hi, try to specify dtype='dict'
In [4]: pt.radgyr(traj, mask='.CA tensor', dtype='dict')
Out[4]:
OrderedDict([('RoG_00000',
array([ 8.10916061, 7.7643485 , 8.09693108, ...,
6.38061648,
6.24139008, 6.48994552])),
('RoG_00000[Tensor]',
array([[ 5.12036852, 49.83322051, 10.8048967 ],
[ 5.64622381, 48.2239143 , 6.41496946],
[ 5.11853422, 54.45380463, 5.98795407],
...,
[ 11.75586745, 17.82494893, 11.13145023],
[ 11.66407102, 17.60610764, 9.68477152],
[ 12.31941738, 20.41890689, 9.38106854]]))])
Hai
On Thu, Sep 21, 2017 at 7:29 AM, Domenico Marson <domenico87.gmail.com>
wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Sep 21 2017 - 06:00:03 PDT
