The second scenario - I never even see the GUI. I am using jmol.jar, not
the applet (although I gather the distinction between the two or at least
packaging of the applet, has changed recently).
Sincerely,
James Ryley, PhD, Patent Agent
SumoBrain: Intellectual Property Solutions & Data
AcclaimIP <https://www.acclaimip.com/> |
FreePatentsOnline.com<http://www.freepatentsonline.com/>|
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This communication is confidential and may be subject to legal privilege.
Nothing contained herein should be construed as legal or patenting advice.
On Sun, Aug 18, 2013 at 11:56 AM, Rolf Huehne <rhue...@fli-leibniz.de>wrote:
> Am 18.08.2013 17:30, schrieb James:
> > Hi,
> >
> > This is probably a dumb question, but I've gone too long without
> > figuring this out. I'm using Perl, but I assume this would apply to any
> > language other than Javascript where one cannot simply access Jmol's
> > data structures:
> >
> > How do I get data out of Jmol and into my script?
> >
> > Sending commands is not problem, I just print to the command line. But,
> > when I want to know values (e.g., I send "show ORIENTATION" and need to
> > know the results), is there a simple way to do that?
> >
> > I already kludged this once by writing a jmol script on the fly, which
> > saves data to a file, and then my Perl script reads it. E.g.:
> >
> > ======================
> > load $inputFile; # a molecular model
> > x = getProperty("boundBoxInfo.vector"); # a jmol native command that
> > doesn't work in Perl
> > write VAR x "$output_file"; # the jmol write file
> > command
> > =======================
> >
> > That sort of offends the senses, but I guess I could abstract it into a
> > function which would make it fairly transparent for Perl to use the
> > getProperty commands whenever I want. Perhaps the main concern there
> > would be that the getProperty list of commands seems pretty short
> > compared to the overall list of commands. I wonder how much data there
> > is that I can't access that way.
> >
> > It won't surprise me if the answer is "rewrite it in javascript." I was
> > just trying to avoid that since I'm more comfortable in Perl.
> >
> Plese explain a little bit more detailed what you want to do, because it
> didn'nt become clear for me.
>
> Do you want to control Jmol in a similar way with Perl as the applet
> with Javascript in a webpage? With Jmol and Perl running side by side
> and exchanging data/commands?
> Or do you just want to start Jmol with a set of commands with Perl, read
> the results and, after Jmol is finished, process the results with Perl?
>
> Regards,
> Rolf
>
> --
>
> Rolf Huehne
> Postdoc
>
> Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
> Beutenbergstrasse 11
> 07745 Jena, Germany
>
> Phone: +49 3641 65 6205
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