Atom Replacer

This node discards all the labels on structure's atoms and replaces them with the given label. It also discards all stereochemistry from structures.

Supported types:

The node is based on the Indigo cheminformatics toolkit.

Options

Target Column: The column that contains molecule or reaction structures.
Append Column: Appends a new structure column (with the name as specified in the text field) if checked, replaces the original column otherwise.
New atom label: The new atom label which will be put on all structure's atoms (default is "*").
Replace only highlighted atoms: With this options only highlighted atoms will be replaced.
Replace specific atom type: With this options only atoms with specified labels will be replaced. Comma-separated list of atoms is supported.
Replace attachment points: With this options only attachment points will be replaced.
Input type: Treat input as: a molecule, 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.

: Table containing molecule's or reaction's structures as strings or as Indigo objects.

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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:

v5.3

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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