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Indigo Toolkit providing enhanced chemistry SDK

Q: Where can I download the installation package?

Please look at the [Downloads](https://lifescience.opensource.epam.com/download/indigo.html) page for the installation package suitable for your system.

Q: Where can I ask more questions about the solution?

Please submit your inquiry using Solution Request form and you will be contacted.

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Indigo

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Solution Overview

Indigo is a universal molecular lab software that can be used for molecular fingerprinting, substructure search and molecular visualization. Also capable of performing a molecular similarity search, it is 100% open source and provides enhanced stereochemistry support for end users, as well as a documented API for developers. Indigo is based on a cheminformatics library that incorporates a number of unique algorithms developed by EPAM, as well as some standard algorithms well-known in the cheminformatics world. Since the core part of Indigo is written in modern C++ with no third-party code or dependencies except the ubiquitous zlib and libcairo, the toolkit provides outstanding performance and excellent portability. Indigo is used by many corporations and institutions. This includes some Indigo-based commercial tools developed exclusively for our clients. Also, an open source chemical search engine — Bingo — is developed on top of the Indigo library.

Benefits

Portability

Indigo supports Linux, Windows and Mac OS X operating systems

Dual License

Product has open source and commercial availability

Cheminformatics SDK

Extensible API can be used by end users and developers

Molecular Search

Enhanced chemistry structure search and similarity search

Performance

Written in modern C++. Includes unique algorithms for solving problems

Molecular Toolkit

Different molecular features, fingerprinting & rendering

Features

Input formats support: Molfiles/Rxnfiles v2000 and v3000, SDF, RDF, CML, SMILES, SMARTS
Portability: Pre-built binary packages are provided for Linux, Windows and for Mac OS X systems
Molecule and reaction rendering, best picture quality among all available products and easy SVG support
Automatic layout for SMILES-represented molecules and reactions
Canonical (isomeric) SMILES computation
Exact matching, substructure matching and SMARTS matching
Matching of tautomers and resonance structures
Molecule fingerprinting & molecule similarity computation
Fast enumeration of SSSR rings, subtrees & edge subgraphs
Molecular weight & molecular formula computation
R-Group deconvolution and scaffold detection
Pioneer work in computing the exact maximum common substructure for an arbitrary amount of input structures
Combinatorial chemistry
Plugins support in the API — as a reference, please see the Renderer plugin distributed together with the Indigo API
Support for PNG/SVG export of expanded monomers

Additional Information

Version

Tech Requirements

Integrates with

Documentation

Links

Work Better Together

Visualize the chemistry data and edit/query structures with Ketcher and Bingo.

REQUEST PACKAGE

Indigo

Toolkit providing enhanced chemistry SDK

Ketcher

Web-based chemical structure drawing software

Bingo

Integrates chemistry into databases

Questions & Answers

Where can I ask more questions about the solution?

Posted on March 1, 2020 by Julius Stokes

Where can I download the installation package?

Posted on February 2, 2020 by Mahdi Pritchard

Can I use Indigo in my commercial product?

Posted on January 11, 2020 by Kay Burt

Indigo version 1.0.0 was released under GNU General Public License v3.0

Indigo version 1.4.0 was re-licensed under Apache License, Version 2.

The Apache License v2.0 allows Indigo to be used as a component in proprietary software products.

If you need support licensing for the product, or there are any additional features required, EPAM can provide a standard support contract. Price depends on the support requirements and will be defined within an SOW document.

Posted on January 13, 2020 by SolutionsHub Support

Integrates with

Pipeline Pilot

KNIME

Tech Requirements

Windows 7+, Linux, Max OS
Java 1.8+, Python 2.7+, .NET

Version

indigo-1.46.0

Updated on August 24, 2026

Documentation

Indigo Product Overview.pdf

Links

Link to the Solution's site

industries

Life Sciences

license type

Open Source

type

Product

Version History

indigo-1.46.0

Updated on August 24, 2026

Release Notes

New features

#3604 - Add api methods to interact with atoms and bonds in s-groups

Bugfixes and improvements

#3691 - PtrArray hybrid contract implementation
#3661 - BILN import/export special cases
#3299 - System should set Implicit H value for atoms if it comes without hydrogens from CDXML
Port stripSalt and checkSalt from Python to Java API
#3703 - objarray to ptrarray
#3754 - Helm import is case sensitive
#3778 - Update the isoelectric point calculation for peptides

