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

Full Changelog: indigo-1.35.0-rc.1...indigo-1.36.0

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, #3047, #3048, #3054, #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, #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)

Full Changelog: indigo-1.34.0-rc.1...indigo-1.35.0

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

Full Changelog: indigo-1.33.0-rc.1...indigo-1.34.0

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

Full Changelog: indigo-1.32.0-rc.1...indigo-1.33.0

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 suuport 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: <reaction> 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

Full Changelog: indigo-1.31.0-rc.1...indigo-1.32.0

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

Full Changelog: indigo-1.30.0-rc.1...indigo-1.31.0

What's Changed

• #2868 Indigo use wrong rotate parameter name KET files
• #2867 API calculateMacroProperties does not allow to pass parameters for UPC and NAC
• #2860 Copy to clipboard doesn't work if Multi-Tailed Arrow present on the canvas
• #2859 System wrongly reverse reaction order on Calculated Values dialog (and thus - values are wrong)
• #2858 Export to any format doesn't work. System throw exception
• #2851 Macromolecule property Molecular mass wrong calculation
• #2844 Support for "Modification Type" property of monomers
• #2843 Support of "HELM alias" property for monomers
• #2840 Add InChI key method to cpp api
• #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”
• #2772 Saving monomers to SDF v3000 works wrong - system saves every monomer template for every monomer on the canvas (geometry progression)
• #2767 - Add support for Postgres 17
• #2462 Can't save a reaction with Multi-Tailed Arrow to Daylight SMARTS format
• #2047 Saved Ellipse and Line Shapes in CDX, CDXML, Base 64 CDX formats are not correctly displayed after opening
• #1970 - New text entities in KET-format
• #1686 System shows positive charge modificator as extra + in addition to charge modified molecule
• #1683 System shifts text label to the right
• #1679 System ignores carrige return in text blocks in loaded CDX
• #2870 Add support for flip expanded monomer

Full Changelog: indigo-1.31.0-rc.2...indigo-1.32.0-rc.1

What's Changed

• #2591 Reagents are repositioned above the reaction arrow after saving and loading RXN V2000/V3000
• #2832 Load from clipboard ignores RNA/DNA/PEP switcher and always loads DNA ambiguous bases even if RNA mode switched on by
• #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

Full Changelog: indigo-1.31.0-rc.1...indigo-1.31.0-rc.2

Indigo 1.30.1

Released 2025-04-17

Features

• 2790 Support of "expanded" monomer option

Bugfixes and improvements

• 2513 Elliptical arrows can not be saved to the png
• 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

Full Changelog: indigo-1.29.0...indigo-1.30.1

What's Changed

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

Full Changelog: indigo-1.29.0...indigo-1.30.0