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Feature Remover

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

This nodes removes selected features from the given structures

Supported types:

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

The node is based on the Indigo cheminformatics toolkit.


Target Column
The column that contains molecule or reaction structures.
Append Column
Appends a new structure column (with the name as specified in the text field) if checked, replaces the original column otherwise.
Discard the isotopes in the structure.
Remove information about chiral centers.
Remove information about cis-trans double bonds.
Reset the highlighting on the structure's atoms and bonds.
Remove the pseudoatoms, placing implicit hydrogens instead.
Remove the R-sites, placing implicit hydrogens instead.
Attachment points
Remove the R-group fragment's attachment points, placing implicit hydrogens instead.
Repeating units
Make the polymer non-polymer by removing its brackets.
Data S-groups
Remove attached and detached data sgroups.
Minor components
Remove all the minor components, leaving the largest one.

Input Ports

Table containing molecule or reaction structures.

Output Ports

The same as input, but with selected features removed.

Best Friends (Incoming)

Best Friends (Outgoing)



To use this node in KNIME, install Indigo KNIME integration from the following update site:


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

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