Molecule Transformation (beta)

This node transforms molecules according to reaction-base set of rules. See the examples for more details.

Supported types:

The node is based on the Indigo cheminformatics toolkit.

Options

Target molecule column: The column that contains molecule structures.
Query Reaction column: The column that contains Indigo query reactions.
Append Column: Appends a new molecule column (with the name as specified in the text field) if checked, replaces the original column otherwise.
Molecule type: Treat input as: a molecule.
Reaction type: Treat input as a query 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 query reaction as SMARTS: Treat input strings for reaction (port 2) as SMARTS.

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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:

v5.2

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

Plugin provider: EPAM Systems, Inc.

Plugin version: 2.1.0.v202404021236

On NodePit since: 2023-12-06

Last update: 2024-04-25

KNIME versions: 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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