just ignore those. They are in the form of comments; for syncing with the
script editor and for command history - (which no one uses....)
2012/3/22 Adrià Cereto Massagué <adrian.cer...@urv.cat>
> It works!
>
> I had to use 'set syncscript on' instead of 'sync script'.
>
> But when I enter any command from the Jmol console, in data[1] I have:
> mycommand## EDITOR_IGNORE ## #NOSYNC;
>
> What does that '## EDITOR_IGNORE ## #NOSYNC;' thing mean? Am I doing
> something wrong?
>
> Here's my code: https://gist.github.com/2158139
>
> Adrià
>
> El 22 de març de 2012 11:48, Adrià Cereto Massagué <adrian.cer...@urv.cat>ha
> escrit:
>
> Thank you! I'll try the JmolStatusListener approach.
>>
>> I think it would be helpful for others to have this on the wiki.
>>
>> Regards,
>>
>> Adrià
>>
>> El 22 de març de 2012 3:39, Robert Hanson <hans...@stolaf.edu> ha escrit:
>>
>> Ah, I see. Let's work on this.....
>>>
>>> That's very interesting, and it's easy. Absolutely no hacking of Jmol
>>> code. It's all ready for you. A couple of options:
>>>
>>> 1) create a JmolScript function with the command name. That's your
>>> starting point. it doesn't matter what this function does. maybe nothing.
>>>
>>> Function myCommand () {}
>>>
>>> Now the user can type;
>>>
>>> mycommand whatever whatever whatever....
>>>
>>> 2) Now, in your application's JmolStatusListener, you need to tell Jmol
>>> that you are interested in listening for script commands and also process
>>> those. That's called a SYNC callback. See the Export.java example:
>>>
>>> class MyStatusListener implements JmolStatusListener {
>>>
>>> public boolean notifyEnabled(EnumCallback type) {
>>> // indicate here any callbacks you will be working with.
>>> // some of these flags are not tested. See
>>> org.jmol.viewer.StatusManager.java
>>> switch (type) {
>>> case SYNC:
>>> return true;
>>> default:
>>> return false;
>>> }
>>> }
>>>
>>> @SuppressWarnings("incomplete-switch")
>>> public void notifyCallback(EnumCallback type, Object[] data) {
>>> switch (type) {
>>> case SYNC:
>>> ...
>>> break;
>>> }
>>> }
>>>
>>>
>>> now issue the Jmol script command;
>>>
>>> sync script
>>> sync ON
>>>
>>> and watch every script command come your way.
>>>
>>> The command from Viewer.StatusManager will be this:
>>>
>>> void syncSend(String script, String appletName, int port) {
>>> if (port != 0 || notifyEnabled(EnumCallback.SYNC))
>>> jmolCallbackListener.notifyCallback(EnumCallback.SYNC,
>>> new Object[] { null, script, appletName, Integer.valueOf(port)
>>> });
>>> }
>>>
>>> So the script command will appear as data[1].
>>>
>>> I realize this is not at all obvious. But it is very powerful and
>>> flexible.
>>>
>>> Another option would be within your function to use the JAVASCRIPT
>>> command. That will return a string value to Jmol. And, come to think of it,
>>> we could set that up to return anything in the form of a ScriptToken. So
>>> for example:
>>>
>>>
>>> Function getCharges (atoms) {
>>> return javascript("exec getES: " + atoms.label("%i %e %[xyz]")
>>> }
>>>
>>> Now if in Jmol the user enters:
>>>
>>> print getcharges({helix})
>>>
>>> they will see the result after your end processes that command. Of
>>> course, if you want, rather than just returning the result, you could do
>>> anything you want with it.
>>>
>>> More possibilities: Maybe you would like to connect with Jmol over a
>>> socket? We do that in the molecular playground. It works great, and you can
>>> receive and send commands to Jmol using the SYNC command with a port number:
>>>
>>> SYNC -30000
>>>
>>> Now Jmol is listening on port 30000 for NIOS calls. Now you can connect
>>> a client and off you go.
>>>
>>> more about that if you are interested. No documentation on that I think.
>>>
>>> Bob
>>>
>>>
>>>
>>> Bob
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> listen for your command and do anything with it you want to.
>>>
>>> The "registering" in jmol is just the definition of
>>>
>>> You would just ignore all the commands you aren't interested in
>>> processing.