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.45.0-rc.1...indigo-1.46.0

v.1.43.0

Updated on May 13, 2026

Release Notes

Indigo 1.43.0

Release Notes:

Features

#3526 - Update SDF and KET format to include information about preset phosphate position
#3525 - Expose ability to calculate fully expanded large molecule into chemical structures
#3562 – Add api to iterate through attachments points of S-groups of 'SUP' type
#3554 - Implement multi-threading in Bingo NoSQL substructure search

Bugfixes and improvements

#3307 - If the selected group is forming an n-agon with 6 or more than 6 points, then the bases should be located inside of the circular structure
#3308 - If the selected group is forming an n-agon with 12 or more than 12 points, the bases should be located inside of the circular structure
#3304, #3305 Fixed monomer of cycle on layout should be top left monomer
#3496 - Fixing the issue during reading of the molecule data and parse it.
#3301 - System provides invalid SDF content (missing semicolon) on mono…
#3449 - Bond length become wrong after Arrange as a Ring option applied
#3329 - Sequential application of “Create cyclic structure” to different segments of one chain leads to overlapping and distorted topology
#3584 - Deadlock in multithread subsearch.
#3622 - Fix Bingo-nosql matcher sub tau speed issue
#3268 - Cyclic layout issues
#3353 - System ignores Implicit H count value in export to SVG/PNG
#3303 - Wrong monomer re-layout

Full Changelog: indigo-1.42.0-rc.1...indigo-1.43.0

Indigo 1.42.0

Release notes:

Features

#3461 - Export/import multi-tailed arrows to/from CDX/CDXML
Enable tau fingerprints in Bingo NoSQL

Bugfixes and improvements

#3528 - Bingo NoSQL database format different in Windows and Linux

Full Changelog: indigo-1.41.0-rc.1...indigo-1.42.0

Indigo 1.41.0

Release notes:

Features

Run sonarqube only by request

Bugfixes and improvements

#3437 - Turn off specific indigo wrappers using cmake
#3352 - System should count O and U peptides in Amino Acid natural analog grid
#3465 - Substructure match: add parameter to limit tautomer chain search only by matched struct
#3446 - Export to CDXML replaces multi-line text labels to many one-line text labels stacked one over another

Full Changelog: indigo-1.40.0-rc.1...indigo-1.41.0

v.1.40.0

Updated on February 23, 2026

Release Notes

Features

#3375 - Improve the alignment logic

Bugfixes and improvements

#3360 - CIP labels aren't added correctly when loading from a cdxml file with no CIP labels
#3362 - 13C isotope not recognised in molecular formula when loading from cdxml

v.1.39.0

Updated on February 20, 2026

Release Notes

Features

#3211 - Introducing alignment of sense and antisense chains
#3273 - Circular structures improvement - formation of fused rings
#3250 - Alignment of sense and antisense strings in AxoLabs format
#3337 - Bingo NoSQL tautomer substructure search support

Bugfixes and improvements

#3282 - Can't use indigo as a git submodule
#3297 - Random '$$$$V2.0' empty return from conversion to HELM
#3306 - Saving to HELM doesn't work for cycled structures consist of nucleosides
#3177 - System can't calculate Calculate properties window values for Amino acids with query bonds
#3299 - System should set Implicit H value for atoms if the comes without hydrogens from CDXML
#3343 - Export to Mol v3000 works wrong for stereo bonds between monomers
#3369 - Bingo NoSQL treat empty flags as NONE instead of ALL
#3363 - The layout algorithm returns different coordinates on macOS for some tests
#3342 - Export ot SVG and PNG doesn't work for stereo bond between monomers, system throws an error: pool: access to unused element
#3344 - Export to SVG/PNG works wrong for stereo bonds between monomers

v.1.38.0

Updated on February 20, 2026

Release Notes

New features

#3227 - Introducing Copolymer S-group type
#3272 - SDF files for library/monomer information
#3196 - Support formation of circular structures in flex mode - PoC

