From 51ceaf8a4b9e7de2b04f1760a2bfa732fd81760a Mon Sep 17 00:00:00 2001 From: Aliaksandr Dziarkach <18146690+AliaksandrDziarkach@users.noreply.github.com> Date: Fri, 14 Feb 2025 11:24:33 +0300 Subject: [PATCH] Update CHANGELOG.md (#2768) --- CHANGELOG.md | 507 ++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 506 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b72ea58beb..407f875b42 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,508 @@ +# 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 \ +* #2141 use \ 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 '<', "' 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 @@ -43,7 +548,7 @@ Released 2023-01-31 * 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  +* #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