RDKit Two Component Reaction

Applies a reaction to two RDKit Mol columns.

The output table contains a row for each product produced by applying the reaction to the inputs.
Each row contains the product molecule, index information, and the reactant molecules that were used.

The reaction can either be defined by a SMARTS pattern in the dialog or by providing a Rxn value at the third input port.



Reactants 1 RDKit Mol column
The column containing the first reactant molecules
Reactants 2 RDKit Mol column
The column containing the second reactant molecules
Rxn column
The column from the second table containing the Rxn
Reaction SMARTS
A reaction SMARTS describing the reaction.
For a description of the format, please have a look in The RDKit Book.


Randomize reactants
If checked, random reactants will be picked for the reactions.
Maximum number of random reactions
Specify here the maximum number of reactions to be calculated. Note: When picking a number higher than a million and switching on Matrix expansion this may cause memory issue and freeze KNIME.
Random seed (or -1 to be ignored):
Specify here a seed for the random number generator or -1 to use it without a seed.

Other Options

Uniquify products
Enable this option to filter out duplicates of products caused by symmetry in molecules. Only the first of multiple encountered products will show up in the result table.
Do matrix expansion
If checked, each reactant 1 will be combined with each reactant 2 yielding the combinatorial expansion of the reactants. If not checked, reactants 1 and 2 will be combined sequentially, with the shorter list determining the number of output rows.

Input Ports

Data with RDKit Mol column
Data with RDKit Mol column
Table with reaction values; if there are multiple rows only the first row is considered

Output Ports

Product molecules


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