FragGenie

FragGenie provides a simple codebase and application for generating a list of theoretical chemical fragments which can be used to generate theoretical mass spectra of chemical compounds.

FragGenie can be accessed directly through the underlying Java code or run from the command line.

An example script for running the application is provided (test.sh) along with a simple example input file test_input.csv.

The test.sh example script runs the more general fragment.sh script with the following parameters:

./fragment.sh test_input.csv test_output.csv smiles 3 80.0 256 1000000000 true METFRAG_MZ

where:

• test_input.csv is the input file name.
• test_output.csv is the output file name.
• smiles is the header name of the column in the input csv file containing SMILES string representations of the chemicals of interest.
• 3 is the fragmentation recursion depth.
• 80.0 is the minimum fragment mass to return.
• 256 is the maximum length SMILES string to consider.
• 1000000000 is the maximum number of SMILES strings to analyse.
• true is a flag to indicate whether to run the script in silent mode.
• METFRAG_MZ specifies that masses (mz) values should be generated. Other options are METFRAG_FORMULAE which generates fragment formulae and METFRAG_BROKEN_BONDS which generates a list of bonds broken for each fragment. Any combination of these three parameters may be specified.