Macs in Chemistry

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Over 1000 downloads of iBabel

 

I just noticed that the latest version of iBabel has been downloaded over 1000 times, this is fantastic news and it certainly allows me to justify the effort put into creating the application.

3dviewers

iBabel started out as an AppleScript Studio application designed as a front-end to OpenBabel DOI, this was updated several times and is now an ApplescriptObjC application built with Xcode. As well as acting as a front-end to OpenBabel it also provided a front-end to tools built on OpenBabel and a molecule viewer using a selection of javascript viewers via an embedded web view.

I’m occasionally asked about the best way to install OpenBabel and I usually refer people to the page I wrote on installing cheminformatics tools on a Mac, this gives instructions on how to install a wide variety of cheminformatics toolkits and applications.

If you only want to install Openbabel then the best way is to use Homebrew.

Homebrew is a package manager for Mac OSX that installs packages in it’s own directory then symlinks the files to /usr/local. To install Homebrew you first need to have access to the command line tools for Xcode, the easiest way to do this is to download Xcode from the Mac Appstore

  1. Start Xcode on the Mac.
  2. Choose Preferences from the Xcode menu.
  3. In the General panel, click Downloads.
  4. On the Downloads window, choose the Components tab.
  5. Click the Install button next to Command Line Tools. You are asked for your Apple Developer login during the install process.

Or You can download the Xcode command line tools directly from the developer portal as a .dmg file. https://developer.apple.com/downloads/index.action. On the "Downloads for Apple Developers" list, select the Command Line Tools entry that you want.

To install Homebrew type this command in the Terminal

ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"

Then type

brew doctor

The 'brew doctor' command checks everything is fine. e.g. it will warn if the developer tools are missing, and if there are unexpected items in /usr/local/bin and /usr/local/lib that may clash and might need to be deleted.

It is a good idea to first update the package list

brew update

To install a range of cheminformatics packages we can use a custom “tap” created by Matt

brew tap mcs07/cheminformatics

Then to specifically install Openbabel use

brew install mcs07/cheminformatics/open-babel

To check OpenBabel is working type this in a Terminal window:

obabel -:'C1=CC=CC=C1F' -ocan 
Fc1ccccc1   
1 molecule converted

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iBabel 3.6 is released

 

Bable

iBabel started out as an AppleScript Studio application designed as a front-end to OpenBabel DOI, this was updated several times and is now an ApplescriptObjC application built with Xcode. As well as acting as a front-end to OpenBabel it also provided a front-end to tools built on OpenBabel and a molecule viewer using a selection of java applets and plugins via an embedded web view.

This all worked perfectly for a while but various security issues mean that java applets and plugins via an embedded web view no longer function, in addition calls to remote web servers to provide javascript viewers also cause security issues. In addition OpenBabel has been substantially rewritten so that many of the small programs built on OpenBabel are no longer supported. This functionality has not been lost however, they have now been incorporated into the main OpenBabel program. Security updates, Sandboxing and changes within El Capitan also meant I had to update a number of features.

Now things have settled down a bit I've restarted work on iBabel and an update is now available.

I've transitioned most of the calls to babel over to obabel the differences are highlighted here and replaced the calls to the tools based built on OpenBabel with the new corresponding calls to obabel.

Updating the viewers however has taken more time than I expected with new security features in Mac OSX updates causing unexpected issues. Whilst not yet complete, I have removed all the java or plugin-based molecular viewers and replaced them with javascript versions.

Full details are here.

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