Substructure Matcher

This node accepts a table with structures (supports reactions and molecules) and a table with query structures, and divides the first table into three sets: one with all rows that contain the specified query structures as a substructure, the other with all structures that do not contain it, the last one gathers all the rows with invalid data.

Supported types:

Molecule: String, SDF, Smiles, CML, Mol, InChI
Reaction: String, RXN, SMILES

The node is based on the Indigo cheminformatics toolkit.

Options

Target column: The column that contains molecule or reaction structures.
Query structures column: The column that contains the query structure.
Substructure settings: Substructure settings that needs to be satisfied for all query structures or at least for a specified number of them.
Append queries row ID column: The column that contains all the meeting the conditions rows.
Append match count column: The column that contains the appropriate molecules amount.
Input type: Treat input as: a molecule, as a reaction.
Treat X as pseudoatom: Treat the "X" atoms in Molfiles as pseudoatoms, not as "any halogen" query atoms.
Ignore stereochemistry errors: Ignore incorrectly specified stereochemistry on input structures, rather than sending the structures with stereochemistry errors to the "invalid molecules" table.
Treat input query string as SMARTS: Treat input string to create a query as SMARTS.

Input Ports

: Table containing molecules or reactions.
: Table containing the query structure.

Output Ports

: Rows with matched structures.
: Rows with unmatched structures.

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Installation

To use this node in KNIME, install the extension Indigo KNIME integration 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: EPAM Systems, Inc.

Plugin version: 2.1.0.v202406240930

On NodePit since: 2024-07-11

Last update: 2024-11-15

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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