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Generate Unique Smiles

Schrödinger extension for KNIME Workbench version 19.4.12.201912161038 by Schrödinger

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

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

Options

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.
Stereochemistry
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

Views

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

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.1
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Developers

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