Bob,
That's a great idea but I still want to check in to make sure that I am not
over complicating this for myself.
Essentially, I want a feature (menu item, jbutton, etc) that will print to a
file the distances between each hydrogen atom for each model that is
currently loaded in a format like this:
#model x
H1 H2 0.243
H1 H3 0.343
...
#model y
...
Using your suggestion from before, my next course of action is to run the
following script:
measure all (hydrogen and */n) (hydrogen and */n)
where n will be iterated across the model numbers for a particular loaded
file. Taking the return value from the JmolViewer.script method, I was
planning on parsing it to attain the atom numbers, that would then be used
to index into the atomNames array in the JmolViewer's modelSet object to get
the name of each particular hydrogen atom. Does this seem like too much of
a workaround? Is there a simpler way to attain this data?
Any suggestions would be greatly appreciated.
Thanks.
On Mon, Jun 16, 2008 at 10:41 AM, Bob Hanson <[EMAIL PROTECTED]> wrote:
> Brian, why not just do it with a simple Jmol script:
>
> measure ALL {*} {*}; show measurements
>
>
>
>
> Brian Ramos wrote:
>
> > Hi,
> >
> > (Since this is a different question, I figured I'd start a different
> > thread.)
> >
> > I'm trying to add a reporting feature that will calculate distances
> > between all pairs of atoms in each model of either an sdf or mol
> > file. I've never really worked on a project this big so I'm having
> > trouble wrapping my head around jmol's internal representation of sets
> > of atoms for a given model. In essence, how would I go about
> > iterating through each model in a file in such a way that I can
> > iterate through all the atoms in each model individually and get the
> > atom info(xyz coords) for each atom? I am currently looking through
> > the source and am getting lost when it comes to modelsets vs. atoms
> > vs. models. How exactly do I get atom info for a model that is not
> > currently being displayed?
> >
> > Thanks in advance,
> > Brian
> >
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>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
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