Indigo 1.43.0

May 14, 2026 · View on GitHub

Released 2026-05-13

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: https://github.com/epam/Indigo/compare/indigo-1.42.0-rc.1...indigo-1.43.0

Indigo 1.42.0

Released 2026-05-13

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: https://github.com/epam/Indigo/compare/indigo-1.41.0-rc.1...indigo-1.42.0

Indigo 1.41.0

Released 2026-05-13

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: https://github.com/epam/Indigo/compare/indigo-1.40.0-rc.1...indigo-1.41.0

Indigo 1.40.0

Released 2026-02-23

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

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.39.0-rc.1...indigo-1.40.0

Indigo 1.39.0

Released 2026-02-20

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
#3343 - Export to Mol v3000 works wrong for stereo bonds between monomers
#3344 - Export to SVG/PNG works wrong for stereo bonds between monomers

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.38.0-rc.1...indigo-1.39.0

Indigo 1.38.0

Released 2026-02-20

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

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.37.0-rc.1...indigo-1.38.0

Indigo 1.37.0

Released 2026-02-19

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

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.36.0-rc.1...indigo-1.37.0

Indigo 1.36.0

Released 2025-10-16

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 recognised 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 clipcoard
#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: https://github.com/epam/Indigo/compare/indigo-1.35.0-rc.1...indigo-1.36.0

Indigo 1.35.0

Released 2025-09-19

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: https://github.com/epam/Indigo/compare/indigo-1.34.0-rc.1...indigo-1.35.0

Indigo 1.34.0

Released 2025-08-21

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: https://github.com/epam/Indigo/compare/indigo-1.33.0-rc.1...indigo-1.34.0

Indigo 1.33.0

Released 2025-08-14

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: https://github.com/epam/Indigo/compare/indigo-1.32.0-rc.1...indigo-1.33.0

Indigo 1.32.0

Released 2025-06-18

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: 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 (geometry progression)
#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: https://github.com/epam/Indigo/compare/indigo-1.31.0-rc.1...indigo-1.32.0

Indigo 1.31.0

Released 2025-06-17

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: https://github.com/epam/Indigo/compare/indigo-1.30.0-rc.1...indigo-1.31.0

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: https://github.com/epam/Indigo/compare/indigo-1.29.0...indigo-1.30.1

Indigo 1.29.0

Released 2025-03-26

Features

#1844 - Implement GenBank/GenPept sequences import
#2552 - "Calculate Properties" for macromolecules
#2713 - Support for the star atom (*)

Bugfixes and improvements

#2739 - Wrong stereochemistry when reading cdxml reaction
#2744 - Indigo ignores alternate name for templates in MOL v3000
#2716 - Valid CXSMILES rejected
#2732 - V2000 Mol file loader skips essential SGroup line in certain cases
#2589 - Jump on uninitialised value
#2763 - System should ignore spaces before line indexes on GenBank/GenPept sequences import
#2798 - Peptide sequence not pasting directly on canvas

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.28.0-rc.1...indigo-1.29.0

Indigo 1.28.0

Released 2025-02-13

Bugfixes

#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
Revert "#2657 - Add ES6 options for WASM build (#2658)"

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.26.0-rc.1...indigo-1.27.0

Indigo 1.27.0

Released 2025-02-12

Features

#2559 Read Name and Reaction Conditions from RDF Metadata as a text
#2404 Save Name and Reaction Conditions to RDF Metadata
#2657 Add ES6 options for WASM build
#2652 Skip Name and/or Reaction Conditions metadata fields on save to RDF if no data is available
#2574 Support for Collapsed monomers

Bugfixes

indentation errors in docstring description

#2654 Arrow size become 2 bonds length after indigo changed default arrow size to 1
#2665 Margins are missing if no reaction result
#2664 Vertical margin for catalyst is wrong
#2662 Arrow size is wrong if reaction loaded from SMARTS
#2653 Indigo should send to ketcher different bond size for macromolecules
#2647 Reaction's name or conditions text wraps incorrectly in specific cases: the last line before truncating, removing of special symbols, empty line instead of "..."
#2583 Not correct length of Multi-Tailed and Single arrows for reactions with atoms after loading from RDF or Layout actions
#2519 The length of the arrow becomes 2 bonds after layout but should be 1
#2624 Elliptic arrow rendered wrong while expotring to PNG in remote mode
#2497 Test fail on compare CML file for R-group

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.26.0-rc.1...indigo-1.27.0

Indigo 1.26.0

Released 2025-01-10

Features

#2460 Load/save hydrogen bonds from/to HELM, KET and MOL
#2575 Saving atom to monomer connections to Mol and HELM
#2472 Support for three letter sequences

Bugfixes

#2491 Update ketcher to newer version for indigo-service frontend
#2519 The length of the arrow becomes 2 bonds after layout but should be 1
#2520 The length of arrow should be 1 bond after importing reaction from rxn file
#2458 The reaction with catalysts is displayed incorrectly with ACS style setting and after layout
#2681 Molfile V3000 with SGROUP type DAT fails to load in Ketcher due to missing spaces in FIELDDISP
#2654 Arrow size become 2 bonds length after indigo changed default arrow size to 1

