This is an old page please use the link above.
Not Just File Conversion
The status of iBabel
It seems there is a problem with Mac OS X 10.7.x
I've asked a few people and we can find no obvious issues.
So I've used XCode to build a version specifically for Mac OS 10.7. As far as I can tell there are no differences and no issues reported but lets see.
It can be downloaded from here.
The version for Mac OS X 10.8.x can be download from here iBabel3
SMARTCyp is a new addition and allows you to view the most likely sites for oxidative metabolism developed by Patrik Rydberg as shown below.
Patrik Rydberg, David E. Gloriam, Jed Zaretzki, Curt Breneman, Lars Olsen, SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism, ACS Med. Chem. Lett., 2010, 1 (3), pp 96-100.
Patrik Rydberg, David Gloriam and Lars Olsen, The SMARTCyp cytochrome P450 metabolism prediction server, Bioinformatics, 2010, 26, 2988-2989
Another change is that instead of using Pubchem to get structures from identifiers iBabel now uses the Chemical Identifier Resolver(CIR) by the CADD Group at the NCI/NIH a web service that performs various chemical name to structure conversions. The service works as a resolver for different chemical structure identifiers and allows one to convert a given structure identifier into another representation or structure identifier. It can help you identify and find the chemical structure if you have an identifier such as an InChIKey or CAS Number. The input identifier can be a chemical name, SMILES, CAS Number, InChi etc and the returned representation can be SMILES, sdf, png etc. this is achieved by using a combination of OPSIN, ChemSpider and CIR's own database.
The tools section has been updated and includes several excellent tools from silicos-it
The latest version can be downloaded from here iBabel
The silicos tools need to be downloaded and compiled, and installed in usr/local/bin with the openbabel tools.
A brief installation guide
Download iBabel and add to the applications folder Install OpenBabel, you can compile from source but the easiest way to get going is to install ChemSpotlight which includes OpenBabel, a Spotlight metadata importer and a Quicklook plugin.
By default Gatekeeper will prevent opening since this was not downloaded from the App store, more info here at the moment you will need to :
- In Finder, Control-click or right click the icon of the app.
- Select Open from the top of contextual menu that appears
Once any bugs have been sorted I’ll arrange to the app to be signed.
If you want to use JSmol you need to download from here download from here, the the folder jsmol needs to be put in Macintosh HD:Public:jsmol. In the jsmol folder you will also find a series of test pages that allow you to explore the capabilities
The silicos-it tools can be downloaded from here silicos-it they need to be compiled, and installed in usr/local/bin with the openbabel tools (I think this is the default install).
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 2 of the License.
The latest changes to Java seem to have broken the ability to use java plugins in a web view. Until I can find a fix I’m afraid you will have to use SVG or ChemDoodle as the viewer/
March 2012 Update to iBabel
I’ve been doing a little work to update iBabel, I’ve updated all the tools developed by Silicos-it to use the new names and options.
I’ve also been looking at the Molecule Viewers, I’ve disabled the ChemDraw plugin because it does not support the now standard 64-bit mode Safari :-(
On the other hand SVG support in Openbabel has undergone significant improvements due to the brilliant efforts of Noel O’Boyle and Chris Morley in particular the ability to colour a substructure within a molecule. This requires installation of the development version of OpenBabel at present.
ChrisMacbookPro:~ prompt$ obabel -L highlight One of the ops highlight Highlight substructures in 2D depictions Usage: --highlight "SMARTS1 color1 [SMARTS2 color2 ...]" Valid colors are black, gray, white, red, green, blue, yellow, cyan, purple, teal and olive. Additional colors may be specified as hexadecimal RGB values preceded by #. The following will color the phenyl group green, and the carboxyl group orange: obabel -:"c1ccccc1CCC(=O)O" -O mol.svg --highlight "c1ccccc1 green C(=O)O #FFA500"
You can see it in action in the movie below.
The new beta can be downloaded from here. (30 MB)
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.
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.
Update: 13 March 2011
Here is the latest version of iBabel (3beta3), the big changes are I've written the on the fly conversion of SMILES to 2D structures so ChemDoodle will now render SMILES in the Viewer panel. I've also rewritten the PubChem search since the they changed some of the field names, there is now a movie of this facility in action here.
Update: 21 Feb 2011
I’ve just uploaded a new beta (3beta2), there are a couple of minor bug fixes and I’ve added the ability to use wild cards in the input file for file conversions.
If you include a wild card in the input string then normally you get this error if you look at the Terminal.
/usr/local/bin/babel -ismiles '/Users/swain/Desktop/tes*.smiles' -osdf '/Users/swain/Desktop/output.sdf' --gen3D ============================== *** Open Babel Error in OpenAndSetFormat Cannot open /Users/swain/Desktop/tes*.smiles 0 molecules converted 1 errors
This is because the input file path is in single quotes, if you click the check box then the file path is not in single quotes and you can use wild cards. A word of caution, if you are going to use wild cards then you must ensure that the entire file path does not include any unacceptable characters (* & % etc.).
/usr/local/bin/babel -ismiles /Users/swain/Desktop/tes*.smiles -osdf '/Users/swain/Desktop/output.sdf' --gen3D 4 molecules converted 308 audit log messages
Update: 14 Feb 2011
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, so that is now available in the “Convert” pane. 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.
It also support JME as the editor but you need to get a copy from Peter Ertl directly and put it in the “Macintosh HD:Public” folder or” User: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.
64318-79-2 iodobenzene trinitrotoluene anisaldehyde 170729-80-3 nonsense Clomipramine Loratidine 108-86-1 63-75-2 Promethazine Chlorpromazine
The result is two files on desktop 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.
The “Tools” tab has been extensively modified now giving access to the many tools that have been built on top of the OpenBabel library.
Since each of the tools needs a different set of input parameters the “Options” box is updated each time you choose another tool, the advantage of doing this is that I can easily add further tools as they become available.
I’d be delighted to hear of any bugs (honest) and any suggestions for how iBabel might be improved.