I’ve put out an updated version (1.0.1) of the CDK descriptor calculator that now supports drag ‘n drop of the input file – just drag an appropriate file onto the UI and the input file text field should be automatically populated. In addition, all file dialogs let OS X users specify a file name manually.
The current version also supports a, frequently requested, command line batch mode. It’s a little limited compared to the GUI since you can’t specify individual descriptors, only descriptor categories (such as ‘all’, ‘topological’ etc) and the only output format is tab delimited.
$ java -jar CDKDescUI.jar -h
usage: cdkdescui [OPTIONS] inputfile
-b Batch mode
-o Output file
-t Descriptor type: all, topological, geometric, constitutional,
-v Verbose output
CDKDescUI v1.0.1 Rajarshi Guha <email@example.com>
By default, output is dumped to output.txt and all descriptors are evaluated. If errors occur for a given molecule and descriptor they are reported at the end (i.e., the program continues)