

from itertools import chain

class FrameIter:
    def __init__(self, trajs):
        self._trajs = trajs

    @property
    def top(self):
        # assume all trajs have the same topology
        return self._trajs[0].top

    def __iter__(self):
        for frame in chain(self._trajs):
            yield frame

In [25]: traj = pt.datafiles.load_tz2()

In [26]: traj2 = pt.datafiles.load_tz2()

In [27]: pt.compute(['rmsd @CA', 'radgyr'], FrameIter([traj, traj2]))
Out[27]: 
OrderedDict([('RMSD_00000',
              array([  1.94667955e-07,   2.54596866e+00,   4.22333034e+00, ...,
                       4.97189564e+00,   5.53947712e+00,   4.83201237e+00])),
             ('RoG_00001',
              array([  9.4451051 ,   9.57459712,  10.19233494, ...,   7.48343543,
                       7.43238185,   7.62039157])),
             ('RoG_00001[Max]',
              array([ 15.79878713,  16.75193828,  16.92138667, ...,  13.66140902,
                      13.25220774,  12.69288639]))])

[pindakaas42]

Hallo, first thank you for your answers the second one is a great idea. As for an example for functions that take lists of trajectories distance and angle , also dihedral and angle, come to mind, although for example rmsd or drmsd don't take lists.

[hainm]

As for an example for functions that take lists of trajectories distance and angle , also dihedral and angle, come to mind, although for example rmsd or drmsd don't take lists.

Thanks. I did not realize that those methods can accept a list of trajs. It's side effect. :D I will recommend user to follow 2nd solution above. Thanks for trying. Cheers and I close this issue now.

[hainm]

Reopen until I update example of passing list of trajs for the docs of pytraj.compute.

[pindakaas42]

It's actually also mentioned in the documentation. That's how I started doing it in the first place.

[hainm]

Ha, I see, my bad.