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CDK to Molecule

KNIME CDK Integration version 1.5.700.v202006231106 by KNIME GmbH, Konstanz and EMBL-EBI, Cambridge

Converts the CDK molecules in one of the input table's columns into various string representations (SDF, Mol2, Smiles, CML).

This node uses CDK classes to parse and display structures.

Options

CDK Column: The column that contains the CDK molecules.
Replace Column: Select this to replace the CDK column with the column containing the converted string representations. Otherwise a new column will be appended.
New column name: Enter the name of the new column here if the original column is not replaced (see option above).
Destination format: Select the destination format here.

Input Ports

: Table containing CDK molecules

Output Ports

: Table with the molecules' converted string representations

Best Friends (Incoming)

Best Friends (Outgoing)

SDF Writer (21 %)
RDKit From Molecule (9 %)
~~CSV Writer~~ (5 %) StreamableDeprecated
Molecule to CDK (4 %)
OpenBabel (4 %)
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Workflows

_01_ChemicalLibraryEnumeration (KNIME Hub)
Convert XLS to SDF (KNIME Hub)
KNIME_project14 (KNIME Hub)

Installation

To use this node in KNIME, install KNIME-CDK from the following update site:

KNIME 4.3

A zipped version of the software site can be downloaded here.

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Developers

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