Macs in Chemistry

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Safari Extensions for Chemists

With Safari 5 one of the most interesting new features is the support for Extensions. If you’ve ever used Firefox or Chrome you might be familiar with these. For more details you might want to take a look at Mac OS X Tips, where there is a detailed description and links to useful Extensions. There is also the Apple Developer page that gives more details of how to create your own extension. There is a tutorial on creating Safari extensions here.

There are a couple of sites that have sprung up that give listings of available extensions. Apple now have a new Extensions website.

However there are not many Extensions that would be useful for chemists, but I had a few ideas, so with help from Matt at Mac OS X Tips I now have the first extensions available.

Update

Apple have released a new version of Safari, possibly the most important feature is that Extensions are now enabled by default.

Only needed for older versions of Safari.

First you need to enable extensions, to do this, first go to Preferences in the Safari menu. In the Advanced section, click the checkbox at the bottom to enable the Develop menu.

enable_extensions Go to this menu (it should just appear in the menubar) and the select third item in the list, “Enable Extensions.” Now, when you go back to the preferences there is a new Extensions section.

enable_extensions_dev

Available Chemistry Extensions

Chemspider :- Displays structure of highlighted chemical/drug and links to ChemSpider page.
PubChem :- Search PubChem for the highlighted compound
eMolecules :- Search eMolecules for the highlighted compound
Chemicalize :- Submit the current URL to chemicalize.org
DrugBank :- Search DrugBank for the highlighted compound
Opsin :- Chemical name to structure and display.
ChEMBL :- Displays structure of highlighted chemical/drug and links to ChEMBL page
Chemistry Reference Resolver :- This adds a toolbar to your browser as well as adds a right-click menu option for reference resolving
oaDOI :- Searches for OpenAccess versions of publications

If anyone knows of any others that would be useful for chemists let me know, or if you have ideas about extensions you would like written drop me a line and I’ll add them to my list. The value of these extensions is that add value to legacy documents.

Updating Extensions

When updates are available they will appear on the preference pane, you can go to the extension and then complete the update.

extension_update

Writing Extensions

One of the best ways to learn how to create extensions is to examine other peoples creations, you can't do this directly because they are stored as compressed archives, Mac OS X Tips has a step by step guide to extracting these archives using the Terminal. However if you are not comfortable using the Terminal then this Applescript will do this for you. If you are working with them however it is a bit of a pain to check which are installed and which are enabled. This applescript is a very neat way of getting a report, it also serves as a demonstration of how to link to shell scripts, in particular using the unix command cat, a standard Unix utility that concatenates and lists files, to generate the report.

If you want to write your own Safari Extensions there is a tutorial here.

Windows Users

A number of Windows Users have asked me about the extensions and based on a little experimentation using Windows XP under VMWare Fusion it looks like Safari on Windows supports these extensions. First you need to show the Develop menu in the Advanced Preference Pane. win_safari_pref

Then select “Enable Extensions” from the Develop menu.

win_safari_enable

You should then be able to download the extension and install them.

Updated 17 November 2016