Bugfixes and improvements

#3239 - System doesn't save monomer expand/collapse state in Mol v3000 for user created monomers (they always come in collapsed state)
#3261 - indigoSaveCdxml doesn't support reaction molecules
#3269 - System ignored HELM alias for bases on monomer load to Library
#3256 - Metals loaded from cdxml are always represented with hydrogens
#3237 - Stackoverflow iterate components
#3277 - System adds broken Preset to the library (part2)
#3278 - System doesn't allow to add monomers with the same structure but different names (part2)
#3286 - CHEMBUGS-64 Automapping fails to guard against contradictory reaction center annotation, corrupts future structure export data
#3297 - Random '$$$$V2.0' empty return from conversion to HELM
#3293 - Library update works wrong if we use empty SDF file
#3292 - Save to SDF v2000 works wrong for created monomers
#3291 - Layout works wrong
#3267 - Export to sugar monomer to AxoLabs error message is wrong
#3265 - System should be able to load unknown monomer on any position
#3338 - System losts stereo bonds on monomer load to Library
#3247 - SVG/PNG: Export of any atom with Isotope (atomic mass) value set doesn't work

v.1.37.0

Updated on February 19, 2026

Release Notes

New features

#3161 - SDF files for library/monomer information
#3152 - AxoLabs format support
#3146 - IDT export: use hardcorded nucleotides instead of standard ones

Bugfixes and improvements

#2922 - Performing an exact match search results in PostgreSQL termination
#3193 - Missing valence of 0 in mol file
#3016 - Valence 0 is not taken into account by Molfile export via API
#3079 - Export to SVG/PNG doesn't work for molecules with "star" atom. System throws an error: molecule render internal: Query atom type 4 not supported
#3141 - One time exception on export to RXN: molecule: casting to molecule is invalid
#3178 - Unable to copy user created monomer, exception: Convert error! molecule: casting to molecule is invalid
#3070 - Saving to RXN v2000 encloses Polymer labels into double quotes
#3206 - Export (or import) to (from) Mol v3000 works wrong for CHEM monomers
#3200 - System allows to export not a purely amino acid to Sequence (3-letter code)
#3210 - System loads Sequence with numbers in middle
#3102 - System can't load sugar-phosphate preset from HELM if sugar provided with HELMAlias name
#3220 - System ignores implicitly provided file format on load content thru Paste From Clipboard way
#3187 - Export to HELM works wrong for custom monomers imported from HELM with inline SMILES (part 2)
#3228 - Loading of AxoLabs with last monomer in brackets doesn't work
#3234 - Unable to add user`s peptide, nucleotide and CHEM to the library
#3235 - System adds broken Preset to the library
#3238 - Monomer name is missed if updated from the API
#3212 - Export to RXN disorganize the reaction

v.1.36.0

Updated on October 16, 2025

Release Notes

New features

#905 - Support for pagination in Bingo Elastic
#3092 - Avoid overwriting cmake output directories variables
#3099 - Support dev container
#2893 - Reaction data support in KET-format
#3136 - No attachment points check should be performed for terminal CHEMs on IDT import/export
#3135 - Mark undefined stereocenters using the standardize function
#3085 - HELM annotations support

Bugfixes and improvements

#3065 - Indigo build fails when trying to build indigo-depict
#3060 - CH labels are recognized as pseudo-atoms when parsing cdxml
#3096 - Expand monomer works wrong with selection
#3105 - bingo-elastic-python filter broken for exact/substructure
#3130 - Bingo-postrgress-fingerprints tests are failing
#3071 - Export to RDF V2000 doesn't work if "star" atom on the canvas. System throws exception: Convert error! std::bad_cast
#3067 - System can't load HELM with inline SMILES if it has r-site star atom without square brackets
#3120 - bingo-elastic-python reaction exact search do not use postprocess actions
#3150 - Exception during molecules loading in test fixture
#3123 - Unable to paste FASTA content from clipboard
#3159 - Export to HELM works wrong for custom monomers imported from HELM with inline SMILES
#3068, #3080, #3082, #3086, #3087, #3088, #3090, #3084 - System can't load atom properties (Charge, Isotope and Valence) in SMARTS with "star" atom. System throws exception.
#3144, #3147 - Export to IDT baseless preset and modified phosphate
#3148 - Export to IDT shouldn't work if monomer at the end has no 3' position IDT code
#3169 - Export to IDT doesn't work if R1-only CHEM stays on five prime position

v.1.35.0

Updated on September 19, 2025

Release Notes

New features

#2894 - Saving expanded monomers into MOL-files
Update monomer expand to follow Indigo structure

