Subject: Molecular Inventor, Java, and other WWW developments

From: Joseph Landman <[email-masked]>
Date: Wed, 10 Apr 1996 08:28:50 -0400 (EDT)

Given my affiliation, I have been staying out of this debate, though I 
have my own personal opinions on this..

On Tue, 9 Apr 1996, Paul Weber wrote:

[...]

> "News") at www.sgi.com.   I'm also surprised to see the attention focused
> just on Java -- if all you want to do is look at a molecule, you might
> consider VRML as well as Molecular Inventor for getting a much improved
> display quality.  VRML and MI formats are pretty easy to write too, so
> general support in the future seems to be a good bet.
> 

This is true.  I wrote a quick xyz-Open Inventor translator about 6 
months ago to show my GaAs systems.  I halted any forther work after 
seeing molecular inventor demos, figuring on taking advantage of it when 
released.  It is good database format for display, and is non-proprietary 
(in the sense of OpenInventor being *open*, and Template Graphics and 
others having ports to MANY platforms, including all flavors of Windows, 
Linix, possibly OS/2, Mac, etc)

I believe that MI may solve some of the thornier issues about portability 
of models, including the connectivity data, between formats and programs.
Actually I am of the opinion that the Molecular Browser/Interactor is 
somewhat seperate from the question of the data type.  There is no doubt 
as to the potential for a Java app/applet to do a reasonable job at 
browsing, rotating, etc a molecule.  However, the implementation still 
needs to be done, and levels of functionality need to be defined.
What is good for the undergrad may not be good for the graduate 
student/researcher/professor.

So, is there any support for defining quantised levels of functionality 
in a browser? 

e.g:

Level 1)	Browsing: rotation, translation, panning.  Advantages are 
		that this is small and fast, without excess code needed for
		operations that will not be performed at this level.  Intended
		for large scale audiences who simply need to see the molecule.

Level 2)	Interaction:  All of level 1, plus atom selection, distance
		and angle calculation, marking sub-parts (chains/ribbons/etc)
		of larger molecules.

Level 3)	All of level 2 including hooks into your favorite renderer,
		as well as trajectory information for dynamics runs, and 
		much more.

(this is quite rough, feel free to hack away)

> Now about Java -
> 
> The download times are a drawback that many have noted, and many are
> working on.  Downloading the classes once and storing locally is
> probably the best bet, as long as the application remembers to check
> to see if it is still up to date.

We could set up a directory site at CCL that the application checks at 
least once a month for latest versions of Java code.

[...]

> vendors.  Thus, a "plug and play" of applications.   The real issue then
> is will there be a common data format to drag and drop between applets?
> Again, I think the Molecular Inventor format from SGI comes the closest
> to what we could use (and Tripos is using it, as well as MSI and probably
> other vendors, too).

Given the Template Graphics port (as well as others) to many platforms, 
one should be able to do a drag and drop between the viewer and their 
word processor (I am assuming OLE or OpenDoc style linkage).  Most of 
SGIs own productivity tools are like that now (in terms of being able to 
import/export these open formats) and this is certainly a benefit in my 
opinion.

[...]

> I think that it is a good time for the community to search for acceptable
> standards, such as SGI's Molecular Inventor, Tripos's SLN, DayLight's
> SMILES, or the PDB (yuck). The chemistry community could then promote the
> use of these standard formats by all software producers, whether garage-shop,
> grad student, or public company.

> Paul L. Weber, Ph. D.
> Vice President, Product Development      Phone: 314 647 1099
> Tripos, Inc.                               Fax: 314 647 9241
> 1699 S. Hanley Rd 
> St. Louis MO 63144 USA               Email: [email-masked]

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