Generate Unique Smiles

Generate unique SMILES strings for the input structures for the first output, repeated structures are listed in the second output. This node also automatically extracts the smiles property for both outputs. The "Retain Duplicates" option can be unchecked to filter duplicates based on the generated SMILES strings.

Backend implementation

The command line tool uniquesmiles is used to implement this node.


Column containing input structure
Select the column in the input data table that contains the input molecules.
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

Retain duplicates
If checked (by default), all SMILES strings are calculated for the input structures and are passed to the first output. If not checked, only the inputs that have unique SMILES strings are written to the first output, the duplicates are written to the second output.
Can be 'none' (don't include stereochemistry in the SMILES), '3d' (derive stereochemistry from the 3d structure), 'annotation' (derive stereochemistry from pre-existing mmstereo properties), or 'auto' (use pre-existing mmstereo properties if present, but fall back to '3d' if not). Default is '3d'.

Input Ports

Molecules in Maestro format

Output Ports

Unique Molecules in Maestro format
Duplicate Molecules in Maestro format


Std output/error of Unique Smiles
Std output/error of Unique Smiles




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