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iBabel 3.0 beta

As I mentioned a little while ago I’m in the process of rewriting iBabel using AppleScriptObjC, and thanks to the invaluable help of AppleScriptObjC Explored by Shane Stanley and the contributors to the MacScripter website I now have the first beta available.
It can be downloaded from
here (24MB), this version requires Mac OS X 10.6 or higher and OpenBabel 2.3
Much will seem familiar to previous users of iBabel and the
screenshots of the old version give a good overview of the capabilities, whilst the images below highlight a few of the new features.
The “Add title and index” option appends a title (default is Mol, but you can edit this in the adjacent text box) and an index number to multi-molecular files, e.g. Mol 1, Mol 2, Mol 3 etc. This is essential if you want to search files displayed in the “Viewer” since you need a unique identifier for each structure. In many cases the molecules will already have a molecule id.

Another new feature with OpenBabel 2.3 is the ability to generate 2D and 3D coordinates.
Perhaps the biggest changes have come with the “Viewer”, by storing the table data in an array we can use some of the cool ObjC functions such as the continuously updating selection count and the live searching of the “Name” text field. To import records identify the input file using the input button and then click the “Import” button.

The buttons highlighted in green allow the user to delete the highlighted row, delete all the “Selected” rows or clear all records completely. The selection can be modified using the buttons highlighted in pale blue.
There are a selection of supported viewers chosen using the iBabel Preferences. ChemDoodle is an included lightweight javascript library that works very well for most file formats but does not at present support SMILES (you can of course use iBabel to convert SMILES to sdf using the generate 2D option). I’m looking at doing this on the fly but I need to see what the performance hit will be.
For the other viewers, JMOL/JChemPaint are in the application bundle. ChemBioDraw needs to be in the Application folder but only works on some machines (something to do with only supporting 32-bit which I think we will have to wait for CambridgeSoft to address). Because of Java security issues Marvin has to be in the same file structure as the htm page, I think you only need to put an alias to Marvin in the Macintosh HD:Public folder or User:Public folder. the 2D and 3D radio buttons allow you to choose an appropriate display.

It also support JME as the editor but you need to get a copy from Peter Ertl directly and put it in the Public folder.

The PChem button pulls structures from PubChem, this can either be a single structure of a list (here is an example
caslist.txt you can download to try).
As you can see the list contains a mixture of systematic names, trivial names, drug names and CAS numbers but the smart people at PubChem sort all that out nicely.


The result is two files on your output.smi which contains the successful searches and NoStructure.txt which contains cases where no structure was found. You can then import the file to view the structures.

I’d be delighted to hear of any bugs (honest) any suggestions for how iBabel might be improved.
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