[AMBER-Developers] [jason.swails.gmail.com: redundant redundancies]

From: case <case.biomaps.rutgers.edu>
Date: Mon, 13 Jun 2011 22:16:45 -0400

I agree with Jason's comments below. I'm happy to let him get started as
proposed, but I hope everyone will help out in working on simplification.
There are both types of issues outlined below, plus much bigger issues, e.g.:

   tleap vs sleap
   ptraj vs cpptraj
   python vs perl versions of mm-pbsa

I don't have any magic answers, but cleanup and simplification of both code
and documentation should be a high priority for the next release.

[On Jason's specific points, we can probably retire top2mol2, top2ff,
and maybe some of the other minor antechamber scripts.]


----- Forwarded message from Jason Swails <jason.swails.gmail.com> -----

Date: Mon, 13 Jun 2011 14:53:59 -0600
Subject: redundant redundancies
From: Jason Swails <jason.swails.gmail.com>

I'm going through Amber and AmberTools right now and adding a section of the
manual that more or less lists all of the programs that exist in each
package right now that gives a short (1-sentence) description of its
functionality and where in the manual you should look for its description.
In doing so, though, I've found numerous redundancies. For instance:

extractFrcmod.py and top2ff do the same thing (although the first one
provides a more complete FF file from a given prmtop). top2mol2 mimics
ambpdb with the -mol2 flag. I can provide a more complete list after I'm
done, though I think we should start thinning out the number of provided
programs; at the very least eliminating redundancies. There are 97 (!)
programs installed with AmberTools (just serial).


----- End forwarded message -----

AMBER-Developers mailing list
Received on Mon Jun 13 2011 - 19:30:04 PDT
Custom Search