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.24.0-rc.1...indigo-1.25.0

Indigo 1.25.0

Released 2024-11-18

Features

#2236 Import/export multi-tails in KET
#2162 Add support for rendering embedded SVGs while exporting to PNG
#2129 Render Multi-tail Arrows for Pathway Reactions in PNG and SVG
#2176 add ACS style reaction layout
#2209 SVG image support in CDX/CDXML
#2237 Save multi reactions (pathway, single, edge cases) to RDF
#2175 Adjust the rendering of PNG and SVG formats for ACS style

Bugfixes and improvements

#2293 Export IDT doesn't work for natural ambiguous monomers
#2383 update lunasvg
#2309 Update layout for pathway reaction on canvas
#1989 Convert api does not recognise format during autodetection
#2070 Settings for the "attachment point tool" don't update with changed pixel settings
#2457 The reaction is not in the center of the picture after saved in png (svg)
#2444 The thickness of the arrow is incorrect when saving to png(svg)
#2447 single up and single down bonds are displayed incorrect when save to PNG(svg)
#2257 Unable to save CHEM SS3 to IDT format
#2312 Export of ambiguous monomers doesn't work (error appears) to any export format (even to SVG/PNG) except KET
#2433 Issues with Saving and Opening Structures with Multi-Tailed Arrow in CDX and CDXML Formats
#2512 Equilibrium Half Arrows are displayed incorrect when saved to PNG (svg) by default size
#2217 The wrong direction of the arrows when exporting from CDXML (or CDX, base64 cdx) format and two retrosynthetic arrows
#2422 Indigo functions doesn't work prorerly: Aromatize, Dearomatize, Layout, Clean Up, Hydrogens, Auto-Mapping Tool
#2458 The reaction with catalysts is displayed incorrect with ACS style setting and after layout
#2440 System shouldn't allow user to export alternatives ambiguous monomers to IDT (since only mixtures are supported)
#2331 System should throw an error in case of wrong IUBcode
#2122 Sugar R should not save in the IDT format
#2446 Sub font size is incorrect when save to png (svg)
#2407 The ordering of branches of cascade reactions and reactions themselves should be the same on Load/Save from/to RDF
#2478 The arrow is displayed incorrect when import from rxn file
#2603 Unknown 'a' CIP stereochemistry cause error in CDXML parser

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.24.0-rc.1...indigo-1.25.0

Indigo 1.24.0

Released 2024-10-04

Features

#2096 Support retrosynthetic arrows - PNG/SVG rendering
#2097 Add retrosynthetic arrow import/export for cdx/cdxml formats
#2031 Build a data structure for a reaction tree
#1619 Import/export of variant monomers from IDT
#2052 Position pathway reaction on canvas
#2015 Import/Export of variant monomers from Fasta/Sequence
#2028 PNG image support in CDX/CDXML
#2128 Add Multi-tail Arrows to Pathway Reactions Loaded from RDF
#2188 HELM 2 support: variant monomers
#2189 HELM 2 support: support for SMILES

Bugfixes

#2232 System replace arrows of diffrent types with Open Arrow type while loading from PPTX(CDX)
#2249 Arrow Open Angle changes to Arrow Filled Triangle after saving and opening in CDX/CDXML
#2120 Export the structure for nucleotides 2-Amino-dA does not work correctly
#2266 Error message is wrong for missing ratio number (PEPTIDE1{(A:+C:0.1)}$$$$V2.0)
#2300 HELM loading doesn't work in remote version
#2293 Export IDT doesn't work for natural ambiguous monomers
#2336 Ribose sugar doesn't allow to load IDT custom mixed bases
#2358 Import of monomer with only one connection point (R2) doesn't work
#2321 Export of multi-character monomer IDs inside ambiguous monomer works wrong
#2375 Export to IDT doesn't work at all for mixed bases
#2356 Library ambiguous peptides loaded as mixtures from FASTA
#2357 Export to HELM doesn't work if we connect peptide TO molecule
#2303 Import of variant monomers from Sequence doesn't work for RNA and FASTA for RNA/DNA
#2355 Import of HELM with fractional ratio mixture values doesn't work - system expects integer
#2421 Incorrect stereo-label placement for (E) and (Z) (indigo part)
#2417 The layout is incorrect with retrosynthetic arrow

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.24.0...indigo-1.23.0

Indigo 1.23.0

Released 2024-09-06

Features

#2134 Store monomer library as API object
#2144 Import/export images in KET
#2071 add retrosynthetic arrow
#2034 Introduce variant monomers in a model
#2030 Load RDF Format as simple list of reaction

Bugfixes

#1944 Fullerene and 3D molecules are not represented as 3D in the Miew 3D window
#2213 Layout for 1-step reactions is broken

Improvements

#2131 Create Indigo WASM bundle with removed rendering part
#2139 use <filesystem>
#2141 use <chrono> instead of nano

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.23.0...indigo-1.22.0

Indigo 1.22.0

Released 2024-09-06

Features

#1912 Support unresolved IDT monomers (no structure, IDT only)
#1919 Support of unsplit nucleotides
#1188 HELM ver 1 scope: support multiple sequences and connection tables (import and export)
#1188 HELM ver 2.04 support API for ketcher

