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Fragments from Molecules

Schrödinger extension for KNIME Workbench version by Schrödinger

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

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


Maximum number of open bonds allowed in a fragment
Remove duplicate fragments
Keep only one copy of identical fragment but with different coordinates.
Cut bonds between ring-carbon and hetero atoms
Allows cutting of bonds between ring-carbon and hetero atoms.

Input Ports

Input data table containing molecules in Maestro format

Output Ports

Molecules in Maestro format


Std output/error of fragment_molecule.py
Std output/error of fragment_molecule.py

Best Friends (Incoming)

Best Friends (Outgoing)


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