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
Updated on June 28, 2024
Release Notes
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
Bugfixes and improvements
-
#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
-
#1802 - bad performance during the parsing of large sequences
Updated on April 30, 2024
Release Notes
What's changed?
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 '<', "#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
Updated on January 30, 2024
Release Notes
What's Changed
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
Updated on October 2, 2023
Release Notes
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: indigo-1.12.0...indigo-1.13.0
Updated on Jul 10, 2023
Release Notes
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 the 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
Updated on Jun 20, 2023
Release Notes
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 the preview and in saved files
- #932 Reagents: When opening Daylight SMILES and Extended SMILES files with reagents 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 the inversion type is chosen in the atom's properties, it is not saved
- #955 Copy Image: Saved bonds do 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 saving a 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)
Updated on March 23, 2023
Release Notes
Features
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
Updated on February 1, 2023
Release Notes
Features
- Add support of R-groups to the CDX loader. by @even1024 #36
- cdx import in scope of current KET/CDXML features support by @even1024 #885
- core: replace MultiMap in MoleculeRGroupsComposition class by @loimu #521
- core: replace MultiMap in MolfileLoader class by @loimu #521
Bugfixes
- MDL Molfile v3000 encoding: Automatic selection of MDL Molfile v3000 encoding doesn't work if the structure contains Enhanced stereochemistry by @mkviatkovskii #924
- Structures with the arrow lose their integrity when pressing 'Layout' by @even1024 #938
- Abbreviations are not supported by @even1024 #685
- api: tests: IronPython update to 3.4.0, fix tests by @mkviatkovskii #934
- CDX import: Reaction arrows disappear when opening a file by @even1024 #943
- CDX import: Aromatized structures are not recognized when Pasting from Clipboard by @even1024 #950
- CDXML parser memory leak by @even1024 #966
- Error opening MOL and RXN files with RBC/SUB/UNC queries by @even1024 #928
- CDX Import, CDXML Import: parsing error when superatom starts with 'R' symbol by @even1024 #960
- CDXML: When opening a saved file with text, the Font size enlarges by @even1024 #961
- CDXML: When opening a file saved with 'Any atom', 'Atom Generics' or 'Group Generics' structure loses its integrity by @even1024 #968
- CDXML import fails to load rectangle primitives by @even1024 in #979
- CDXML: File containing Functional Groups or Salts and Solvents cannot be opened and causes a convert error by @even1024 in #963
- CDXML import: nodes with radicals are not getting parsed by @even1024 #990
- CDXML import: fails to import some cdxml files with multiple text objects related to different fragments by @even1024 #992
- CDXML import: 'superscript' and 'subscript' is not displayed correctly #962
- Improve ssl bingo elastic by @MysterionRise #863
- bingo: postgres: add support for Postgres 15, drop support for Postgres 10 by @mkviatkovskii
- fix auto-saving to CTAB v3000 by @mkviatkovskii #929
Updated on December 6, 2022
Release Notes
Bugfixes
- CDXML import: Molecule above plus sign in #915
Updated on November 29, 2022
Release Notes
New features and improvements
- SMARTS support for implicit hydrogens specifier 'h'
- CDXML enhanced stereochemistry #861
- CDXML abbreviations #862
Bugfixes
- Dearomatize query onload #891
- Multistep to rxn-smiles #870 and #871
