Thanks to Dan pointed out, I've just added support to pytraj with a command
pytraj.radgyr_tensor.
Please see here for example: https://github.com/Amber-MD/pytraj/pull/1423
And here for how to install development version of pytraj to amberhome:
http://amber-md.github.io/pytraj/latest/installation.html#update-to-amberhome
(check: "From github development version" section)
Enjoy
Hai
On Thu, Sep 21, 2017 at 1:08 PM, Domenico Marson <domenico87.gmail.com>
wrote:
> 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
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > *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 - 22:00:03 PDT
