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Canonical SMILES

Indigo extensions for KNIME Workbench version 2.0.0.v201603210922 by EPAM Systems, Inc.

This node takes a table containing a column with molecules or reactions as a target and append new column with these objects in canonical SMILES format (string representation).

Supported types:

  • Molecule: String, SDF, Smiles, CML, Mol, InChI
  • Reaction: String, RXN, Smiles, CML

The node is based on the Indigo cheminformatics toolkit.

Options

Target column
The column that contains molecules or reactions.
Append column
Name for the new column that contains the molecules/reactions in canonical SMILES format.
Input type
Treat input as: a molecule, a reaction.
Treat X as pseudoatom
Treat the "X" atoms in Molfiles as pseudoatoms, not as "any halogen" query atoms.
Ignore stereochemistry errors
Ignore incorrectly specified stereochemistry on input structures, rather than sending the structures with stereochemistry errors to the "invalid molecules" table.

Input Ports

Table containing molecules or reactions.

Output Ports

The same as input, but with a new string column containing canonical SMILES representations.

Best Friends (Incoming)

Best Friends (Outgoing)

Update Site

To use this node in KNIME, install Indigo extensions for KNIME Workbench from the following update site:

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