Bugfixes

#1993 Micro and macro structures connected through attachment points cannot be opened after save in CDXML format in micro mode
#1986 System breaks IDT export line if it is longer than 80 chars by
#2106 Export monomer with R2, R3, R4 APs resulted in monomer with R2, R3 if exported to mol v3000
#2110 The structure changes when saved in SVG/PNG formats

Improvements

#877 api: wasm: indigo-ketcher: prepare 2-files wasm+js package

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.22.0...indigo-1.21.0

Indigo 1.21.0

Released 2024-08-27

Features

#1903 Introduce IDT alias for monomers and RNA presets in Ket format
#1901 Receive monomer library from Ketcher upon import/export IDT notation
#1900 Export of modified RNA to IDT notation (modified IDT monomers)
#1899 Import of modified IDT monomers

Bugsfixes

#1974 Preview: User can save IDT with 5' phosphate but cannot open this file again.
#1972 Can't save KET with nameless superatom
#1996 Cannot open IDT with MOE sugar.
#1960 Fix error message in the SequenceLoader for an invalid sequence
#1928 Support monomer to molecule connections type
#1878 The structure saved in CML format does not open
#1843 FASTA export: 80 chars limit
#2000 Exporting a CDX file to ChemDraw loses information about charge on atoms
#1997 Export to IDT doesn't work at all for remote indigo
#1993 Micro and macro structures connected through attachment points cannot be opened after save in CDXML format in micro mode
#2004 Errors occur when trying to save a macro structure connected to a micro structure to MOL V3000
#1994 Micro and macro structures connected through attachment points cannot be opened after save in CDX and Base 64CDX format in micro mode
#1992 Micro and macro structures connected through attachment points cannot be saved in Extended SMILES format in micro mode
#1990 Micro and macro structures connected through attachment points cannot be saved in CML format in micro mode
#1984 Error message is wrong if in case if position indicator in IDT code contradicts real position of the monomer in the chain
#1982 Cannot open some expected IDT.

Improvements

#1976 Too slow monomer library load

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.21.0...indigo-1.20.0

Indigo 1.20.0

Released 2024-07-01

Features

#1654 Export of RNA presets to IDT notation (standard IDT monomers)
#1588 Import of standard IDT monomers
#1466 Export as sequence string for RNA, DNA and PEPTIDEs

Bugs

#1891 Bug Report | When building api/http container, it cannot run due to mismatch in pydantic version
#1598 Macro: V3000 export: leaving groups are displayed as side chain connections for standard presets added to canvas
#1579 Unable to add hydrogens for aromatic bonds outside the ring - system throws exception
#1910 Indigo incorrectly calculates RNA coordinates with data from FASTA/Sequence file
#1950 Empty headers appear when exporting to FASTA

Improvements

#1802 bad performance during the parsing of large sequences

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.19.0...indigo-1.12.0

Indigo 1.19.0

Released 2024-05-02

Features

#1755 Import and export fasta format for RNA, DNA and PEPTIDES
#1466 Export as sequence string for RNA, DNA and PEPTIDEs

Bugs

#1787 Some Bonds from ChemDraw don't open in the Ketcher
#1776 Cannot add to Canvas saved in the Ketcher CDX file with Bond structures
#1775 Save to CDX converts triple bond to Single/Double Aromatic bond
#1774 Save to CDX converts aromatic benzene ring to dashed ring
#1425 Indexing of a substantial quantity of molecules instigates the indexing process for the entire file.
#1575 Basic hydrogen layout problem - angles of hydrogens are not perfect
#1771 Bingo version does not return current tag
#1761 Can't export sequence with 1 monomer to molv3000
#1598 Macro: V3000 export: leaving groups are displayed as side chain connections for standard presets added to canvas
#1477 sequence id calculation for molv3000
#1563 Unable to load mol file: System throws exception: Convert error! Unexpected token '<', "<!DOCTYPE "... is not valid JSON
#1852 Macro(Export FASTA): The header 'Sequence N' is missing, and '>' symbol is located at end of the first sequence
#1822 Fasta: All Peptides should be saved to FASTA format and (use N/X symbol as well).
#1851 Macro(Import FASTA): The ';' symbol is not recognized as a comment
#1786 Some bonds from Ketcher don't display correctly in the Ketcher and the ChemDraw for CDXML format.
#1777 Some bonds don't display correctly in ChemDraw when opening a saved Ketcher CDX file.
#1849 Macro(Import FASTA): The ' * ' symbol occurring between two letters is not recognized as a break in peptide chain
#1850 Macro(Import FASTA): The '>' symbol is not recognized as indicating a new sequence
#1802 bad performance in WASM during the parsing of large sequences
#1848 Cannot save FASTA using the Remote mode
#1791 Aromatic is lost from Benzene while save to CDX/base64 CDX formats
#1774 Save to CDX converts aromatic benzene ring to dashed ring
#1773 Save to CDX converts plus and arrow into lone pair and line
#1796 Some bonds from ChemDraw don't display correctly in the Ketcher.
#1814 Macro: System ignore spaces and line breaks when importing a sequence through Paste from Clipboard
#1801 No monomer full name when import from a sequence
#1161 bingo unable to index on sql server
#1773 Save to CDX converts plus and arrow into lone pair and line
#1774 Save to CDX converts aromatic benzene ring to dashed ring
#1796 Some bonds from ChemDraw don't display correctly in the Ketcher.
#1881 Macro: Cannot load Peptides from our Library that are not connected by bonds using FASTA file

