Thanks Hai,
Unfortunately the command isn't working. I paste here the error message I
get:
gyr = pt.radgyr(traj=traj, mask=":8P3,8FP,8CP tensor")
/Users/domenico/amber16/lib/python2.7/site-packages/pytraj/utils/decorators.pyc
in inner(*args, **kwd)
9 .wraps(f)
10 def inner(*args, **kwd):
---> 11 return f(*args, **kwd)
12
13 inner._is_parallelizable = True
/Users/domenico/amber16/lib/python2.7/site-packages/pytraj/utils/get_common_objects.pyc
in inner(*args, **kwargs)
304 except IndexError:
305 args.append(mask)
--> 306 return f(*args, **kwargs)
307
308 inner._is_super_dispatched = True
/Users/domenico/amber16/lib/python2.7/site-packages/pytraj/all_actions.pyc
in radgyr(traj, mask, top, nomax, frame_indices, dtype)
670 command = " ".join((mask, nomax_))
671 c_dslist, _ = do_action(traj, command, c_action.Action_Radgyr)
--> 672 return get_data_from_dtype(c_dslist, dtype)
673
674
/Users/domenico/amber16/lib/python2.7/site-packages/pytraj/utils/get_common_objects.pyc
in get_data_from_dtype(d0, dtype)
68 return DSL(d0)
69 elif dtype == 'ndarray':
---> 70 return d0.to_ndarray()
71 elif dtype == 'dict':
72 return d0.to_dict()
pytraj/datasets/c_datasetlist.pyx in
pytraj.datasets.c_datasetlist.DatasetList.to_ndarray
(pytraj/datasets/c_datasetlist.cpp:11851)()
ValueError: don't know how to convert to ndarray
On Tue, Sep 19, 2017 at 12:18 PM, Domenico Marson <domenico87.gmail.com>
wrote:
> Hello,
> I'm really glad you have developed pytraj, it has positively changed the
> processing of my trajectories.
>
> In cpptraj it is possible to obtain the gyration tensor of a selection
> simply giving the appropriate option to the "radgyr" command. I'm trying to
> achieve the same thing in pytraj, but I'm not able to find any way of doing
> it... Am I missing something or it's an option not implemented? Can someone
> point me in the right direction?
>
> Many thanks for your help,
>
> Regards,
> Domenico.
>
> --
> *Domenico Marson, Ph.D.*
> Department of Engineering and Architecture (DEA) Postdoctoral Fellow
> Molecular Simulation Engineering (MOSE) Laboratory
>
> University of Trieste
>
> Skype: domenicomars
>
--
*Domenico Marson, Ph.D.*
Department of Engineering and Architecture (DEA) Postdoctoral Fellow
Molecular Simulation Engineering (MOSE) Laboratory
University of Trieste
Skype: domenicomars
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Received on Thu Sep 21 2017 - 05:00:02 PDT
