Hi Hai,
It works!
Many thanks.
Vivek
On Mon, Apr 30, 2018 at 3:26 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> Hi,
>
> pytraj does not natively support 'theta' yet. But you can add 'theta' to
> `method` keyword and pick dtype='dict'
>
> Example
>
> In [11]: import pytraj as pt
>
> In [12]: traj = pt.load('Pyranoid.mol2') #
> https://github.com/Amber-MD/cpptraj/blob/master/test/Test_
> Pucker/Pyranoid.mol2
>
> In [13]: pt.pucker(traj, method='cremer theta', dtype='dict',
> pucker_mask=('C1', 'C2', 'C3', 'C4', 'C5', 'O5'))
> Out[13]:
> OrderedDict([('pucker_res1', array([-176.8910242])),
> ('pucker_res1[Theta]', array([ 5.13193415]))])
>
>
> Let me know if that works for you.
> Cheers
>
> Hai
>
> On Mon, Apr 30, 2018 at 2:13 PM, Vivek Bharadwaj <
> vivek.bharadwaj.gmail.com>
> wrote:
>
> > Hi all,
> >
> > I am trying to calculate the pucker of a sugar ring using pytraj.
> >
> > While using ptraj (not pytraj) I can specify to calculate the 'theta'
> > values. Does this option not exist in pytraj?
> >
> > I only seem to get 1 array of values (which I assume is the phi values)
> > while running pucker using pytraj.
> >
> > The code I am using reads as follows:
> >
> > import pytraj as pt
> > traj=pt.iterload(aligned_file,top=top_file,stride=500)
> > pucker_data = pt.pucker(traj, pucker_mask=("C1", "C2", "C3", "C4", "C5",
> > "O5"),resrange=[213],range360=True,method='cremer')
> >
> > pucker_data is a single numpy array.
> >
> > Anybody else also encounter a similar problem? Any help will be much
> > appreciated.
> >
> > Thank you.
> > Vivek
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> >
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Received on Tue May 01 2018 - 08:00:04 PDT
