0 ×

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)


To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:


You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform. Browse NodePit from within KNIME, install nodes with just one click and share your workflows with NodePit Space.


You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.