Thank you, Bob.
I have checked the readers in org.jmol.adapter.readers. For example, in
XyzReader.java, Jmol read in the coordinates and atom types from the xyz
files. But there are no bound information in Xyz file. How did Jmol know
which atoms are bounded together when it display it?
Is it possible for you to mention the class or the function name which deal
with that?
> Message: 6
> Date: Thu, 16 Jan 2014 10:26:25 -0500
> From: Robert Hanson <[email protected]>
> Subject: Re: [Jmol-users] Jmol-users Digest, Vol 92, Issue 7,Message 4
> To: "[email protected]"
> <[email protected]>
> Message-ID:
> <
> caf_yuvv8cpjeljj_cbxeadjvbvn_0xzujc1r+wyuw2xfcor...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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 is a somewhat-out-of-date graphic at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
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