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.18.0...indigo-1.19.0

Indigo 1.18.0

Released 2024-02-29

Features

#1412 Nucleotide splitting for V3000 molfile SCSR
#1450 No naturalAnalogShort in KET for basic aminoacids during conversion MOLV3000 -> KET
#1436 Expose Fold/Unfold hydrogens function in indigo API
#1440 Add support for query features in MOL, SDF and RXN formats (Marvin extension)
#1426 Import sequence format for RNA, DNA and PEPTIDES
#1589 Apply hydrogens folding/unfolding with respect to selected atoms

Bugs

#1307 Error in DevTool console about memory access out of bound when call 'ketcher.getRxn()'
#1431 Crash during parsing query mol-file
#1439 Indigo can't parse KET with R-Site as a leaving group
#1232 Multi-line reaction cause access violationg exception.
#1423 Common atoms loaded as aliphatic in SMARTS mode
Update bug_report.md
#1458 Failed UT api\indigo_test.py:test_convert_smarts
#1460 ImplicitH set to zero casue error loading query molecule from ket
#1446 Dearomatization does not work with query features
PostgreSQL 11 EOL support
#1465 Unable to load specific mol-file
#1484 Query molecule convert implicit/explicit hydrogens cause error
#1512 Broken string-formats support for wasm
#1452 Convert from implicit hydrogens change layout
#1463 Macro: Some molecules are not perfect on preview tooltip
#1524 Dearomatizing doesn't work for molecula with custom query fetures
#1568 Wrong molecule nodes enumeration in KET-file
#1476 Aromatization/Dearomatization wipes out SOME Ring bond count values
#1478 Dearomatization causes exception in case of Implicit H count query feature set to 4 (i.e. more than 2)
#1525 System attach two explicit hydrogens to aromatized ring
#1573 Add/Remove explicit hydrogens can't be applied to fullerene C60 - system throws exception
#1567 System can't copy atom with custom query feature to clipboard
#1534 Presence of stand alone H2 molecule on the canvas breaks Add explicit hydrogens feature (it stops working)
#1468 Valence lost on loading molfile with MRV extension.
#1472 Dearomatization wipes out Aromaticity query property
#1504 Molfile MRV extension generated for "H count"
#1500 Atom Query feature export: System replace "Ring membership" values with "Ring Bond Count" ones for value 0 - export to SDF V2000 file
#1564 Add/Remove explicit hydrogens wanishes "Chirality" value
#1598 Macro: V3000 export: leaving groups are displayed as side chain connections for standard presets added to canvas
#1533 System attach two explicit hydrogens to atoms connected to "any type" bonds
#1608 convert_explicit_hydrogens response doesn't comply with the ket schema
#1538 Add/Remove explicit hydrogens feature doesn't work if atom with problem valence present on canvas (crash happens)
#1614 Adding hydrogens doesn't work for bonds with No center value of Reacting Center
#1550 Add/Remove explicit hydrogens feature doesn't work for "Any Atom" molecule with valence value set
#1593 Macro: V3000 import: removed 5' phosphate is displayed in Ketcher
#1483 Unable to past empty reaction (arrow only) from clipboard to canvas
#1607 Unable to load large base64 CDX content to canvas if remote indigo used`
#1536 Add/Remove explicit hydrogens feature doesn't work for reactions on canvas (crash happens)
#1652 Unfold hydrogens does not select added bonds
#1640 System adds hydrogens for only one atom among many selected by
#1634 Add/Remove hydrogens doesn't work for atoms with Radical=Triplete if atom with query feature present on the canvas
#1629 Add/Rmove hydrogens process should count R-Group attachment point as hydrogen
#1695 CDX loader failed if object with zero id follow by reaction
#1697 CDX loader crashed on some files with abbreviations by
#1684 System put on the canvas two arrows (one above other) per each arrow on target CDX
#1724 Fold hydrogen in reaction with selection works wrong by
#1730 UT cano/permutations is too slow by
#1576 Bad molecule layout after adding hydrogens (Chlorophyll A)
#1685 System shows attached abbreviation group in wrong position

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.16.0...indigo-1.18.0

Indigo 1.16.0

Released 2024-01-30

Features

#1185 Macromolecules export from MolV3000 to KET
#1381 Macromolecules import from KET

