VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 17 2008 - 16:14:35 CDT

Hi guys,
  The patch looked fine as a starting point. I'll see about
integrating it in the next few days after I'm back in town again.
Regarding the legal aspects, tiny patches like this that go against
the existing core code of VMD end up being considered owned by
UIUC since they are derived from the existing source code and UIUC IP,
and are not otherwise a "standalone" piece of code. Larger works of code
that could be used independently of VMD would be a different issue and
would likely have to be more formally contributed to be on the safe side.
The VMD plugins, with one or two exceptions are all open source,
so they are typically even less of an issue than small patches like this one.

Cheers,
  John

On Thu, Jul 17, 2008 at 12:19:09PM +0100, FX wrote:
> Hi Axel,
>
> >there are a few
> >constructs that are legal c++ code, but don't work so well across
> >platforms. i keep forgetting of those every once in a while, but
> >john is a nice guy and always fixes it.
>
> OK. I welcome all comments about legality, portability or style,
> because it's actually the first time I write C++ (I started reading
> "Thinking in C++" last week).
>
> >when compiling, i see that the variable "j" is not used, but other
> >than that is compiles find and works fine and looks pretty cool,
> >particularly when using a transparent material on a GLSL capabable
> >graphics card. so i wholeheartedly second including this feature.
>
> I also tried it with tachyon and povray rendering, and it does indeed
> look quite nice when it's transparent.
>
> >the one possible improvement that i am seeing (and i've been
> >suggesting
> >something similar for dynamic bonds as well for quite a while now)
> >would
> >be to have _two_ selections. one for the center and one for the
> >"neigbors". but i would expect that to matter only in very rare
> >cases, e.g. when the corner atoms are actually small molecules
> >(h2o, nh3)
> >and yon only want the "center" of the molecule be used. which is true
> >for the specific system i was testing, but even then with a careful
> >choice of the cutoff radius it does the right thing.
>
> I think in theory it would be the most useful thing to do. I actually
> contemplated it, but it looked to me like the "selection" code is too
> far from the place where drawing happens for this to be easy to
> implement. (Now, I really am new to the codebase, so that opinion is
> not worth a lot, of course.)
>
> >nobody has asked me to sign over something so far. i implicitly assume
> >that i'm assigning ownership to UIUC (see license), but it is not like
> >you are submitting something to a "political" project like the
> >GCC. ;-)
>
> Yep, it's amazing how political the development of GCC can be at
> times (and not only the paperwork).
>
> FX
>
> --
> François-Xavier Coudert
> http://www.homepages.ucl.ac.uk/~uccafco/
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078