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Reaction Based Enumeration

Schrödinger extension for KNIME Workbench version by Schrödinger

Set up the reaction or reaction sequence. Three methods are available for creating the reaction sequence: PathFinder analysis, which decomposes a structure by looking for reactions to synthesize it; choice of reactions from a library of reactions; and sketching the reaction sequence in the Sketcher.

Backend implementation

$SCHRODINGER/run combinatorial_synthesis.py


Column containing input
Select the column containing input structures
Output Column Structure
Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaced within Input columns - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

On clicking "Settings" button, this node brings up the "Reaction-Based Enumeration" python panel for configuration.
Parameter flow variables
Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Flow variable prefix keyword: ReactEnum
Note: To specify an option as flow variable, the flow variable name should be like:
keyword-option_name for single-dash option
keyword--option_name for double-dash option

To add a new option with value, specify the option_name and the corresponding value through flow variable.

To add a new option without value, specify the option_name and the value as _on_ through flow variable.

To override an existing option's value in the command line, just specify the option_name and the new value through the flow variable.

To remove an existing option without a value, specify the option_name and the value as _off_ through the flow variable.

To remove an existing option with a value, specify the option_name and the value as _rm_ through the flow variable.

Input Ports

Input in Maestro format

Output Ports

Output in Maestro format


Log output
Log output

Best Friends (Incoming)

Best Friends (Outgoing)



To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:


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