Bugs

#1395 Class and naturalAnalog of KET monomerTemplate should be optional
#1405 Valence is lost for Mol and Rxn files
#1415 Incorrect S-Group count in MOL V3000 header if ImplicitH is set
#1346 Extended SMILES: Atropisomer is displayed incorrectly
#1304 Indigo accepts [#6] notation in SMILES mode
#1355 Error appears when pressing 'Layout'
#1330 Implicit H count is not added to the SMARTS file
#1358 Error while loading [!#6,!#7,!#8] smarts
#1357 Wrong atom list when paste structure as SMARTS
#1292 valid SMARTS with cycles cause error in loader
#1349 Symbol for topology chain is missing in SMARTS file
#1351 Error returned when try to convert structure with custom query for bond into SMARTS format
#1283 wrong chirality generated by SMARTS load/save
#1329 Aromacity is incorrectly marked in the SMARTS file
#1325 Indigo should return warning for some attributes
#1328 Chirality is not added to the SMARTS file
#1281 Support SMARTS "or unspecified" bond property in custom queries
#1321 When saving a structure with set up Implicit H count and any other atom attribute then an error appears
#1309 Error appears while trying to save some element with set up H count and implicit H count
#1319 Directional bonds are encoded incorrectly in SMARTS
#1183 Support monomer templates import from KET-format
#1184 Support monomer templates export into KET-format
#1310 Error appears while opening SMARTS file with query which contains comma
#1322 Reaction cannon be saved in convert function
#1303 Return original format from convert and layout function
#1316 SMARTS saver miss component level grouping
#1254 SMARTS with component-level grouping saved without '()'
#1252 SMARTS loader load grouped components as separate molecules
#1245 Reaction/Molecule autoloaders don't load SMARTS
#914 Why is the code InChI=123 valid?
#1224 Different indent after loading reaction from file and after layout it.
#1221 An empty structure is returned given incorrect InChi string

Improvements

#1338 Use docker image for building npm packages and apply tags while publish

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.14.0...indigo-1.16.0

Indigo 1.14.0

Released 2023-11-07

Features

#1217 Support SDF-format for Indigo-Ketcher API
#1257 Enhanced stereo labels on atropisomers are lost when opening saved Extended SMILES

Bugs

#887 When saving in PNG and SVG format, files have low resolution when opened (Ketcher Remote)
#1200 MolfileSaver add Data S-Groups to molecule at saveMolecule()
#1199 CanonicalSmiles saver contains extended part.
#1161 Bingo unable to index on SQL Server
#1040 SMILES/SMARTS import: Files with S-Group Properties cause an error
#1145 CDX import: letter is duplicate and 'superscript' and 'subscript' become the same size as the letter
#1191 Bingo-elastic: Cannot search at elastic using custom-index
#731 Warnings in the Structure Check window doesn't display for molecules with R-Groups
#1230 Unable to save file if the canvas has a reaction arrow and a Functional Group
#1249 Incorrect order of aliases in SMILES saver
#1240 Unable to open the CDX file with an R-Group added to the whole structure
#1239 CDX: An abbreviation appears in the upper left corner of a Function Group or Salt when opening a saved file
#1287 New S-Group type Query component level grouping
#1260 SMARTS saver works incorrectly for non-query entities if atom valence or radical present
#1300 Stereobond is not preserved after pasting a SMILES structure
#1277 Atropisomer centers support
#1347 When pasting Extended SMILES with coordinates enhanced stereochemistry is lost

Improvements

#1037 Indigo Toolkit information in the 'About' section that is not relevant for the users
#1197 Migrate indigo-knime nodes to KNIME Analytics Platform 5.1

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.13.0...indigo-1.14.0

Indigo 1.13.0

Released 2023-10-04

What's Changed

Bugfixes

#1205 Reagent located at the bottom of the arrow when opening the RXN V2000 and V3000 files are located on top of the arrow
#1168 Error message when trying to save structure with Multiple Group type applied to entire structure
#1166 CDX: file with R-Group label saved in Ketcher opens without part of structure
#1159 [CDX] IndigoException: stoi when reading USPTO CDX file
#1155 [CDX] Indigo header files doesn't appear in msvc solution.
#1152 No module named tzdata while running indigo service
#1139 core dumped when reading CDX file downloaded from USPTO
#1113 RXN 3000 import: When importing, the structure becomes unreadable
#1094 Structure with R-Group isn't opened correctly from v3000 mol file
#1061 [Bingo-Elastic] Cannot create custom index in python bingo-elastic
#1026 [Bingo-Elastic] SVG/PNG: Contracted 'Functional Groups' and 'Salts and Solvents' are rendered expanded when saved
#926 CDXML import: 'superscript' and 'subscript' appears below the letter

Features

#1182 Enhanced stereo labels on atropisomers are lost when opening molfiles
#1158 Ketcher needs to correctly serialize/deserialize attachment point information for super atoms for mol v3000 & ket format

Improvements

#1111 api: add method for copying RGroups for Java and .NET
#1124 SMILES format does not store alias information

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.12.0...indigo-1.13.0

Indigo 1.12.0

Released 2023-07-09

What's Changed

Bugfixes

#965 MDL Molfile v3000: when opening files containing 'Salts an Solvents', names are truncated and abbreviation is expanded
#1036 SMILES import: general chiral specification labels (TH, AL, SP, TB, OH ) don't work
#1051 Opening file with a superatom label saved in RXN v3000 format only the first part of the label is displayed
#1114 Atoms of Benzene ring become Monoradicals when opened from file saved in Daylight SMARTS
#1132 SMILES loader uninitialized heap fix
#1102 When pasting Extended SMILES structure with stereochemistry there are two &1 centers instead of an ABS and an &1
#1135 C library macro - va_end() is missing before return statement.
#1126 Segfault when iterating CDX file from USPTO downloads
#1144 Unable to save the structure after clicking 'Save', an error appears