>>>
>>>
>>>
>>> 2012/3/21 Adrià Cereto Massagué <adrian.cer...@urv.cat>
>>>
>>>>
>>>>
>>>> El 21 de març de 2012 19:31, Robert Hanson <hans...@stolaf.edu> ha
>>>> escrit:
>>>>
>>>> That's Jmol script, not JavaScript. Yes, essentially exactly like
>>>>> pyMol. You can write any macro you want.
>>>>>
>>>>
>>>> I didn't explain well.
>>>> I can implement some of that functionality using JmolScript, but not
>>>> everything I want.
>>>> I would like to map commands to, or directly call ,Java (not JavaScript
>>>> nor JmolScript) functions from the Jmol console.
>>>> With pymol one can register any python function as a command available
>>>> from pymol's console.
>>>> Here it's explained: http://www.pymolwiki.org/index.php/Extend
>>>>
>>>>
>>>> Is there something similar in Jmol?
>>>>
>>>>
>>>>
>>>>
>>>>>
>>>>>
>>>>> 2012/3/21 Adrià Cereto Massagué <adrian.cer...@urv.cat>
>>>>>
>>>>>>
>>>>>>
>>>>>> El 21 de març de 2012 1:45, Robert Hanson <hans...@stolaf.edu> ha
>>>>>> escrit:
>>>>>>
>>>>>> Custom commands can be simply set up by defining a function with that
>>>>>>> command name. is that what you mean -- sort of a macro?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> function colorMeBlue(atoms) {
>>>>>>>
>>>>>>> color @atoms blue
>>>>>>>
>>>>>>> }
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> colorMeBlue {helix}
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> Thank you. I have some commands I can implement in JmolScript, and
>>>>>> therefore defien as functions,
>>>>>> but I would like to call or execute an external Java method. Can it
>>>>>> be done?
>>>>>>
>>>>>> In PyMol it is possible to map a python function to a script command.
>>>>>> Is there something similar in Jmol?
>>>>>>
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 2012/3/20 Adrià Cereto Massagué <adrian.cer...@urv.cat>
>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I am new to Jmol, and I am developing an application which relies
>>>>>>>> on it (the Integration.java example has been very useful)
>>>>>>>>
>>>>>>>> I want to have some custom commands available from the scripting
>>>>>>>> console. Is there an easy way for doing so?
>>>>>>>>
>>>>>>>> I have tried extending AppConsole and overriding the enterPressed()
>>>>>>>> method and checking AppConsole.text for the last line, but then I have
>>>>>>>> no
>>>>>>>> way no clear the custom command from the console unless i call
>>>>>>>> super.enterPressed(), which prints a script error about (obviously) not
>>>>>>>> recognizing the command.
>>>>>>>>
>>>>>>>> Thank you in advance,
>>>>>>>>
>>>>>>>> Adrià
>>>>>>>>
>>>>>>>> --
>>>>>>>> *Adrià Cereto Massagué*
>>>>>>>> Ph.D Student
>>>>>>>> Nutrigenomics Research Group
>>>>>>>> Biochemistry and Biotechnology Department
>>>>>>>> Building N4, Campus Sescelades
>>>>>>>> Universitat Rovira i Virgili
>>>>>>>> Tarragona, Catalonia
>>>>>>>>
>>>>>>>> Languages: Català, Español, English, Français, Deutsch, Português
>>>>>>>>
>>>>>>>> Nota
>>>>>>>> importante<http://www.gnu.org/philosophy/no-word-attachments.es.html>|
>>>>>>>> Important
>>>>>>>> Notice <http://www.gnu.org/philosophy/no-word-attachments.html>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> This SF email is sponsosred by:
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>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> This SF email is sponsosred by:
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>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
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>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> This SF email is sponsosred by:
>>>>> Try Windows Azure free for 90 days Click Here
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>>>>>
>>>>> _______________________________________________
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>>>>> Jmol-users@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>>
>>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
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>>>>
>>>>
>>>
>>>
>>> --
>>> 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
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> This SF email is sponsosred by:
>>> Try Windows Azure free for 90 days Click Here
>>> http://p.sf.net/sfu/sfd2d-msazure
>>>
>>> _______________________________________________
>>> Jmol-users mailing list
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>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>
>
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--
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
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