Notice how information has been lost (the reaction arrow and text) in this conversion due in part to impedance mismatch between the CDX format and the molfile format. The output is an SD file in which the first molecule is benzene and the second is aniline: benzene-to-aniline-reaction.cdx This generates a properly formatted molfile: benzene.cdxīabel -icdx benzene-to-aniline-reaction.cdx -omol benzene-to-aniline-reaction.mol
If you downloaded the examples, you might use: babel -icdx benzene.cdx -omol benzene.mol Change into the directory containing the CDX files. With a selection of CDX files in hand, we can now convert them.
To save even more time, you can download the files I created. In the interest of time and money, I decided to go with Option (3) for now. Free to use with no installation required. It does, however, read CDX files quite nicely. Unfortunately, the 30-day free trial does not support writing CDX files. Chemdoodle is a full-featured desktop chemical drawing package.
#INTORUDCTION TO CHEMDOODLE SOFTWARE#
After taking the time to download it, the installer looked sufficiently non-standard on my Mac to make me re-think letting this software loose on my system. I'm not sure if CDX writing is supported in the evaluation version.
#INTORUDCTION TO CHEMDOODLE INSTALL#
I'm running MacPorts, so it was this simple: sudo port install openbabel If you haven't done so already, install Open Babel on your system. In this tutorial, we'll be using the command line utility to read CDX files generated by a drawing program. Open Babel is both a command line utility and a developer toolkit. Given the ubiquity of CDX files, how can we read them in an inexpensive way? This article describes one approach that uses Open Babel. It also described the important role this file format plays in the business and science of chemistry. The previous article in this series gave a brief introduction to the ChemDraw CDX file format. Reading and Translating ChemDraw CDX Files with OpenBabel T00:00:00.000Z
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