Improvements

#1098 api: add method for copying RGroups

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.11.0...indigo-1.12.0

Indigo 1.11.0

Released 2023-06-19

What's Changed

Features

#1053 Split publish job in "Indigo CI" GitHub Action
#310 Support stereo CIP calculation in Ket format
#957 Support of Korean, Chinese and Japanese characters in Standalone.
#995 Automated memory leaks testing

Bugfixes

#1044 SVG/PNG: Reaction arrows are not visible without structures at preview and in saved files
#932 Reagents: When opening Daylight SMILES and Extended SMILES files with reagent the original structure is distorted
#1084 Can't open mol v3000 files with 'S-Group Properties Type = Generic' and 'S-Group Properties Type = Multiple'
#1083 Indigo Service: enable of using Indigo Options
#910 MDL Molfile v3000 encoding: Automatic selection of MDL Molfile v3000 encoding doesn't work if the number of atoms (or bonds) exceeds 999
#956 Copy Image: When inversion type is chosen in the atom's properties, it is not saved
#955 Copy Image: Saved bonds does not have Reacting Center marks
#1052 Set "Indigo Docker images preparation" GItHub Action to start manually only add version tag to Docker images
#1064 Keep implicit hydrogens information in KET-format
#1048 Memory leak in 3rd party library
#1056 RXN2000/3000 should not serialize INDIGO_DESC fields for s-groups
#1050 Memory leak in StringPool code
#1031 Calculate CIP: Hovering over the label R/S displays Indigo system information
#1049 Memory leak in the SMILES loader code
#973 Daylight SMARTS: Error when save file in SMART format with reaction arrow and reagent
#1017 imagoVersions is undefined
#899 Add restrictions on size to be less than 1000
#1015 Cannot test CDX export with certain files
#944 CDX import: Greek letters, Celsius and Fahrenheit signs are replaced with question marks
#1093 python binding memory leak from 1.8.0 (and still present in 1.10.0)

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.10.0...indigo-1.11.0

Indigo 1.10.0

Released 2023-03-22

What's Changed

Features

#941 CDX export

Bugfixes

#1003 Some texts are not rendered and may lead to Indigo crash
#987 docker-indigo-tester image build failed
#994 Some UTF-8 characters from Ketcher Text panel are not displayed in Indigo WASM
#889 When saving in PNG and SVG format UTF-8 text display incorrectly (Ketcher Standalone)
#1032 Combine molecules that are related to a single s-group into one in .Ket format
#974 SVG/PNG: Molecule reagent located below arrow is displayed in preview above arrow
#1039 Opening file with a superatom label saved in RXN v3000 format removes a custom s-group
#1063 Structure saved in CDX and Base64CDX with reaction arrow cannot be opened
#1068 CDX-loader crash

Full Changelog:https://github.com/epam/Indigo/compare/release/1.9...release/1.10

Indigo 1.9.0

Released 2023-01-31

MDL Molfile v3000 encoding: Automatic selection of MDL Molfile v3000 encoding doesn't work if the structure contains Enhanced stereochemistry by @mkviatkovskii in #924
cdx import in scope of current KET/CDXML features support by @even1024 in #885
Structures with the arrow lose their integrity when pressing 'Layout' by @even1024 in #938
Abbreviations are not supported by @even1024 in #685
#934: api: tests: IronPython update to 3.4.0, fix tests by @mkviatkovskii in #940
Add support of R-groups to the CDX loader. #36 by @even1024 in #946
CDX import: Reaction arrows disappear when opening a file #943 by @even1024 in #948
CDX import: Aromatized structures are not recognized when Pasting from Clipboard #950 by @even1024 in #953
CDXML parser memory leak #966 by @even1024 in #967
Error opening MOL and RXN files with RBC/SUB/UNC queries #928 by @even1024 in #969
CDX Import, CDXML Import: parsing error when superatom starts with 'R' symbol #960 by @even1024 in #975
CDXML: When opening a saved file with text, the Font size enlarges #961 by @even1024 in #982
CDXML: When opening a file saved with 'Any atom', 'Atom Generics' or 'Group Generics' structure loses its integrity #968 by @even1024 in #985
CDXML import fails to load rectangle primitives #979 by @even1024 in #980
CDXML: File containing Functional Groups or Salts and Solvents cannot be opened and causes a convert error #963 by @even1024 in #984
CDXML import: nodes with radicals are not getting parsed #990 by @even1024 in #991
CDXML import: fails to import some cdxml files with multiple text objects related to different fragments by @even1024 in #993
CDXML import: 'superscript' and 'subscript' is not displayed correctly #962
Improve ssl bingo elastic by @MysterionRise in #901
bingo: postgres: add support for Postgres 15, drop support for Postgres 10 by @mkviatkovskii in #903
#521: core: replace MultiMap in MoleculeRGroupsComposition class by @loimu in #917
#521: core: replace MultiMap in MolfileLoader class by @loimu in #911�
#929: fix auto-saving to CTAB v3000 by @mkviatkovskii in #931