Bugfixes and improvements

#2900 - CIP labels are always rendered from cdxml
#3012 - Create IUPAC Compliant Chemical Formula
#3050 - Loading monomer chain from SDF file works wrong - bonds between monomers got lost/Export RNA monomers from MOLv3000 doesn't work for ACCLDraw export
#3047 - Loading monomer chain from SDF file works wrong - bonds between monomers got lost/Export RNA monomers from MOLv3000 doesn't work for ACCLDraw export
#3048 - Loading monomer chain from SDF file works wrong - bonds between monomers got lost/Export RNA monomers from MOLv3000 doesn't work for ACCLDraw export
#3054 - Loading monomer chain from SDF file works wrong - bonds between monomers got lost/Export RNA monomers from MOLv3000 doesn't work for ACCLDraw export
#3051 - Loading monomer chain from SDF file works wrong - bonds between monomers got lost/Export RNA monomers from MOLv3000 doesn't work for ACCLDraw export
#2928 - Isoelectric Point calculation should take into account occupied leaving groups (exclude them)
#3053 - Calculate properties doesn't work for "rich" sequences
#3049 - Stereo labels got missied on export to SVG result
#3056 - HELM load fails if it contains more than one instance of monomers with aliasHELM property
#3045 - Adding substituents to reactants breaks chemical property calculations
#3061 - System can't recognize single rebose or phosphate if loaded from HELM
#3062 - System can't recognize single rebose or phosphate if loaded from HELM
#3069 - Export to RXN doesn't work, system throws exception: Error: memory access out of bounds
#3094 - Export of expanded CHEMs works wrong (system losts CHEM type)

v.1.34.0

Updated on August 21, 2025

Release Notes

New features

#2899 - Peptide sequence should be auto-deceted at insert
#2958 - Map molfile monomers onto library monomers on import
#2967 - Support for marking of nucleotide components
#2952 - Expand c api to return CIP labels

Bugfixes and improvements

#2929 - Isoelectric Point calculation formula seems to be wrong
#2964 - System loads base as sugar
#2985 - Incorrect Implementation of PKA calculation
#2926 - Atom weights in indigo should be updated according to last IUPAC data
#2936 - System doesn't calculate melting temperature for mix of nucleotides/nucleosides and unsplit nucleotides/unsplit nucleosides
#2965 - System shouldn't allow to export molecules to 3-letter sequence format
#2989 - Export (and import) of sequence of nucleosides to HELM works wrong (doesn't work for import)
#2993 - System shouldn't consider closing bracket as part of name
#2998 - Input fields for ion concentration and oligonucleotides become inactive after entering excessively long number
#2970 - Rendering CIP labels breaks the generated svg for firefox
#3014 - Wrong bingo-postgres-linux version

v1.33.0

Updated on August 14, 2025

Release Notes

New features

#2890 - Conda support
#2835 - Loading HELM with monomers with multi-character IDs without brackets
#2836 - Loading monomer NOT from the library as Unknown monomers (in the same manner as it works in IDT)

Bugfixes and improvements

#2933 - Melting temperature calculation works wrong
#2748 - Substituents are displayed backwards if appearing on the left of the molecule
#2934 - Melting temperature should not be defined for one RNA/DNA nucleotide chain lenght
#2927 - Molecule formula atom order wrong
#522 - core: replace Obj with standard smart pointer
#2937 - System doesn't calculate melting temperature for mix of nucleotides/nucleosides and phosphates
#2720 - Reaction SMILES lossily handles enhanced stereochemistry
#2968 - Melting temperature calculation works wrong
#2969 - Export of unknown for Ketcher monomers works wrong
#2923 - System doesn't substract from mass of monomer mass of leaving group atom(s) if an attachment point is occupied
#2966 - Load from HELM doesn't work for two side chain connected sequences
#2986 - Don't calculate Melting temperature for one pair of double stranded DNA/RNA nucleotides

v.1.32.0

Updated on June 31, 2025

Release Notes

New features

#2767 - Add support for Postgres 17
#1970 - New text entities in KET-format
#2843 - Support of "HELM alias" property for monomers
#2844 - Support for "Modification Type" property of monomers
#2870 - Add support for flip expanded monomer
#2840 - Add InChI key method to cpp api

