Talk:MediaWiki

Please, post your suggestions concerning the Jmol extension here.

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Adding other components

Suggestion

List of components to add (feel free to add other components) :

• Checkbox
• Radio button
• Link
• Menu
• Button opening a popup window with Jmol Applet in it DONE → <jmolAppletButton>

Reading files

Suggestion

In the first version, the only way of giving a datafile to the applet is directly through the <onlineContents> tag.

Other ways need to be available:

• Accessing a file previously uploaded in MediaWiki DONE → <uploadedFileContents>
• Accessing a file stored as a Wiki Page DONE → <wikiPageContents>
• Accessing a file through an URL. That may require several other modifications: DONE → <urlContents>
  • Possibility to disable this feature in LocalSettings.php DONE
  • Possibility to use the signed applet to access a remote file (configurable in LocalSettings.php) DONE

Note: Accessing files directly will also give the possibility to load gzipped files directly since Jmol read gzipped files as well as non-compressed files.

Comments

• all files should be accessible via a common category, this will allow to browse to all files at the same time. In other words, this will allow to build up a data repository, which allows downloading all at once.

<uploadedFileContents> can be used to use uploaded files. In the description of the file, it's possible to add the file in categories. On this Wiki, the category is Molecular Data. --Nico

<wikiPageContents> and $wgJmolForceNameSpace can be used to put all the files in one namespace (not a category). --Nico

• If possible a second tool should be able to generate an archive file out of that.

• Is it possible to extend this approach also to JChemPaint and CDK/JOELib to get 2D drawings and calculate physicochemical properties? E.g. toxicity, solubility, etc.?

Currently, I don't know how JChemPaint and CDK/JOELib work. I won't do it for the first version of the Jmol Extension, but I would happily discuss with people about this. --Nico

Extending to other tools of the Blue Obelisk

Since this approach is quite general for other tools, too. It might be interesting to include also other tools of the Blue Obelisk Movement, e.g.:

• 2D layout and drawings: JChemPaint
• feature calculation: CDK,JOELib
• NMR predictions: CDK
• etc.

Contributors

AngelHerraez, NicolasVervelle, JimHu, Joerg Kurt Wegner, Mevans86, Bduke