Re: [Jmol-developers] Jmol as applet

[Daniel Z. <zah...@dt...>]

E.L. Willighagen wrote:
> (Hens, I've copied you in on this thread as it deals with interaction with the 
> Jmol applet from web pages. See below.)
> 
> On Monday 06 January 2003 18:36, mth wrote:
> 
>>Peter,
>>
>>I am very glad you got in touch with us regarding Jmol use as an applet.
>>
>>
>>>The purpose is to transform a CML document into
>>>a  standalone HTML+SVG+Applet document which can run on any modern
>>>browser.
>>
[...]
>>My *challenge* is that I am a computer scientist, not a chemist.
>>Therefore, I need some end-user input to flesh out the javascript API.
>>
>>Restated: If you tell me what you want I can probably put it in for you
>>and turn it around for you very quickly.
> 
> 
> Hens, you expressed interest in this functionality. I am not sure if you got
> everything working on your webpage as you like it to work, but maybe you
> want to comment on this?

If I could delurk for a moment for a few comments. My group at the 
National Cancer Institute is very interested in the JMol applet. We use 
it already (more below). We have about 250,000 2D chemical structures 
and about 235,000 3D chemical structures available. These are available via:
1)search pages on our site. 2D structures are part of the Basic Chemical 
data search (http://dtp.nci.nih.gov/dtpstandard/ChemData/index.jsp). We 
don't have a 3D structure search page set up, but a general search
(http://dtp.nci.nih.gov/dtpstandard/dwindex/index.jsp) will provide a 
link to the 3D structure if it exists for the input query.

2)our servlets, general form http://dtp.nci.nih.gov/dtpstandard/servlet/XXXX
where XXXX is the servlet name. Probably of most interest here are 
Chem2D, Chem3D, and Smiles. Servlet parameters include
1)searchtype - NSC for NCI registration number, CAS, NAMECONTAINS for 
substring search, NAMESTARTS for substring search a start of name and
HELP for a full list of parameters for the particular servlet and examples
2)searchlist - the list of values to search
3)outputformat - HTML uses the Jmol applet for display of 3D structures 
and JME for 2D structures; XML sends stuff back in CML and SDF will work 
for the structure files. So you (or a program) can construct a URL to 
get back any data you want in a variety of formats.

3) a world readable Oracle database. All the data we have is stored in a 
single set of relational database tables. We call this our datawarehouse 
project (See http://dtp.nci.nih.gov/dw/dw_main.html). The sql to 
generate the tables as well as all our JAVA code is available. We have 
tested things pretty extensively in Oracle and Posgresql. You can set up 
your own instance or connect to our public instance.

4) all underlying data is available for download in bulk files so you 
can put it into whatever database you wish.

We are just finishing some new additions and will be spending the next 
month or two cleaning up code, docs, data, etc. in preparation for a 
"1.0" release in time for the April AACR meeting. As soon as that work 
is done, we plan a number of things, including getting more involved 
with Jmol. I can't say we have clear set of TODOs, but obviously the 
first step is to catch up with all the new code and make sure we can 
effectively use it for our 3D display. We are also very interested in 
scripting and we would prob want to get involved in that area.

So we have a bunch of stuff going on, some of which involves Jmol 
directly and even more which would prob be of interest to the people on 
this list. As I mentioned above, we are only starting a focused effort 
to clean up code and docs, but we'd be very happy to hear from anyone 
who would like to wander around our stuff with whatever questions or 
comments you have.

DanZ.


-- 
/**********************************************************************
  *  Dan Zaharevitz
  *  Chief, Information Technology Branch
  *  Developmental Therapeutics Program
  *  National Cancer Institute, Rockville, MD 20892-7444
  *  email:  zah...@dt...      phone:  (301)496-8747
  **********************************************************************/