Bugfixes and improvements

#2805 - Saving of 3:3 reaction to SDF v2000 causes exception: Convert error! core: is not a base molecule
#2781 - Ketcher fails to save structure in MOL V3000 format when encountering custom attachment labels like “Ch”
#2851 - Macromolecule property Molecular mass wrong calculation
#2772 - Saving monomers to SDF v3000 works wrong - system saves every monomer template for every monomer on the canvas
#2860 - Copy to clipboard doesn't work if Multi-Tailed Arrow present on the canvas
#2858 - Export to any format doesn't work. System throw exception
#2047 - Saved Ellipse and Line Shapes in CDX, CDXML, Base 64 CDX formats are not correctly displayed after opening
#2868 - Indigo use wrong rotate parameter name KET files
#2867 - API calculateMacroProperties does not allow to pass parameters for UPC and NAC
#2859 - System wrongly reverse reaction order on Calculated Values dialog (and thus - values are wrong)
#2462 - Can't save a reaction with Multi-Tailed Arrow to Daylight SMARTS format
#2892 - API calculateMacroProperties does not work if only molecule passed as a parameter without monomers
#2888 - Unable to export single expanded monomer to SVG Image, system throws error: array: invalid index 0
#1679 - System ignores carrige return in text blocks in loaded CDX
#1683 - System shifts text label to the right
#2897 - Calculated Values doesn't work if reaction arrow overlaps reactant bounding box
#2931 - Calculated values doesn't work for "rich" monomer chain
#2917 - Molecular mass and Molecular formula are not calculated for Molecule (custom CHEM)
#2939 - System doesn't calculate melting temperature for GC nucleotides pair
#2930 - System shouldn't count bases that are not part of a nucleotide/nucleoside as RNA/DNA
#2947 - System "caches" PNG/SVG of canvas and stops reflect rotation/flip chanages if any
#2987 - Melting temperature value missed if UPC or NAC value set to zero
#2946 - Non-standard connections cause chain break in macromolecule properties calculation
#2902 - Indigo does not calculate properties for Peptides tab if Phosphate is missing in mixed chain
#2903 - Indigo fails to calculate properties when two chains are connected via a microstructure
#2904 - Indigo fails to calculate properties when two chains are connected via a CHEM
#2905 - Incorrect Calculate Properties result when monomers are connected via not a R2-R1

v.1.31.0

Updated on June 17, 2025

Release Notes

Features

#2788 - Support for PNG/SVG export of expanded monomers

Bugfixes and improvements

#2150 - Can't save a schema with some elements from Periodic Table in PNG and SVG format
#425 - Smiles with attachment points is not read correctly (valences are wrong)
#2747 - Incorrect substituent position
#1680 - System can't load CDX with (unsupported) brackets inside
#1631 - Add/Remove hydrogens changes Radical value from Diradical (triplet) to Diradical (singlet)
#2755 - Error occurs on click of "Remove Explicit Hydrogens" in reaction
#1686 - System shows positive charge modificator as extra + in addition to charge modified molecule
#2810 - Unnecessary rearrangment of cdxml reaction
#2807 - Missing label from cdxml
#2801 - Can't render reactions which contain brackets
#2778 - Can't render fragments with multiple external connections
#2815 - CIP labels are not rendered
#2591 - Reagents are repositioned above the reaction arrow after saving and loading RXN V2000/V3000 files
#2832 - Load from clipboard ignores RNA/DNA/PEP switcher and always loads DNA ambiguous bases even if RNA mode switched on
#2845 - Export to PNG/SVG works wrong for labels
#2722 - Monomer could be saved to RDF V3000 format but can't be loaded back - exception

1.30.0

Updated on April 22, 2025

Release Notes

Features

#2790 - Support of "expanded" monomer option

Bugfixes and improvements

#2741 - Image missing stereochemistry information when using abbreviations
#2513 - Elliptical arrows can not be saved to the png by
#2412 - User can't correctly save (or make a layout) to RDF/RXN reaction several products or with separate positioned molecules
#2746 - Incorrect phosphorus valence
#2708 - Export to SMILES works wrong if loaded from MOL
#2707 - Atom Query feature export: System lost MOST "Substitution count" values
#2702 - Export molecule which contains atom with five neighbors and stereo-bond cause error
#2704 - System losts one stereo label if load from MOL
#2699 - R Group logic condition is wrong if loaded from MOL
#2816 - Format recognition order of content from clipboard should be changed for Sequence mode canvas
#2818 - Library ambiguius RNA bases loaded from HELM as bases with % label
#2826 - Unable to load ambiguous RNA and ambiguous DNA monomers with same name from HELM

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Indigo Toolkit providing enhanced chemistry SDK

Solution Overview

Benefits

Features

Additional Information

Work Better Together

Questions & Answers