Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
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.
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
- Start Xcode on the Mac.
- Choose Preferences from the Xcode menu.
- In the General panel, click Downloads.
- On the Downloads window, choose the Components tab.
- 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)"
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
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
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.
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.