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

: Table containing molecules or query molecules

Output Ports

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

Popular Predecessors

Popular Successors

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RDKit Canon SMILES8 %
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RDKit Two Component Reaction5 %
Reaction Automapper4 %
Reaction Based Enumeration4 %
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N_arylation_49b1 %
Atom Replacer1 %
Combinatorial Reaction Enumeration (beta)1 %
Highlighter1 %
Indigo Fingerprint1 %
MCS Scaffold Finder1 %
SMILES Writer1 %
Reaction Fingerprint1 %
~~Joiner~~1 %
Column Filter (legacy)1 %
Reaction Decoder Mapper1 %
Rxn to RInChI1 %
RInchI To Rxn1 %

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Workflows

USPTO_Yield_Conversion_Lowe_SchwallerKNIME Hub

Developers

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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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