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.8.0...indigo-1.9.0

Indigo 1.8.2

Released 2022-11-28

What's Changed

core: SMARTS support for implicit hydrogens specifier 'h' added by @mkviatkovskii
Feature/#861 cdxml enhanced stereochemistry by @even1024
Feature/#862 cdxml abbreviations by @even1024
Bugfix/#891 dearomatize query onload by @even1024
Bugfix/#870 and bugfix/#871 multistep to rxn-smiles by @even1024

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.8.0...indigo-1.8.2

Indigo 1.8.0

Released 2022-10-14

What's Changed

ci: fix npm versioning according to semver by @mkviatkovskii in https://github.com/epam/Indigo/pull/741
Fixed mistypes by @SunFellow in https://github.com/epam/Indigo/pull/743
Rename indigo-ketcher.zip artifact to indigo-wasm.zip by @SunFellow in https://github.com/epam/Indigo/pull/744
api: added TPSA calculation by @mkviatkovskii in https://github.com/epam/Indigo/pull/745
api: added numRotatableBonds, numHydrogenBondAcceptors, numHydrogenBondDonors by @mkviatkovskii in https://github.com/epam/Indigo/pull/748
api: added logP and molarRefractivity, removed Python implementation by @mkviatkovskii in https://github.com/epam/Indigo/pull/750
Text cipfix by @even1024 in https://github.com/epam/Indigo/pull/739
api: added atom hybridization calculation by @mkviatkovskii in https://github.com/epam/Indigo/pull/751
api: renamed cLogP to logP by @mkviatkovskii in https://github.com/epam/Indigo/pull/752
api: bingo-nosql: fix partitioning in exact search by @mkviatkovskii in https://github.com/epam/Indigo/pull/754
api: c: another stage of abandoning self-written red-black tree collections by @mkviatkovskii in https://github.com/epam/Indigo/pull/756
api: cpp: replace multiple Indigo*Iterator classes to single template one; add Bingo.Part test by @mkviatkovskii in https://github.com/epam/Indigo/pull/757
metadata refactoring by @even1024 in https://github.com/epam/Indigo/pull/755
core: ket: text rendering support by @even1024 in https://github.com/epam/Indigo/pull/760
core: molecule auto loader: cdx enable; text for reaction fix (#706) by @even1024 in https://github.com/epam/Indigo/pull/763
core: base64 support for binary formats, uninitialized data and #764 fix by @even1024 in https://github.com/epam/Indigo/pull/766
#768: api: add hash() method for molecules and reactions, improve reaction hash to decrease number of collisions by @mkviatkovskii in https://github.com/epam/Indigo/pull/769
Bingo Elastic search by @AATDev21 in https://github.com/epam/Indigo/pull/772
#770: reduce list of exported symbols to avoid conflicts with other shared libraries by @mkviatkovskii in https://github.com/epam/Indigo/pull/793
#791: core: molecule: Lee-Crippen SMARTS pKa calculation method implemented by @mkviatkovskii in https://github.com/epam/Indigo/pull/792
#794: ci: add version changing script and update version to 1.8.0-dev by @mkviatkovskii in https://github.com/epam/Indigo/pull/795
core: render2d: text renderer fixes, UTF-8 support, subscript/superscript, all arrows styles, fix for #355 by @even1024 in https://github.com/epam/Indigo/pull/776
#777: utils: indigo-service: reorganize codebase, simplify docker compose, update ui by @mkviatkovskii in https://github.com/epam/Indigo/pull/796
#798: api: python: reorganize codebase by @mkviatkovskii in https://github.com/epam/Indigo/pull/799
#163: api: added test by @mkviatkovskii in https://github.com/epam/Indigo/pull/802
Issue #520: api: replace RedBlackMap in IndigoDeconvolution by @AStepaniuk in https://github.com/epam/Indigo/pull/803
#808: render2d: equilibrium arrows rendering supported by @even1024 in https://github.com/epam/Indigo/pull/801
Fix for Indigo-WASM build by @SPKorhonen in https://github.com/epam/Indigo/pull/828
Restore indigo service by @AlexanderSavelyev in https://github.com/epam/Indigo/pull/858
Issue #520: core: replace RedBlackMap and RedBlackSet implementation by @AStepaniuk in https://github.com/epam/Indigo/pull/804
Issue #520: core: replace RedBlackMap for GraphEmbeddingsStorage by @AStepaniuk in https://github.com/epam/Indigo/pull/805
Issue #520: core: replace RedBlackMap in SimpleCycleBasis by @AStepaniuk in https://github.com/epam/Indigo/pull/806
Issue #520: core: replace RedBlackMap for MangoPg by @AStepaniuk in https://github.com/epam/Indigo/pull/809
Issue #520: core: replace RedBlackMap in MoleculeRGroupsComposition class by @loimu in https://github.com/epam/Indigo/pull/810
Issue #520: core: replace RedBlackMap in CanonicalSmilesSaver by @AStepaniuk in https://github.com/epam/Indigo/pull/811
Issue #520: core: replace RedBlackMap in BaseMolecule class by @loimu in https://github.com/epam/Indigo/pull/812
Issue #520: core: replace RedBlackMap for Molecule3dConstraints by @AStepaniuk in https://github.com/epam/Indigo/pull/813
Issue #520: core: replace RedBlackMap in MoleculeGrossFormula class by @loimu in https://github.com/epam/Indigo/pull/814
Issue #520: core: replace RedBlackMap in MultipleCdxLoader class by @loimu in https://github.com/epam/Indigo/pull/816
Issue #520: core: replace RedBlackMap in MolfileSaver class by @loimu in https://github.com/epam/Indigo/pull/819
Issue #520: core: replace RedBlackMap in BaseReactionSubstructureMatcher class by @loimu in https://github.com/epam/Indigo/pull/820
#843 Make core List moveable by @AStepaniuk in https://github.com/epam/Indigo/pull/844
Fix indigo-service for config not found message issue by @AlexanderSavelyev in https://github.com/epam/Indigo/pull/873
CDXML agents and reactions support. #832, #836, #837, #835, #834, #832, #830, #853 by @even1024 in https://github.com/epam/Indigo/pull/872
S-Groups support for extended SMILES (#874) by @even1024 in https://github.com/epam/Indigo/pull/875

