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Atom Signatures

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

This node generates atom signatures describing the neighbourhood of carbon or hydrogen atoms in CDK molecules. There are two types of signatures available, HOSE codes or atom signatures. If the minimum and maximum height of the signature are not specified, the signatures will be calculated for height 6. If the signature of a specified height cannot be calculated, the signature with the maximum possible height for that atom will be reported. The first column of the output table contains the atom IDs. To visualise the atom IDs in the molecule cell go to "File > Preferences." In the drop-down list go to "KNIME > Chemistry > CDK" and then select an option to "show atom numbers for" the atoms you are interested in. In case you change the "Atom number type" after running the node, the atom IDs will only be updated upon reset of the node.


Column with molecules
Select the column containing the molecular structure
Signature type
Chose the type of signature to be generated
Atom of interest
Chose for which type of atom is the signature going to be generated
Set signature height
Customise the minimum and maximum height of the signature

Input Ports

Table containing molecular structures

Output Ports

As input but with new rows for each atom in the CDK molecule for which the signatures were calculated

Best Friends (Incoming)

Best Friends (Outgoing)


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


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

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