Jmol/debugging - Revision history

Eric Martz: /* Techniques specific to JSmol run in a browser */

2021-04-12T16:35:03Z

Techniques specific to JSmol run in a browser

← Older revision		Revision as of 16:35, 12 April 2021
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	You can use the JSmol Console to query variable values:		You can use the JSmol Console to query variable values:

	<nowiki>print [jmol-expression]</nowiki>		<nowiki>print jmol-expression</nowiki>

	or		or

Eric Martz: /* Techniques specific to JSmol run in a browser */

2021-04-12T16:34:37Z

Techniques specific to JSmol run in a browser

← Older revision		Revision as of 16:34, 12 April 2021
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	== Techniques specific to JSmol run in a browser ==		== Techniques specific to JSmol run in a browser ==
			When JSmol is running in a browser, bugs can occur either in the browser javascript that sends commands to JSmol, or in the JSmol commands themselves. To look for bugs in javascript, open the browser's console. For example, in Firefox: Tools, Web Developer, Browser Console.

	You can use the JSmol Console to query variable values as		To open the JSmol Console: Right click in JSmol so that the menu appears, and then click on Console.

			You can use the JSmol Console to query variable values:

			<nowiki>print [jmol-expression]</nowiki>

			or

	<nowiki>javascript alert(javascript-expression)</nowiki>		<nowiki>javascript alert(javascript-expression)</nowiki>

			<!-- I don't think this makes any sense because if you are in the JSmol Console, you can use the
			above 'print' command. -Eric Martz 4/12/2021
	or		or

	<nowiki>javascript alert(jmolEvaluate(jmol-expression))</nowiki>		<nowiki>javascript alert(jmolEvaluate(jmol-expression))</nowiki> -->

	== Acknowledgements ==		== Acknowledgements ==

	Some of these techniques were suggested by [https://sourceforge.net/p/jmol/mailman/message/37260020/ Bob Hanson] and [https://sourceforge.net/p/jmol/mailman/message/37259976/ Eric Martz] in response to a query on the Jmol listserv.		Some of these techniques were suggested by [https://sourceforge.net/p/jmol/mailman/message/37260020/ Bob Hanson] and [https://sourceforge.net/p/jmol/mailman/message/37259976/ Eric Martz] in response to a query on the Jmol listserv.

Eric Martz: /* General debugging techniques */

2021-04-12T16:27:29Z

General debugging techniques

← Older revision		Revision as of 16:27, 12 April 2021
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	== General debugging techniques ==		== General debugging techniques ==

	There are multiple ways to insert breakpoints into Jmol scripts, pausing the script to verify the script ~~progresses to~~ a certain point, and allowing you to check the state of variables at this point. The "pause" command pauses the script and gives control to you until you type "resume" in the console. The "prompt" command, given without parameters, opens a pop-up screen with the stack trace of the script.		There are multiple ways to '''insert breakpoints''' into Jmol scripts, pausing the script to verify the script progress at a certain point, and allowing you to check the state of variables at this point. The "pause" command pauses the script and gives control to you until you type "resume" in the console. The "prompt" command, given without parameters, opens a pop-up screen with the stack trace of the script.

	There are a variety of commands described under "set (debugging)" in the [https://chemapps.stolaf.edu/jmol/docs/#setdebugging manual] that help with debugging and analyzing program crashes. For example, you can use the history function in the Jmol console to see which commands executed after setting the historyLevel to a non-zero value.		There are a variety of commands described under "'''set (debugging)'''" in the [https://chemapps.stolaf.edu/jmol/docs/#setdebugging manual] that help with debugging and analyzing program crashes. For example, you can use the history function in the Jmol console to see which commands executed after setting the historyLevel to a non-zero value.

	Of course, it is also possible to add strategic "print" statements to the script but the techniques described above are more flexible because they pause the script or give you a chance of a post-mortem analysis.		Of course, it is also possible to add '''strategic "print" statements''' to the script but the techniques described above are more flexible because they pause the script or give you a chance of a post-mortem analysis.

	== Techniques specific to the Jmol application ==		== Techniques specific to the Jmol application ==

Karsten Theis: User:Karsten Theis/Jmol/debugging moved to Jmol/debugging: So others can edit

2021-04-11T21:46:27Z

User:Karsten Theis/Jmol/debugging moved to Jmol/debugging: So others can edit

← Older revision	Revision as of 21:46, 11 April 2021
(No difference)

Karsten Theis: /* Techniques specific to JSmol run in a browser */

2021-04-11T21:45:15Z

Techniques specific to JSmol run in a browser

← Older revision		Revision as of 21:45, 11 April 2021
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	You can use the JSmol Console to query variable values as		You can use the JSmol Console to query variable values as

	<nowiki>javascript alert(javascript-expression)</nowiki>		<nowiki>javascript alert(javascript-expression)</nowiki>

	or		or

	<nowiki>javascript alert(jmolEvaluate(jmol-expression))</nowiki>		<nowiki>javascript alert(jmolEvaluate(jmol-expression))</nowiki>

	== Acknowledgements ==		== Acknowledgements ==

	Some of these techniques were suggested by [https://sourceforge.net/p/jmol/mailman/message/37260020/ Bob Hanson] and [https://sourceforge.net/p/jmol/mailman/message/37259976/ Eric Martz] in response to a query on the Jmol listserv.		Some of these techniques were suggested by [https://sourceforge.net/p/jmol/mailman/message/37260020/ Bob Hanson] and [https://sourceforge.net/p/jmol/mailman/message/37259976/ Eric Martz] in response to a query on the Jmol listserv.

