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
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).
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.
The source code can be accessed at https://anonymous:firstname.lastname@example.org/svn/nodes4knime/trunk/com.ggasoftware.indigo.
The Indigo extension is released under GPLv3.