[AMBER-Developers] Discussion: CPPTRAJ: AT12 updated manual issue

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 29 Aug 2012 13:09:47 -0600

Hi All,

It appears the AT12 manual was updated from the master branch
post-release, so lots of the functionality I was adding to cpptraj
(and documenting) after the official release made it into the manual.
Unfortunately, this has led to situations like the one today, where a
user tries to use a documented function that is not actually present
in the code. I can see this being rectified one of four ways:

1) The simplest(?) thing may be to correct the manual and post
something about it on the mailing list.

2) Patch cpptraj so that the missing functionality is added back in.
This could be a real pain in the neck since there is a decent amount
of new code; some are new commands (like avgcoord etc) and some
existing commands have new functionality (hbond, nastruct, etc), and
the infrastructure of cpptraj has changed enough from AT12 to now to
make back-porting a chore.

3) Release an updated cpptraj by itself, outside the normal AmberTools
release cycle. This has the advantage of all the upgraded
functionality, but could potentially cause headaches. Cpptraj is
relatively orthogonal w.r.t. the rest of AmberTools and does have its
own configure, so the framework is there. However I don't know if this
is a precedent we want to set.

4) As a last resort a mega-patch could be used to bring AT12 cpptraj
up to date with what's in the code, but honestly I don't really like
that idea. Even with the new patch distribution system the patch
itself would be enormous, which == lots of places for things to go

My first thoughts are to do a combo of 1 and 3; inform users of the
issues with the manual, then make a development version of cpptraj
available as a separate download for advanced users who would like the
functionality mentioned in the manual. There are a lot of new analysis
methods that Tom and I have been working on which people may get some
use out of.



Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
AMBER-Developers mailing list
Received on Wed Aug 29 2012 - 12:30:03 PDT
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