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RDKit Fingerprint

StreamableRDKit Nodes for Knime version 4.0.1.v202006261025 by NIBR

Generates hashed bit-based fingerprints for an input RDKit Mol column and appends them to the table. Several fingerprint types are available. Not all settings are used for each type. Settings that are not supported by a fingerprint type will be disabled/hidden and will have no effect. The settings a fingerprint gets generated with are made available as column properties and can be visualized with the RDKit Interactive View Node.


Fingerprint type
The type of fingerprint to generate. Choices are:
  • Morgan: Circular fingerprint based on the Morgan algorithm and connectivity invariants (ECFP-like)
  • FeatMorgan: Circular fingerprint based on the Morgan algorithm and feature invariants (FCFP-like)
  • AtomPair: Atom-pair fingerprint
  • Torsion: Topological-torsion fingerprint
  • RDKit: Daylight-like topological fingerprint
  • Avalon: Fingerprint from the Avalon toolkit (http://sourceforge.net/p/avalontoolkit/)
  • Layered: An experimental substructure-matching fingerprint (see LayerFlags defintion below)
  • MACCS: RDKit implementation of the 166 public MACCS keys
  • Pattern: Substructure screening fingerprint based on small number of very generic SMARTS patterns
More details about different RDKit fingerprint implementations can be found here: https://www.rdkit.org/docs/RDKit_Book.html#additional-information-about-the-fingerprints
RDKit Mol column
The column containing reactant molecules
New Column Name
Name of the fingerprint column in the output table.
Remove source column
Toggles removal of the input RDKit Mol column in the output table.


Fingerprint Settings - Num Bits
Number of bits in the fingerprint.
Fingerprint Settings - Path length
Path length to be used (Torsion only).
Fingerprint Settings - Radius
The radius of the atomic environments considered.
Fingerprint Settings - LayerFlags
Which atomic layers should be included. This value is the total of the following layer flag values: 0x01 pure topology, 0x02 bond order, 0x04 atom types, 0x08 presence of rings, 0x10 ring sizes, 0x20 aromaticity. The default value of 7 (0x01 pure topology + 0x02 bond order + 0x04 atom types) allows classic substructure searches.
Fingerprint Settings - Min Path Length
Minimum length (in bonds) of the paths to be considered.
Fingerprint Settings - Max Path Length
Maximum length (in bonds) of the paths to be considered.
Rooted Fingerprints - Create rooted fingerprint
Check this option to create a rooted fingerprint based on an atom list. This option is not applicable to all fingerprint types.
Rooted Fingerprints - Atom list column for rooted fingerprints
The column containing the atom lists that are necessary when calculating rooted fingerprints. Instead of a list it is also possible to provide an integer column with a single atom index.
Rooted Fingerprints - Include atoms
Check this option to include the atoms when calculating rooted fingerprints or uncheck to exclude them.

Input Ports

Data with RDKit Mol column

Output Ports

Data with fingerprint column

Best Friends (Incoming)

Best Friends (Outgoing)



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