RDKit Substructure Filter

Applies a substructure filter to an input RDKit Mol column. The substructure query is given as a single SMARTS pattern. Molecules that match the pattern appear in the first output table, molecules that don't match appear in the second output table.

Options

RDKit Mol column: The column containing the molecules
SMARTS query: A SMARTS string describing the query.
Do exact match: If this is set, only molecules containing the same number of atoms as the substructure query can match. This isn't exactly equivalent to an exact structure match, because query features in the query molecule can still be used, but it's close.
Use chirality: If this is set, information about stereochemistry will be used in the substructure search.
Match handling: Specify here, if an additional column with details about the match shall be added. It is possible to add the Atom List of the First Match or of all matches (overlaps possible).
Column name for matching atom list: The column name of the for the atom list column, if enabled.

Input Ports

: Table with RDKit molecules

Output Ports

: Molecules matching the substructure query
: 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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