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SD-to-Smiles

Schrödinger extension for KNIME Workbench version 20.3.139.202008121324 by Schrödinger

Converts each structure in the SD input into SMILES.

Backend implementation

$SCHRODINGER/utilities/canvasConvert
canvasConvert is used to convert the SD input to SMILES output.

Options

Include Input
All columns in the input table are included in the output
Produce unique, canonical SMILES strings
Produce unique, canonical SMILES strings.
Produce kekulized SMILES strings
Generate SMILES which have explicit double and single bonds. The use of a kekulized SMILES as a SMARTS will not work properly in most cases.
SD field used to overwrite the name of a molecule
Field in a SD file that can be used to overwrite the name of a molecule (usually the top line). e.g. "ID" or "library-ID" or any existing field in a SD file.
Use V3000 format
Use V3000 format

Input Ports

Icon
Molecules in SD Format

Output Ports

Icon
Molecules in Smiles format (2nd column is Molecule title)

Views

Std output/error of SD-to-Smiles
Std output/error of SD-to-Smiles

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

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

KNIME 4.2
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