RDKit Molecule Substructure Filter

Applies a substructure filter to an input RDKit Mol column. The patterns are given as SMARTS, SMILES, SDF or RDKit molecules in the second input table. You can choose either a minimum number of patterns to match or to require that all match.

Options

RDKit Mol column
Select the column from the first input table that contains the RDKit molecules
Query Mol column
Select the column from the second input table that contains the query molecules. Acceptable types are SMARTS, SMILES, SDF and RDKit Mol.
Use chirality
If this is set, information about stereochemistry will be used in the substructure search.
Use enhanced stereochemistry
If this is set, information about enhanced stereochemistry will be used in the substructure search.
Matches
Select the minimum number of patterns that must match for each molecule so that it is included in the first output table
New column name for matching substructures
Enter here the name of the new column that will contain a list of all matching substructure row indices

Advanced

Fingerprint screening threshold
Substructure search performance can be improved using fingerprints. This makes sense when there are many different query molecules and a lot of input molecules. In this case the node can pre-calculate fingerprints once for all input and query molecules and do some pre-screening for substructure matching. The fingerprint screening threshold value defines the number of query molecules (table 2) that must be present in order to enable fingerprint calculation and pre-screening. Set it to 0 to disable fingerprint screening completely for this node. Set it to -1 to always use the RDKit Nodes default behavior (the standard setting).
Use row keys as substructure match information
The column for matching substructure indices contained (for historic reasons) the row index, which turned out not to be too useful. Click this flag to use row keys instead, which is today the default for new nodes.

Input Ports

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Table with RDKit molecules
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Table with SMARTS, SMILES, SDF or RDKit Mol molecules to use as queries

Output Ports

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Molecules matching the substructure query
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Molecules not matching the substructure query

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Installation

To use this node in KNIME, install the extension RDKit Nodes Tests Feature from the below update site following our NodePit Product and Node Installation Guide:

v5.3

A zipped version of the software site can be downloaded here.

Plugin provider: Novartis
Plugin version: 5.0.0.v202407311957
On NodePit since: 2024-09-28
Last update: 2024-11-21
KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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