A simple Python script that uses the BRICS algorithm from the RDKit library to generate fragments from a chemical compound in SMILES format.

The generated fragments are stored in tri-dimensional SDF, ready to be incorporated into further pipelines, such as molecular docking and/or molecular dynamics experiments.

The program also generates partial reconstructions of the generated fragments and stores them in the same manner.

Finally, chemical representations of the original compound together with its fragments are generated in PNG format.

Simply

./BRICS.py your_compound.smiles

A SMILES file for aspirin, for example, would contain just the SMILES entry in one row:

CC(=O)OC1=CC=CC=C1C(=O)O

which is all the script needs.

The following are the generated fragments:

And the following are the reconstructed fragments: