Brood includes a default database of approximately six million molecular fragments that are carefully selected to be medicinally relevant. While this database is quite thorough, we recognize that some users may want to supplement the default database with fragments generated from their own proprietary molecule collections. To facilitate this process, the Brood distribution includes two programs, CHOMP and BroodMerge.

CHOMP allows users to fragment molecules, filter the fragments, generate 3D conformations, organize and index the fragments for rapid searching, and write a Brood database. This process can be carried out from start to finish using a Brood license and does not require access to OMEGA, FILTER, MolProp, or OEChem licenses. BroodMerge, a utility that allows users to merge their own corporate databases with the OpenEye default database, will be covered in detail in the following chapter.

At its simplest, CHOMP takes molecules as input and fragments them to generate Brood databases: simply specify the molecules you want to use to generate fragments using the -in flag and the output database you want to create with the -out flag.

By default, CHOMP assumes you want to create a database from your proprietary collection in order to augment the default database. CHOMP does not automatically remove any duplicates from the generated database. To remove duplicates, you can specify the database of fragments from which you would like to eliminate duplicates with the -userUnique flag.

The output from CHOMP will be a directory filled with a Brood database. To search the database with Brood, specify the directory name with Brood’s brood -db flag.

While the basic use of CHOMP is straightforward, there are many options for controlling the CHOMP process and filtering the fragments.


CHOMP input molecules are pKa normalized, i.e., set to pH=7.4 ionization state.