Indigo Nodes for KNIME

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About the nodes

These nodes provide functionality for organic structures, allowing users to create high-performance workflows for completing standard cheminformatics tasks. The nodes are based on the Indigo toolkit. The functionality provided in the initial release is the following:

  • Conversion from/to SDF(Mol), SMILES, and CML formats
  • Detection of structure drawing mistakes (valence, stereochemistry)
  • High-quality depiction of structures
  • Generation of 2D coordinates (keeping the stereochemistry information from both 0D and 3D structures)
  • Conversion to aromatic and Kekule form
  • Addition and removal of explicit hydrogens
  • Substructure and SMARTS matcher (also matching tautomers and resonance structures)
  • Highlighting and alignment of matched structures by the given substructure
  • Generation of Indigo fingerprints
  • Fingerprint similarity computation
  • Calculation of molecule properties: MF, MW, H count, and 20 others
  • R-Group decomposition (automatic detection of scaffold possible)
  • Murcko scaffold computation
  • Separation of components
  • Discarding isotopes, stereochemistry, and other chemical features

More nodes are to be added in the future. If you have any suggestions for new nodes or bug-reports for the existing ones, please let us know either on the KNIME Indigo forum or in our Google groups.


Some example workflows can be found on the KNIME Public server that is accessible from within each KNIME installation (look for 099_Community/07_Indigo).

About Indigo

Indigo is a universal organic chemistry toolkit developed by GGA Software Services LLC. It contains first-class tools for end users, as well as a documented API for developers. Indigo is completely free and open-source (GPLv3), while also available on a commercial basis.

Since the core part of Indigo is written in modern C++ with no external dependencies except the ubiquitous zlib and libcairo, the toolkit provides outstanding performance and excellent portability. Indigo provides wrappers for C, .NET, and Python, and also a Java wrapper which is used in the KNIME nodes.

Indigo API is highly configurable and extensible. You can write C/C++/C#/Java/Python plugins for it and distribute them independently.

Indigo has got support from the cheminformatics community. Any question or comment you have, you can always post it publicly and get a timely reply from the developers' team.

Source Code

The source code can be accessed at


The Indigo extension is released under GPLv3.