New Contributors

@AStepaniuk made their first contribution in https://github.com/epam/Indigo/pull/803
@loimu made their first contribution in https://github.com/epam/Indigo/pull/810

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.7.0...indigo-1.8.0-rc.1

Indigo 1.7.0

Released 2022-05-26

Features

API web service: added /render endpoint for rendering compounds and reactions
API: added logP calculation to Python API
API: added atom hybridization calculation to Python API
API: added salt stripping method to Python API
Core: added support for multistep reactions
Ketcher WASM API: added InChIKey calculation method
API: Added Jupyter notebooks with examples of using Indigo in machine learning
API: Added initial version of graph neural networks featurizers

Improvements

ZLib updated to 1.2.12
LibPNG updated to 1.6.37
TinyXML updated to TinyXML2 9.0.0
Bingo PostgreSQL support to Postgres 13 and 14 added, thanks @SPKorhonen; dropped support for Postgres 9.6

Bugfixes

Bingo Elastic: fixed exact search (#644)
Core: Ketcher format loader: options handling fixed (#588)
API: Fixed name() calling for RXNV3000 format (#678)
Numerous fixes for Ketcher data format (#689, #711, #733, #734)
API web service: fixed descriptors calculation

Indigo 1.6.1

Released 2021-12-28

Features

PoC implementation of Indigo modern C++ user API written on top of low-level C API. Later it will be used in Indigo-WASM and probably other languages.
New Indigo service added as preview. Modernized Indigo service implements JSON:API protocol and can be installed as Docker image epmlsop/indigo-service:enhanced-latest.
Indigo API ported to ARM64 processor architecture. Python, Java and C# wrappers now contain required native libraries for macOS (Apple M1) and Linux.
Implemented loader for CDXML format.
Dative and hydrogen bonds are now supported.
Implemented partial aromatization/dearomatization for the structures with superatoms.
Multifragment support for KET-format.
Simple objects support for KET-format.
Atom's aliases and functional groups' attributes support for KET-format.
Indigo-Python: initial version of inorganic salt checker added.

Improvements

Bingo-NoSQL major refactoring with significant multithreading performance improvements.
C++ unittests were separated in API and Core parts.
CMake build system by default tries to enable as many components as possible and warns if building something is not possible on the current platform.
Migrated to modern C++ standard mutexes and locks instead of own-written implementation.
Using thread-safe objects in Indigo API instead of raw mutexes to guarantee thread safety.
C++ code modernization: added 'override', replaced plain C functions with corresponding from std, etc.
Indigo API integration tests engine parallelized.
Indigo WASM API for Ketcher reached stable status and is now published to NPM public repository.
Indigo i386 libraries for Windows prepared.
CI/CD: automatic code style checks and linters added for Python and C++ code.

Bugfixes

Fixed multiple data races in API and especially in Bingo-NoSQL (#476).
InChI library bugfix for empty string support
Multiple small bugfixes in Indigo-Ketcher WASM module and Indigo Service.
Bingo-Elastic-Java: updated all dependencies to fix log4j security issue.
Fixed an occasional error in RPE.
Bingo-NoSQL: fixed enumerateId() in Java.

Indigo 1.5.0

Released 2021-09-06.

Features

InChI updated to 1.06
Added WebAssembly support to run Indigo in a web browser.
Added Java and Python API for Bingo Elasticsearch cartridge
Added JSON-based data format for interacting with Ketcher supporting enhanced stereochemistry, simple graphics, reactions and r-groups.

Improvements

Added C++ unittests.
Added multiple API integration tests.
CMake build system reworked, now all components, including Bingo cartridges and Python, Java, C# API. could be built using single CMake command.
Migrated to standard modern C++ smart pointers. Changed AutoPtr to std::unique_ptr.
Unified molecule check function and changed the result format.
Miscellaneous modern C++ related refactorings: added 'override', replaced plain C functions with corresponding from std.
Optimized the adding of elements to atoms and bonds arrays.
Exposed oneBitsList in .NET API.
Implemented context manager and iterator for Bingo object.
Added Bingo CI for Postgres 9.6.

Bugfixes

api: sessions fixed, now options are session-scoped, not global.

Previous versions: