Bob, I think you are missing the pedagogical point - he is not making
the DNA viewer as part of a real application, this is an educational
exercise. The only way he can learn how to implement a modelling
solution is by building a modelling solution. However, you are
absolutely correct that plowing into the innards of a mature
application is not the way to go.
Pravin, if you are committed to doing this in Java, then look at Java
openGL (Jogl) as your starting point, not JMol. You will need to know
how to decode a PDB file to get atomic coordinates, and if you are
making a bonded representation you will need standard connectivity
information. Then, you need to render geometric primitives.
I use opengl in a C environment, so have not used jogl - however, I am
sure that GLUT-like primitives for spheres and other building blocks
are available. There are a lot of openGL examples on the web that you
can look at to get a general idea as to how to proceed.
Randy
On Mar 14, 2010, at 1:39 PM, Robert Hanson wrote:
Pravin,
Think twice before you go down this path. Unless you have many MANY
hours of time, you are far better off using what is already
available -- a Jmol frame in your application -- than trying to code
all the graphics and user interface yourself from scratch. Project
or not, no one should have to recreate this whole process. Unless, I
guess, this is a school project that is simply for you to
demonstrate that you can write code that other programs have already
done better.... Is there some point to that?
So my basic question is this: Why would you want to rewrite all this
code? Using Jmol code allows you to focus on what might be a far
more interesting project. See some of the examples provided, such as
Integration.java, as a starting point.
Bob Hanson
On Sun, Mar 14, 2010 at 8:56 AM, Jonathan Gutow <[email protected]>
wrote:
Pravin,
The Jmol code is quite opaque because things are reused as
much as possible. Since you've loaded Eclipse I suggest you follow
the code by using the "open declaration" option in the right-button
menu. This will help you dig into what is being done. You probably
want to start with the viewer code as most screen rendering is
passed through there (right, Bob?).
Jonathan
On Mar 13, 2010, at 11:58 PM, Pravin Sonawane wrote:
> Hi Nico..
>
> First of all, thankyou for all your help so far...
>
> I need a 3D molecular viewer as a part of my project. As mentioned
earlier, I want to code it myself.
>
> I want to write a code for a simple 3D molecular viewer that
should have just the basic features like:
> 1. read pdb files (i do not want any other format)
> 2. display DNA molecules in 3D (with mouse dragging as input to
rotate the molecule)
> 3. display the different atoms (carbon, hydrogen, nitrogen,
oxygen) in different colours.
>
> I have Jmol 9 and Jmol 11.8.20 source codes with me... I
downloaded Jmol 9 (source code) because I thought it would a lot
easier to understand this code instead of its 11.8 counterpart...
>
> But, I'm having trouble understanding it(the source code).
>
> It will be very helpful if you suggest me some links or help me
understand the code for the above three requirements.
>
>
>
>
> Hi angel..
>
> yes i realised that we do not need CDK.. i installed subclipse in
eclipse and the Jmol code worked!
>
> Thankyou for replying..
>
> -Pravin
>
------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Jmol-developers mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
_______________________________________________
Jmol-developers mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev_______________________________________________
Jmol-developers mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
Randy J. Zauhar, PhD
ArtemisDiscovery, LLC
Independents Hall
20 N. 3rd Street, Unit 201
Philadelphia, PA 19106
EMail: [email protected]
Phone: 267-303-4766
University:
Depts. of Chemistry & Biochemistry, and
Bioinformatics & Computer Science
University of the Sciences
600 S. 43rd Street
Philadelphia, PA 19104
EMail: [email protected]
Phone: 215-596-8691
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
_______________________________________________
Jmol-developers mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
