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R-Group Decomposer

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

This node performs R-Group decomposition of a given collection of structures, using a scaffold that is common for these structures.

Supported types:

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

The node is based on the Indigo cheminformatics toolkit.


Target molecule column
Column that contains molecule structures.
Scaffold column
Column that contains the scaffold (query molecule).
R-Group column prefix
Each of the new R-group columns will be named with this prefix + number (1,2,3,..).
Aromatize input molecules.
Input type
Treat input as: a molecule
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.
Treat input scaffold string as SMARTS
Treat input string to create a query as SMARTS.

Input Ports

Table containing molecule structures.
Table containing the scaffold (query molecule).

Output Ports

Same as input, with R-Group columns.
Same as input scaffold, but with marked R-sites.

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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