Atto: Chemistry editor

atto_chemistry
Maintained by Picture of Geoffrey Rowland Geoffrey Rowland
Edit chemistry equations in Moodle 2.7, or later, using the mhchem extension to the MathJax or TeX filter. Useful for full and ionic equations, isotopes, equilibrium reactions, thermochemistry and reaction kinetics. Includes a periodic table of element symbols.
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Edit chemistry equations in Moodle 2.7, or later, using the mhchem extension to the MathJax or TeX filter. Useful for full and ionic equations, isotopes, equilibrium reactions, thermochemistry and reaction kinetics. Includes a periodic table of element symbols.

Requirements:

1. The MathJax filter to be enabled (recommended) or the TeX filter enabled (or, in Moodle 2.8, both)

Administration > Site administration > Plugins > Filters > Manage filters

Don't forget to also enable the appropriate filter in the relevant course:

Administration > Course administration > Filters

2. The mhchem  extension to be added to the MathJax configuration:


Edit Administration > Site administration > Plugins > Filters > MathJax > MathJax configuration to include:

TeX: { extensions: ["AMSmath.js","AMSsymbols.js","mhchem.js","noErrors.js","noUndefined.js"] },

 or to the TeX filter configuration:

Edit Administration > Site administration > Plugins > Filters > Tex notation > LaTeX renderer Settings to include:

\usepackage{mhchem}

At this stage you may wish to check the filters are working by, say, typing \(\ce{ H2SO4 }\) into Atto. This should be displayed as H2SO4 when saved.

 3. The chemistry editor button (flask icon) to be added to the Atto editor toolbar:

Edit Administration > Site administration > Plugins > Text editors > Atto HTML editor > Atto toolbar settings > Toolbar config, to give, for example:

insert = chemistry, equation, charmap, table, clear

Immediately after installation and configuration you may need to clear your Moodle server caches:

Administration > Site administration > Development > Purge all caches

and local browser cache for correct display.

Sets

This plugin is part of set MoodleCloud.

Screenshots

Screenshot #0
Screenshot #1

Contributors

Picture of Geoffrey Rowland
Geoffrey Rowland (Lead maintainer)
Please login to view contributors details and/or to contact them

Comments RSS

Show comments
  • Picture of David Mudrák
    Fri, 12 Sep 2014, 8:20 PM
    Hi Geoffrey. Thanks for sharing this plugin with the community. I've been able to successfully set it up using the documentation provided. Let me suggest that the requirements regarding the filter set up are at least shortly mentioned in the plugin description at this page. People might expect it working out of the box.

    I had troubles having the button icon displayed correctly. I think that there should be a code like iconComponent: COMPONENTNAME, added below https://github.com/geoffrowland/moodle-editor_atto-chemistry/blob/master/yui/src/button/js/button.js#L174 as Moodle searches for the icon in the core locations without success. Also, the SVG icon provided does not seem to contain the correct icon. Rather than relying on a font, it would be better to provide plain SVG with the flask shape. Currently, it displays an U+F0C3 character for me for some reason.

    Other thing I noticed are empty lines at https://github.com/geoffrowland/moodle-editor_atto-chemistry/blob/master/settings.php#L301 and below. I'm not sure they are intentional and if so, why.

    The rest of the code looks ok to me. With the hope the issues raised above will be addressed soon, you are cleared to land now. Welcome to the Plugins directory!
  • Picture of Geoffrey Rowland
    Sat, 13 Sep 2014, 6:34 PM
    David
    Thanks for reviewing this so quickly. As requested, I'll update the description.

    I'll also work on getting the icon to display properly. Currently needs to be copied from the plugin pix/e/ location to moodle core pix/e/ folder.

    The empty lines are intentional. They are required for empty buttons to act as spacers to give the periodic table layout. I'm sure this could be done more elegantly, but was a simple way to use the existing editor button layout.
  • Picture of Geoffrey Rowland
    Tue, 23 Sep 2014, 5:20 AM
    Latest release fixes local icons (svg and png). No longer any need to copy to core pix folder
  • Me!
    Tue, 22 Sep 2015, 9:58 AM
    This is another excellent plugin from Geoffrey!

    Thank you very much for creating and sharing this plugin.
  • Picture of Geoffrey Rowland
    Mon, 28 Sep 2015, 7:31 PM
    Glad you appreciate it, Damyon. Then again, the code is mainly from your Atto Equation Editor plugin wink

    In similar vein, I have just released an Atto plugin for TeX/MathJax Matrices and Arrays, which I hope will prove useful.
    https://moodle.org/mod/forum/discuss.php?d=320681

    BTW you should fix MDL-45067, the 2x2 matrix button in the Atto Equation Editor.
    Just needs \\\\ rather than \\ in the relevant line of settings.php. Presumaby an escaping issue (rendered in TeX as \\)
  • Picture of David Conrad
    Sat, 8 Oct 2016, 2:17 AM
    I followed the instructions above and added this plugin v2.9-2 to a moodle 3.0.3 install. For step 2 I used the TeX filter configuration instead of the MathJax configuration. I verified that the filters are On in the course. When the Chemistry editor appears, all the cells are red and each symbol is preceeded by "\ce" in red (such as \ce$⇓$ ). Has anyone else had this problem? I will add a discussion post as well.
  • Picture of Geoffrey Rowland
    Sat, 8 Oct 2016, 4:02 AM
    Hi David

    Do you have LaTex and other dependencies including the mhchem extension installed on your Moodle server?
    Precise details vary depending on your server setup though there is more information at:

    https://docs.moodle.org/31/en/Chemistry_notation_using_mhchem#via_LaTeX

    Get back to me if you still have issues
  • Ricardo Caiado
    Wed, 7 Dec 2016, 8:42 PM
    Any upgrade to Moodle 3.2?
  • Picture of Roel Cantada
    Tue, 20 Dec 2016, 8:06 PM
    The tex \{\ce{ H2SO4 }\} in the description appears to be incorrect. My installation would only parse \(\ce{ H2SO4 }\) wherein the second and last brackets are replaced by parentheses.
  • Picture of Geoffrey Rowland
    Wed, 21 Dec 2016, 12:44 AM
    Thanks Roel. I have now updated the description to use the correct parentheses.
  • Picture of Andreas Schenkel
    Sat, 24 Jun 2017, 6:35 PM
    Is there a version for moodle 3.3?
  • Ricardo Caiado
    Tue, 15 Aug 2017, 10:33 PM
    Hi,

    Teachers on my Institution are asking for a 3.3 version...

    Ricardo
  • Picture of Geoffrey Rowland
    Wed, 16 Aug 2017, 1:07 AM
    Ricardo
    I no longer have full-time involvement in education and Moodle administration/development. So, have not followed the most recent Moodle versions.

    However, I'll take a look at this over the next few weeks and see if I can update for Moodle 3.3. I'm also aware that MathJax mhchem has been updated (https://mhchem.github.io/MathJax-mhchem/). So, I'll explore the implications of this too.

    Cheers

    Geoff
  • Ricardo Caiado
    Wed, 16 Aug 2017, 1:10 AM
    Geoff,

    Thanks so much for the help!!!

    Ricardo
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