Sorry, I was hasty,
this command gives me a dictionary with RoG and Rog[Tensor],
but in this dictionary I only find the XX, YY, ZZ values, XY, XZ and YZ are
missing!
Am I missing something?
Thank you in advance!
On Thu, Sep 21, 2017 at 3:32 PM, Domenico Marson <domenico87.gmail.com>
wrote:
> Hi Hai,
> It works like a charm, thank you very much!
>
>
> On Thu, Sep 21, 2017 at 2:33 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>> 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
>> >
>> _______________________________________________
>> AMBER mailing list
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>>
>
>
>
> --
> *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 - 10:30:02 PDT
