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Getting Started

If you are just getting started with brood, we highly recommend you use the graphical interface. Even if you prefer to use the command-line, walking through the graphical interface one time will give you a good overview of the workflow involved in running BROOD.

Command Line Interface

Required Parameters

-queryMolecule (-queryMol)

Molecular file containing the primary molecule of interest. This parameter was formerly known as the -buildMolecule. This is the molecule for which you would like to generate analogs. If the query molecule has a query fragment already specified from the graphical interface, this is the only necessary parameter.

Optional Parameters

Input Parameters

-db (-database)

Specified the directory containing the BROOD database files. Additional details on the files contained in the directory can be found in the section on the Fragment Database as well as in the section on Database Preparation