Reaction Builder

This node combines the input molecules and creates reactions from given reactants, products and catalysts columns. Defines the output column type automatically.

Supported types:

  • Molecule: String, SDF, Smiles, CML, Mol, InChI
  • Query molecule: String, Smiles, Mol, SMARTS, SDF

The node is based on the Indigo cheminformatics toolkit.

Options

Add reactants
Flag (append or skip) and column selection for molecule reactants.
Add products
Flag (append or skip) and column selection for molecule products.
Add catalysts
Flag (append or skip) and column selection for molecule catalysts.
Result reaction column name
Column name for the output molecules
Input type
Treat input as a reaction or as a query reaction
Output type
Result column type.
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 String as SMARTS
Treat string input for molecule as SMARTS

Input Ports

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Table containing molecules or query molecules

Output Ports

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The same as input, plus the column with the created reactions
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The same as input, contains invalid data (unconvertible to Indigo)

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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: 2024-11-21
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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