Released 2025-02-13
- #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
Released 2025-02-12
- #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
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
Released 2025-01-10
- #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
- #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
Released 2024-11-18
- #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
- #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
Released 2024-10-04
- #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
- #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
Released 2024-09-06
- #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
- #1944 Fullerene and 3D molecules are not represented as 3D in the Miew 3D window
- #2213 Layout for 1-step reactions is broken
- #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
Released 2024-09-06
- #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
- #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
- #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
Released 2024-08-27
- #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
- #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.
- #1976 Too slow monomer library load
Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.21.0...indigo-1.20.0
Released 2024-07-01
- #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
- #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
Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.19.0...indigo-1.12.0
Released 2024-05-02
- #1755 Import and export fasta format for RNA, DNA and PEPTIDES
- #1466 Export as sequence string for RNA, DNA and PEPTIDEs
- #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
Released 2024-02-29
- #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
- #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
Released 2024-01-30
- #1185 Macromolecules export from MolV3000 to KET
- #1381 Macromolecules import from KET
- #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
- #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
Released 2023-11-07
- #1217 Support SDF-format for Indigo-Ketcher API
- #1257 Enhanced stereo labels on atropisomers are lost when opening saved Extended SMILES
- #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
- #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
Released 2023-10-04
- #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
- #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
- #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
Released 2023-07-09
- #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
- #1098 api: add method for copying RGroups
Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.11.0...indigo-1.12.0
Released 2023-06-19
- #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
- #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
Released 2023-03-22
- #941 CDX export
- #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
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
Released 2022-11-28
- 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
Released 2022-10-14
- ci: fix npm versioning according to semver by @mkviatkovskii in #741
- Fixed mistypes by @SunFellow in #743
- Rename
indigo-ketcher.zipartifact toindigo-wasm.zipby @SunFellow in #744 - api: added TPSA calculation by @mkviatkovskii in #745
- api: added numRotatableBonds, numHydrogenBondAcceptors, numHydrogenBondDonors by @mkviatkovskii in #748
- api: added logP and molarRefractivity, removed Python implementation by @mkviatkovskii in #750
- Text cipfix by @even1024 in #739
- api: added atom hybridization calculation by @mkviatkovskii in #751
- api: renamed cLogP to logP by @mkviatkovskii in #752
- api: bingo-nosql: fix partitioning in exact search by @mkviatkovskii in #754
- api: c: another stage of abandoning self-written red-black tree collections by @mkviatkovskii in #756
- api: cpp: replace multiple Indigo*Iterator classes to single template one; add Bingo.Part test by @mkviatkovskii in #757
- metadata refactoring by @even1024 in #755
- core: ket: text rendering support by @even1024 in #760
- core: molecule auto loader: cdx enable; text for reaction fix (#706) by @even1024 in #763
- core: base64 support for binary formats, uninitialized data and #764 fix by @even1024 in #766
- #768: api: add hash() method for molecules and reactions, improve reaction hash to decrease number of collisions by @mkviatkovskii in #769
- Bingo Elastic search by @AATDev21 in #772
- #770: reduce list of exported symbols to avoid conflicts with other shared libraries by @mkviatkovskii in #793
- #791: core: molecule: Lee-Crippen SMARTS pKa calculation method implemented by @mkviatkovskii in #792
- #794: ci: add version changing script and update version to 1.8.0-dev by @mkviatkovskii in #795
- core: render2d: text renderer fixes, UTF-8 support, subscript/superscript, all arrows styles, fix for #355 by @even1024 in #776
- #777: utils: indigo-service: reorganize codebase, simplify docker compose, update ui by @mkviatkovskii in #796
- #798: api: python: reorganize codebase by @mkviatkovskii in #799
- #163: api: added test by @mkviatkovskii in #802
- Issue #520: api: replace RedBlackMap in IndigoDeconvolution by @AStepaniuk in #803
- #808: render2d: equilibrium arrows rendering supported by @even1024 in #801
- Fix for Indigo-WASM build by @SPKorhonen in #828
- Restore indigo service by @AlexanderSavelyev in #858
- Issue #520: core: replace RedBlackMap and RedBlackSet implementation by @AStepaniuk in #804
- Issue #520: core: replace RedBlackMap for GraphEmbeddingsStorage by @AStepaniuk in #805
- Issue #520: core: replace RedBlackMap in SimpleCycleBasis by @AStepaniuk in #806
- Issue #520: core: replace RedBlackMap for MangoPg by @AStepaniuk in #809
- Issue #520: core: replace RedBlackMap in MoleculeRGroupsComposition class by @loimu in #810
- Issue #520: core: replace RedBlackMap in CanonicalSmilesSaver by @AStepaniuk in #811
- Issue #520: core: replace RedBlackMap in BaseMolecule class by @loimu in #812
- Issue #520: core: replace RedBlackMap for Molecule3dConstraints by @AStepaniuk in #813
- Issue #520: core: replace RedBlackMap in MoleculeGrossFormula class by @loimu in #814
- Issue #520: core: replace RedBlackMap in MultipleCdxLoader class by @loimu in #816
- Issue #520: core: replace RedBlackMap in MolfileSaver class by @loimu in #819
- Issue #520: core: replace RedBlackMap in BaseReactionSubstructureMatcher class by @loimu in #820
- #843 Make core List moveable by @AStepaniuk in #844
- Fix indigo-service for config not found message issue by @AlexanderSavelyev in #873
- CDXML agents and reactions support. #832, #836, #837, #835, #834, #832, #830, #853 by @even1024 in #872
- S-Groups support for extended SMILES (#874) by @even1024 in #875
Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.7.0...indigo-1.8.0-rc.1
Released 2022-05-26
- 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
- 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
- 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
Released 2021-12-28
- 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.
- 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.
- 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.
Released 2021-09-06.
- 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.
- 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.
- api: sessions fixed, now options are session-scoped, not global.
Previous versions: