On Wed, Jan 10, 2018 at 12:04 PM, Abdul-Rashid III Sampaco <
absampaco.up.edu.ph> wrote:
> Hello,
>
> So in cpptraj, pseudo-trajectories of covariance matrix eigenvectors can be
> generated using the *modes* command, and the minimum and maximum values are
> found by looking at the histogram of the corresponding components. This is
> well-documented everywhere.
>
>
> But can this be done in pytraj? I've tried looking for a pytraj counterpart
> of the *modes* command, and all I found out is pytraj.analyze_modes, which
> is not very well documented in the github pages.
Blame the guy who wrote that due to his lack of understanding the module. :D
> Maybe it can be done using
> a series of different functions?
Yes I think so.
pytraj provides API to construct the Trajectory
traj = pytraj.Trajectory(xyz=3d_arrary, top=...)
the 3d_array can come from any source (eigenvectors in this case). and the
topology need to have the same number of atoms (3d_array[0].shape[0])
After having that "traj", you can do anything, e.g: (traj.save("your.nc"))
Hopefully pytraj developers can add one example for this.
Hai
> I hope the pytraj developers can shed
> light on this. It will be helpful to me and other people who do most of
> their analysis in pytraj.
>
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Received on Wed Jan 10 2018 - 10:00:04 PST
