[Pipet Devel] using XML

J.W. Bizzaro bizzaro at bc.edu
Wed Dec 9 15:54:30 EST 1998

Thanks Konrad, for all the feedback!

Konrad Hinsen wrote:
> There's nothing to port, MMTK does not deal with user interfaces. MMTK
> is just the library for the computational stuff. I'd like to see TULIP

My mistake.  I saw the screenshot of MMTK, and I thought that it had its own
GUI.  Is that VMD or something displaying the molecule?

> evolve as a complement of MMTK. MMTK handles operations on
> macromolecular structures, but there will be non-structural operations
> as well, which should be implemented in a similar kind of low-level
> library. And then there would be the end-user programs on top of all
> that, which is where GTK comes into play. So TULIP would be both for
> end users and for developers. Or perhaps it might be better to
> separate these two tasks and use different names - but that's not an
> urgent decision.

Hmmm.  A non-graphical, operations library for TULIP.  I haven't considered
that.  We'll keep that in mind!

> But I totally agree in principle: lots of people will produce lots
> of tools for XML, so we would be stupid not to profit from that!


> a nice option where applicable. The main limitation is data manipulation,
> which is either limited to forms or requires Java or JavaScript, and
> that's a big mess.

...for an HTML browser.  Maybe we can go beyond simple text and forms with our
tools.  However, we must not make XML code that incompatible with the big XML
projects, like XML in a Web browser.

> passing complex data structures, XML fits the bill. But let's not
> overdo it; there's no point in sending an XML document where a
> five-character command line argument would be sufficient!

For a non-interactive, non-core tool, a command line argument will be passed, by
user request, to this tool.  I think the main role of XML is in formatting the
data that is *returned*.  So, instead of this program printf-ing plain text as
the output, it adds a few XML markers.  This is why I think XML is so simple. 
It doesn't require any new functions or routines...just a few more print
statements :-)

> Which reminds me: perhaps we can steal browser-type code from Grail!

I thought of that.  Grail is written in Python.  Plus there is a nice HTML
widget for GNOME.  But again, the tools don't have to look like Web browsers to
use XML, do they?

J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/

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