Dear Amberites,
We are pleased to announce the development and now the release of a new
trajectory analysis tool. For years, the program 'ptraj' had been the
principle module for analyzing trajectories in the Amber suite of
programs that recently gave way to a reimplementation in C++ called
cpptraj. We have decided to reimplement this functionality again,
avoiding the headaches of using needlessly complex programming languages
in favor of a far more user-friendly pair of programming languages --
POSIX shell and the popular awk languages.
This new program, shawktraj, couples the advanced technology developed
within ptraj and cpptraj with the power, flexibility, and simplicity of
the shell and awk languages to develop a powerful program for performing
any and all trajectory and data analyses with the natural, expressive,
and easy-to-master interface afforded by shell and awk. Computationally
intensive functionality has been implemented with a combination of C++
and compiled python so that the performance and scalability of shawktraj
at least matches that of its predecessors ptraj and cpptraj. Parallelism
has been implemented with custom SSH/RSH calls and shared files,
allowing use of multiple processors where available.
The user interface of shawktraj was designed to be completely compatible
with the interface developed in cpptraj and can be used as a true
drop-in replacement. The code is currently available under a permissive
open-source license on Github, with the link to the repository given in
the postscript of this announcement. We encourage anybody and everybody
that is interested to visit the Github page and give shawktraj a try.
It is already fully-functional and currently implements all of cpptraj's
functionality.
On behalf of two members of the Amber/SHAWKTRAJ development team,
Jason Swails and Dan Roe
Github address: https://github.com/swails/shawktraj
"shawktraj - it will shawk you..."
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 01 2014 - 04:30:02 PDT
