Mass Frontier supports batch processing for fragment prediction. Fragments without mechanisms can be generated for more than one input structure using *.sdf files. For every input structure stored in a *.sdf file, a set of fragments will be generated and stored in a separate *.sdf file. So for a single *.sdf file with 10 input structures, Mass Frontier will generate 10 new *.sdf fragments files.

The *.sdf file format, defined by MDL (Molecular Design Ltd), is an ASCII file format that can contain multiple compounds in MDL CTfile format.

To generate fragments in batch processing mode, choose the Tools | Batch Processing menu item and then select the particular *.sdf file with input structures.