Indigo is a universal cheminformatics toolkit for working with molecules and reactions.
It offers a broad chemistry-focused SDK for tasks such as molecular rendering, canonicalization, exact and substructure matching, fingerprinting, similarity search, and scaffold-related analysis, and it includes bindings for environments such as Python, Java, .NET, R, and WebAssembly.
This is free and open source software.
Key Features
- Supports common chemistry file and query formats including Molfile/Rxnfile v2000 and v3000, SDF, RDF, CML, SMILES, and SMARTS.
- Provides molecule and reaction rendering, including SVG output and automatic layout for SMILES-based structures.
- Offers exact matching, substructure matching, SMARTS matching, and handling of tautomers and resonance structures.
- Computes canonical isomeric SMILES, molecular fingerprints, molecular similarity, molecular weight, and molecular formulae.
- Includes tools for R-Group deconvolution, scaffold detection, and maximum common substructure analysis.
- Ships with command-line utilities such as indigo-depict, indigo-cano, and indigo-deco.
- Supports multiple language bindings and can be integrated into applications through its documented API.
Website: github.com/epam/Indigo
Support:
Developer: EPAM Systems
License: Apache License 2.0
Indigo is written in C++. Learn C++ with our recommended free books and free tutorials.
Related Software
| Chemistry Tools | |
|---|---|
| GROMACS | Versatile package to perform molecular dynamics |
| tomviz | Process, visualize, and analyze 3D tomographic data |
| Psi4 | Ab initio quantum chemistry software |
| NWChem | Ab initio computational chemistry software package |
| PyMOL | OpenGL molecular graphics system written in Python |
| LAMMPS | Classical molecular dynamics simulator |
| CP2K | Atomistic simulations of solid state, liquid, molecular and biological systems |
| GAMESS | General ab initio quantum chemistry package |
| Avogadro | Advanced molecular editor |
| OpenMM | High-performance toolkit for molecular simulation |
| Gabedit | Graphical user interface to computational chemistry packages |
| Open Babel | Converts and manipulates chemical data files |
| Jmol | Viewer for three-dimensional chemical structures |
| Kalzium | Full-featured chemistry application for KDE 5 |
| XDrawChem | 2D editor for chemical structures and reactions |
| Cantera | Chemical kinetics, thermodynamics, and transport tool suite |
| Orac | OpenMP/MPI molecular dynamics engine to simulate solvated biomolecules |
| MPQC | Computes the properties of molecules, ab initio |
| JChemPaint | Chemical 2D structure editor |
| BKChem | 2D molecule editor written in Python |
| MDynaMix | General purpose molecular dynamics |
| ChemCanvas | 2D chemical drawing tool |
| MoleQueue | Abstract, manage, and coordinate the execution of tasks |
Read our verdict in the software roundup.
 Explore our comprehensive directory of recommended free and open source software. Our carefully curated collection spans every major software category.This directory is part of our ongoing series of informative articles for Linux enthusiasts. It features hundreds of detailed reviews, along with open source alternatives to proprietary solutions from major corporations such as Google, Microsoft, Apple, Adobe, IBM, Cisco, Oracle, and Autodesk. You’ll also find interesting projects to try, hardware coverage, free programming books and tutorials, and much more. Discovered a useful open source Linux program that we haven’t covered yet? Let us know by completing this form. |