VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 27 2010 - 22:16:44 CDT

Jerome,
  Have you looked at whether you can use the existing "gettimestep"
and "rawtimestep" routines from by making Tcl eval calls from
your C++ code without needing to modify VMD itself?

I suspect your problems were caused by hijacking internal program
state from an unsafe point during command processing, but without having
all of the code/patches I can't say for sure.

I would start by looking at whether there's a reasonable way to use
gettimestep and rawtimestep and we can go from there.

Cheers,
  John

On Thu, May 27, 2010 at 02:27:00PM +0200, Jérôme Hénin wrote:
> Hi all,
>
> I have a VMD-hacking problem, which might be similar to what some of
> you have tried. We'd like to have Tcl-wrapped C++ code do some calculations
> efficiently, accessing VMD's atom coordinate data directly. Ideally,
> that would be dynamically loaded, and not require recompiling VMD.
>
> We have a python hack, where the python "timestep" routine (from
> py_numeric.C) is called to get a python array, from which one can
> extract the C pointer and work directly with it.
>
> There is an interestingly ugly Tcl variant where a small Tcl routine
> (added to TclCommands.C) gets the pointer (i.e.
> myMolecule->get_frame(myFrame)->pos), casts it to a long int and
> returns that. The integer is passed to my Tcl-C++ "plugin" (loaded
> from a shared object), which casts it back to (float *), and goes on
> to do the computation. This, on top of being ugly, requires inserting
> this little Tcl hook and recompiling VMD. Amazingly though,
> it works just fine.
>
> In yet another variant, I have tried to eliminate the middle-man and
> the need to modify and compile VMD by accessing VMD's internals
> directly from my dynamically loaded C++ code. This felt a bit dangerous:
> I was surprised that it worked up to a point, and then disappointed
> that it didn't work all the way. Here are a few relevant lines from that
> function:
>
> VMDApp *app = (VMDApp *)Tcl_GetAssocData(interp, (char *)"VMDApp", NULL);
> Molecule *mol = app->moleculeList->top();
> Timestep *ts = mol->get_frame(0);
>
> The result is the following: I do get a pointer to the top molecule,
> but calling methods from that object essentially give me garbage (e.g.
> the returned pointer from get_frame is off). I suppose that these are
> not supposed to be called from external, dynamically loaded code, but
> I don't understand all the details, for example, why the calls to
> VMDApp methods do give me the right answers.
>
> Could anyone point me to information that would help me understand
> this? Does anyone have an opinion on a better way to obtain this kind
> of "lightweight plugin" functionality?
>
> Thanks,
> Jerome 

-- 
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