This is a minor update (26 Feb 2008) that fixes an issue where the viewer displays HTML code rather than the structure, this seems to only effect a very limited number of users but the fix should avoid the problem in the future. You can download the new version here.
iBabel 2.5.1 This is an updated version of the cheminformatics tool iBabel (19 February 2008), this minor update improves compatibility with Mac OS X 10.5 particularly on Intel machines. I've also modified the CAS Number lookup from PubChem, very many thanks to the guys at PubChem who showed me a more reliable way to get the appropriate SMILES strings and how to avoid the formatting issues.
If you are using Mac OS X 10.5 you will need the latest version of ChemDraw to use the plugin in the viewer, it can be downloaded (59 MB) from the support downloads page. Marvin from ChemAxon works perfectly!
The key new feature in version 2.5 is the ability to get the structures corresponding to CAS Numbers from PubChem. It uses the the Entrez Programming Utilities (eUtils). If it proves useful I can look at adding further search facilities using PubChem, there are more details about the CAS lookup and screenshots here. This version also improves compatibility with Mac OS X 10.5 (Leopard). You can download the new version here, or from either MacUpdate or Versiontracker. To get a better idea of the capabilities of iBabel have a look at the screenshots.
Remember you need to install ChemSpotlight to access all functionality, the download here will also install OpenBabel. The full documentation is available here
A Brief Summary of iBabel
- This is an Applescript Studio Application created using Xcode, it is a GUI for the command line driven file conversion application OpenBabel
- The application is available iBabel and the documentation is available. If anyone wants the source code drop me an email, everything will be uploaded to Sourceforge when I have time.
- You can read more about it in this issue of CDK news page 19.
- iBabel was designed to be the interface to OpenBabel and it provides a simple GUI for file conversion and manipulation and supports over 80 different chemical file formats.
- It also provides to a number of tools built using the OpenBabel toolkit, these include very fast substructure and similarity searching using a variety of molecular descriptors, don't worry if you can't write SMARTS queries there are a range of predefined queries available from the drop-down menus and you can use the embedded editor to create more.
- The embedded tools also give access to molecular property calculation, molecular rotamer generation, and energy minimisation.
- Embedded tools allow the user to overlay structures on a template defined by a SMILES string, print chirality or property information.
- The structures can be viewed in 2D or 3D as appropriate using the embeded Jmol or JChempaint applets in addition iBabel also supports the use of Marvin from ChemAxon or ChemDraw from Cambridgesoft.
- I've now added the ability to search using the excellent ChemSpotlight created by Geoff Hutchison this means you can search your hard drive for chemical content.
- Full details can be found in the documentation or you can listen to a podcast describing the application, or read a poster here (3.9 MB)
