Macs in Chemistry

Insanely great science

 

Updated

The latest version of iBabel can be found here

This is an old page please use the link above.

iBabel 3.0

Not Just File Conversion

The status of iBabel

Feb 22

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.

http://macinchem.org/ibabel/iBabel107/iBabel.zip

The version for Mac OS X 10.8.x can be download from here iBabel3

February 2013

As you might have imagined the issues with Java security have made it impossible to support the use of Java Applets as the molecule viewer so I’ve been busy trying out various options. I’ve decided to abandon the use of Java applets and the use of plugins; sorting out which version of a plugin works with which version of browser and/or operating system was becoming a nightmare. So I’m moving to a variety of Javascript based molecule viewers.

The options are shown in the image below. Elemental is 2D molecule viewer/editor from Dotmatics, which I have working but not released yet, JSmol is a javascript version of the very popular Jmol. SVG are the images that are generated by OpenBabel itself, ChemDoodle is a javascript 2/3D molecule viewer and editor. ChemBioDraw may or may not work depending on the factors mentioned above.

viewers

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

smartcyp

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

ibabelTools

The latest version can be downloaded from here iBabel

Remember this version is designed to support Mac OSX 10.8 and requires OpenBabel 2.3. Whilst the javascript libraries for ChemDoodle are included to use JSmol you will need to download from here, I may bundle it in the future but whilst it is still under active development it sees easier for the user to decide on updates. iBabel assumes that the folder containing JSmol is in Macintosh HD:Public:jsmol.

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 :

  1. In Finder, Control-click or right click the icon of the app.
  2. Select Open from the top of contextual menu that appears

menu

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).

Legal Stuff

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.

September 2012

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.

tools

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"

sss

You can see it in action in the movie below.

The new beta can be downloaded from here. (30 MB)