Jiayi,
Yes, I fully appreciate the difficulty.
Be sure to use Eclipse or, if you must, some other programming environment.
Then you can follow function call links forwards and backwards, and walk
through the code using breakpoints. If you don't have this capability, you
will go crazy.
The starting point for all scripting is in org.jmol.script.ScriptEvaluator.
For example, there is a load() method there that is called from execution
of the LOAD command. org.jmol.viewer.Viewer is the central processor. There
is a somewhat-out-of-date graphic at
http://chemapps.stolaf.edu/jmol/viewer.png that may be helpful.
Beyond that, we are talking about hundreds of calls. The Jmol code consists
of 474 classes and 3075 methods.
Your questions:
Q1. atom "types" are all determined in various readers found in
org.jmol.adapter.readers. Not all readers generate atom types.
Q2. structure comparisons are carried out using SMILES matching, with
selective use of chirality. Search the code for "enantiomer" and you will
see how that works.
Bob
On Thu, Jan 16, 2014 at 8:41 AM, jiayi.zhou <[email protected]> wrote:
> Hi, Robert:
>
> I know I have to look into the source code. I think you can understand
> it's really hard to read other's code.
> Is it possible for you to tell me some key functions' names or the
> entrance function names such as:
> 1. The function how Jmol get the atom types even the structure file only
> contains the atoms' coordinators when the user called "load"?
> 2. The function how Jmol know the two structures to be compared are
> isomers?
>
> Thank you.
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
------------------------------------------------------------------------------
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today.
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
