We (SciTouch LLC) recently published our cheminformatics
toolkit called Indigo. It consists of five software products:
Bingo: Cartridge for Oracle database supporting a wide range of searches in
molecule and reaction databases.
Dingo: Molecule and reaction rendering library with cairo backend
Cano: Canonical SMILES computation library
Deco: R-Group deconvolution and scaffold detection library
Nucleo: Nucleotide chain handling
Our site: http://opensource.scitouch.net/indigo/
It is all free and open-source and licensed under the terms
of GPL v3. All was written from scratch in C++, while some
components also are presented with Java and C# libraries
and command-line utilities.
The source code provided contains original implementations
of many algorithms:
- spanning tree building
- biconnected components extraction
- substructure matching (subgraph isomorphism)
- affine transformation matching (Kabsch Alignment)
- chemical conformation matching
- 3D constraints matching
- cycle enumeration, aromaticity perception
- aromaticity matching and de-aromatizaion
- tautomer (sub)structure matching
- resonance (sub)structure matching (pi-systems matching)
- canonical SMILES saver (with stereochemistry)
- 2D layout (conversion from SMILES to well-drawn Molfile)
- maximum common subgraph (MCS) of two structures
- exact MCS of an arbitrary amount of structures
- enumeration of sub-trees
- reaction substructure matcher
- reaction atom-to-atom mapping (AAM)
- molecule and reaction fingerprinting
The supported formats are: Molfiles 2000/3000, Rxnfiles,
SMILES, and Reaction SMILES. Some Chemaxon extensions
for SMILES are supported.
We are very interested in any feedback, including
critics, suggestions of further development, comparison
with existing tools, and bug reports. We will be very
pleased with any possibility of developing the SMILES
format. For near future, we are planning InChI support
and more Java/Ruby/Python interfaces for our components.
We have prepared 3 news-groups for discussing Indigo.
You can see the links on the main page.
With best regards,
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