[AMBER-Developers] Ptraj actions / analyze routines implemented in Cpptraj

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 9 Nov 2011 13:43:23 -0500

Hi All,

Just a quick note to inform you that I have incorporated almost all
the actions and analysis routines (those not already implemented in
cpptraj) from ptraj into the latest version of cpptraj in the GIT
tree. This means that 1) almost all ptraj scripts should now work in
cpptraj and 2) output for actions / analysis routines incorporated
this way match ptraj output exactly. This is essentially a stopgap
measure until these actions can be natively incorporated into the
cpptraj framework.

The ptraj actions currently implemented inside cpptraj include:
atomicfluct, atomicfluct3D, checkoverlap, contacts, correlation,
clusterdihedral, diffusion, dipole, dnaiontracker, echo, grid, matrix,
principal, projection, randomizeions, runningaverage, scale, unwrap,
vector, watershell.

Note that at the moment coordinates are not transmitted back from the
ptraj action routines to cpptraj, so the randomizeions, scale, and
unwrap routines won't function correctly yet (this will happen soon).
The truncoct and cluster routines had larger issues being ported, so
they are not yet functional (although cpptraj does have its own simple
hierarchical agglomerative clustering algorithm in place). Also, since
these actions exist outside the larger framework of cpptraj, they
cannot access the enhanced data format options available to other
cpptraj actions (gnuplot formatted output etc).

All analyze routines except for 'analyze hbond' work just as they do in ptraj.

I have tested the atomicfluct, checkoverlap, clusterdihedral,
contacts, diffusion, and grid actions, as well as the vector ired /
corrired, matrix ired / mwcovar / distcovar, analyze timecorr, and
analyze matrix routines. If anyone has any probems or sees any issues
let me know.


Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ   08854
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Received on Wed Nov 09 2011 - 11:00:04 PST
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