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
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 '$$$$V2.0' empty return from conversion to HELM
- #3306 - Saving to HELM doesn't work for cycled structures consist of nucleosides
- #3177 - System can't calculate Calculate properties window values for Amino acids with query bonds
- #3299 - System should set Implicit H value for atoms if the comes without hydrogens from CDXML
- #3343 - Export to Mol v3000 works wrong for stereo bonds between monomers
- #3369 - Bingo NoSQL treat empty flags as NONE instead of ALL
- #3363 - The layout algorithm returns different coordinates on macOS for some tests
- #3342 - Export ot SVG and PNG doesn't work for stereo bond between monomers, system throws an error: pool: access to unused element
- #3344 - Export to SVG/PNG works wrong for stereo bonds between monomers
Updated on February 20, 2026
Release Notes
New features
- #3227 - Introducing Copolymer S-group type
- #3272 - SDF files for library/monomer information
- #3196 - Support formation of circular structures in flex mode - PoC
Bugfixes and improvements
- #3239 - System doesn't save monomer expand/collapse state in Mol v3000 for user created monomers (they always come in collapsed state)
- #3261 - indigoSaveCdxml doesn't support reaction molecules
- #3269 - System ignored HELM alias for bases on monomer load to Library
- #3256 - Metals loaded from cdxml are always represented with hydrogens
- #3237 - Stackoverflow iterate components
- #3277 - System adds broken Preset to the library (part2)
- #3278 - System doesn't allow to add monomers with the same structure but different names (part2)
- #3286 - CHEMBUGS-64 Automapping fails to guard against contradictory reaction center annotation, corrupts future structure export data
- #3297 - Random '$$$$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
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
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
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)
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
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
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
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
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
Updated on January 16, 2025
Release Notes
Bugfixes and improvements
- #2313 - Indigo functions doesn't work if ambiguous monomer present on the canvas
- #2435 - Export of ambiguous monomers to Sequence/FASTA doesn't work for mixed ambiguous monomers
- #2324 - System loads DNA bases instead of RNA ones during IDT import
- #2387 - After opening a saved HELM file, microstructure name F1 turns into Mod0
- #2062 - HELM loader ignores repeating token
- #2332 - Error message should use "ambiguous monomer" instead of "variant monomer"
- #2338 - System loads HELM inline SMILES phosphate as base (RNA1{R[P%91(O)(O)=O.[*:1]%91 |$;;;;_R1$|]}$$$$V2.0)
- #2436 - System should report an error if we have one or more monomers on the canvas don't have mapping for them in case of export to Sequence/FASTA
- #2427 - Import of unsplit monomers from HELM doesn't work
- #2041 - Monomer could be saved to RXN V3000 format but can't be loaded back - exception
- #2137 - An error occurred while saving the unresolved nucleotides and arrow in the RXN3000 format
- #2195 - Indigo functions doesn't work if query atom and monomer on the canvas at the same time
- #2126 - An error occurred while saving the nucleotide and arrow in the RXN2000 format
- #2330 - Error diagnostic is not clear in case of wrong percent value type
- #2622 - Saving to MOL 3000 cause template data loss that causes wrong export to HELM
- #2361 - Wrong error message if SMILES phosphate has lack of attachemt point
- #2359 - System loads HELM even it it has wrong connection section (PEPTIDE1{[DACys]}|PEPTIDE2{C}$PEPTIDE1,PEPTIDE2,1:R1-1:R2$$$V2.0)
- #2539 - Export of unknown monomer to HELM doesn't work
