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RDKit Chemical Transformation

RDKit Nodes for Knime version 3.8.0.v201906261723 by NIBR

Transforms a structure into another structure by applying several reactions provided as SMARTS values or Rxn Blocks. Every valid reaction found in table 2 will be applied multiple times to every input molecule in table 1. If the result does not change anymore for one reaction, the next one will be applied, and so on. Sometimes, a reaction could be applied forever. To avoid this scenario a maximal number of reaction cycles can be set. If a reaction fails in some cycle the failure will be ignored and the next reaction is being executed on the last successful product. At the very end after all reactions were applied the end product is being sanitized. If this sanitization fails for some reason the result cell will be empty.

Options

Reactant RDKit Mol column (table 1)
The input column with RDKit Molecules.
Reaction column (table 2)
The input column with the reactions (either SMARTS or Rxn).
New column name
The name of the new column, which will contain the calculation results.
Remove source column
Set to true to remove the molecule input column from the result table.
Maximal number of applied reaction cycles
To avoid eternal reaction cycles the number of cycles can be limited.

Input Ports

Table with RDKit Molecule column
Table with reactions to be applied

Output Ports

Transformed molecules

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install RDKit KNIME JUnit Test from the following update site:

KNIME 4.0
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Developers

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