Re: [AMBER] pseudo-trajectory in pytraj

From: Hai Nguyen <>
Date: Wed, 10 Jan 2018 12:54:33 -0500

On Wed, Jan 10, 2018 at 12:04 PM, Abdul-Rashid III Sampaco <> 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: (""))
Hopefully pytraj developers can add one example for this.


> 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
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