Karsten Theis at 21:15, 11 April 2021

2021-04-11T21:15:31Z

← Older revision		Revision as of 21:15, 11 April 2021
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	Debugging refers to finding and fixing errors in programs or scripts. Jmol has an extensive scripting language that implements a dialect of javascript. Because this dialect is not completely compatible with javascript, it is not possible to debug Jmol scripts using debuggers made for javascript.		Debugging refers to finding and fixing errors in programs or scripts. Jmol has an extensive scripting language that implements a dialect of javascript. Because this dialect is not completely compatible with javascript, it is not possible to debug Jmol scripts using debuggers made for javascript. Instead, there are ways to debug right in the Jmol application or in a browser running JSmol.


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	There are multiple ways to insert breakpoints into Jmol scripts, pausing the script to verify the script progresses to a certain point, and allowing you to check the state of variables at this point. The "pause" command pauses the script and gives control to you until you type "resume" in the console. The "prompt" command, given without parameters, opens a pop-up screen with the stack trace of the script.		There are multiple ways to insert breakpoints into Jmol scripts, pausing the script to verify the script progresses to a certain point, and allowing you to check the state of variables at this point. The "pause" command pauses the script and gives control to you until you type "resume" in the console. The "prompt" command, given without parameters, opens a pop-up screen with the stack trace of the script.

	There are a variety of commands described under "set (debugging)" in the [https://chemapps.stolaf.edu/jmol/docs/#setdebugging manual] that help with debugging and analyzing program crashes. ~~Of course~~, ~~it is also possible to add strategic "print" statements to~~ the ~~script but~~ the ~~techniques described above are more flexible because they pause~~ the ~~script or give you a chance of~~ a ~~post~~-~~mortem analysis~~.		There are a variety of commands described under "set (debugging)" in the [https://chemapps.stolaf.edu/jmol/docs/#setdebugging manual] that help with debugging and analyzing program crashes. For example, you can use the history function in the Jmol console to see which commands executed after setting the historyLevel to a non-zero value.

	== Techniques specific to the Jmol ~~app~~ ==		Of course, it is also possible to add strategic "print" statements to the script but the techniques described above are more flexible because they pause the script or give you a chance of a post-mortem analysis.

			== Techniques specific to the Jmol application ==

	You can open the Jmol script editor to step through a script. If you are in an endless loop, you can pause the script to see where you are stuck. After a script crashes, you can open the Java console to see which Java exception was raised.		You can open the Jmol script editor to step through a script. If you are in an endless loop, you can pause the script to see where you are stuck. After a script crashes, you can open the Java console to see which Java exception was raised.

Karsten Theis: New page: Debugging refers to finding and fixing errors in programs or scripts. Jmol has an extensive scripting language that implements a dialect of javascript. Because this dialect is not complete...

2021-04-11T21:07:07Z

New page: Debugging refers to finding and fixing errors in programs or scripts. Jmol has an extensive scripting language that implements a dialect of javascript. Because this dialect is not complete...

New page

Debugging refers to finding and fixing errors in programs or scripts. Jmol has an extensive scripting language that implements a dialect of javascript. Because this dialect is not completely compatible with javascript, it is not possible to debug Jmol scripts using debuggers made for javascript.

== General debugging techniques ==

There are multiple ways to insert breakpoints into Jmol scripts, pausing the script to verify the script progresses to a certain point, and allowing you to check the state of variables at this point. The "pause" command pauses the script and gives control to you until you type "resume" in the console. The "prompt" command, given without parameters, opens a pop-up screen with the stack trace of the script.

There are a variety of commands described under "set (debugging)" in the [https://chemapps.stolaf.edu/jmol/docs/#setdebugging manual] that help with debugging and analyzing program crashes. Of course, it is also possible to add strategic "print" statements to the script but the techniques described above are more flexible because they pause the script or give you a chance of a post-mortem analysis.

== Techniques specific to the Jmol app ==

You can open the Jmol script editor to step through a script. If you are in an endless loop, you can pause the script to see where you are stuck. After a script crashes, you can open the Java console to see which Java exception was raised.

== Techniques specific to JSmol run in a browser ==

You can use the JSmol Console to query variable values as

<nowiki>javascript alert(javascript-expression)</nowiki>

or

<nowiki>javascript alert(jmolEvaluate(jmol-expression))</nowiki>

== Acknowledgements ==

Some of these techniques were suggested by [https://sourceforge.net/p/jmol/mailman/message/37260020/ Bob Hanson] and [https://sourceforge.net/p/jmol/mailman/message/37259976/ Eric Martz] in response to a query on the Jmol listserv.