This script will break up a set of input molecules into fragments based on some simple rules, similar to those described in the original RECAP paper.

1. Never cut a hydrogen-connecting bond.
2. Never cut a bond connecting a ring-carbon and a hetero atom (optional).
3. Never cut ring bonds.
4. Refuse a fragment if it is in the SMARTS file specified by -smarts.
5. Refuse a fragment if the number of open bonds exceeds the specified limit.
6. Refuse a fragment if the number of atoms is less than -number. 

Backend implementation

fragment_molecule.py
The script fragment_molecule.py is used to implement this node.