File containing the molecular connection table for
the known fragment for which bioisosteres should be proposed. File formats are
discussed in the subsequent section. Only the first conformer (query
coordinates are not required) of the first molecule in the query file is
used. All other conformers and molecules in the query file are disregarded.
-db (-database)
File containing 3D conformers of all fragments to
consider in the search for bioisosteres of the query fragment. File formats
are discussed in the subsequent section. If database files without partial
charges are used, Brood will automatically generate MMFF partial charges
on each fragment. Yhis doesn not appreciably slow execution. If a database
file without 3D fragment coordinates is used, Brood will fail to process
any fragment without coordinates.
Brood:
Fragment replacement for Medicinal Chemistry
