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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Received on Mon Apr 30 2018 - 14:30:02 PDT
