Releases: epam/Indigo
Releases · epam/Indigo
indigo-1.15.0
What's Changed
- #1221 An empty structure is returned given incorrect InChi string by @Wadym in #1228
- #1224 Different indent after loading reaction from file and after layout it by @AliaksandrDziarkach in #1227
- #914 Why is the code InChI=123 valid by @Wadym in #1229
- Revert: #1033 CDXML: expanded abbreviation opens as contracted from .cdxm files by @even1024 in #1234
- #1245 Reaction/Molecule autoloaders don't load SMARTS by @AliaksandrDziarkach in #1243
- #1252 SMARTS loader load grouped components as separate molecules by @AliaksandrDziarkach in #1255
- #1254 SMARTS with component-level grouping saved without '()' by @AliaksandrDziarkach in #1266
- #1282 SMARTS load/save errors in Indigo. by @AliaksandrDziarkach in #1284
- #1285 Add new query properties support to KET format by @AliaksandrDziarkach in #1286
- #1287 New S-Group type Query component level grouping by @AliaksandrDziarkach in #1288
- #1278 Indigo-service. Remove Mithril library dependency from UI module by @bodyangug in #1275
- #1302 Pylint cause error "too many arguments" by @AliaksandrDziarkach in #1301
- #1296 Add "customQuery" option support to ket format by @AliaksandrDziarkach in #1297
- #1316 SMARTS saver miss component level grouping by @AliaksandrDziarkach in #1317
- #1303 Return original format by @AliaksandrDziarkach in #1315
- #1310 Error while opening SMARTS contains comma by @AliaksandrDziarkach in #1327
- #1184 Support monomer templates export into KET-format by @even1024 in #1251
- #1183 Support monomer templates import from KET-format by @even1024 in #1335
- #1319 Directional bonds not work with SMARTS by @AliaksandrDziarkach in #1326
- #1338 Use docker image for building npm packages and apply tags while publish by @AlexanderSavelyev in #1339
- #1309 Error appears while trying to save some element with set up H count and implicit H count by @AliaksandrDziarkach in #1336
- #1281 Support SMARTS "or unspecified" bond property by @AliaksandrDziarkach in #1341
- #1328 Chirality is not added to the SMARTS file by @AliaksandrDziarkach in #1343
- #1325 Indigo should return warning for some attributes by @AliaksandrDziarkach in #1344
- #1331 Ring bond count 'As drawn' saved wrong by @AliaksandrDziarkach in #1352
- #1351 Error returned when try to convert structure with custom query… by @AliaksandrDziarkach in #1353
- #1349 Symbol for topology chain is missing in SMARTS file by @AliaksandrDziarkach in #1354
- #1292 valid SMARTS with cycles cause error in loader by @AliaksandrDziarkach in #1356
- #1358 Error while loading [!#6,!#7,!#8] smarts by @AliaksandrDziarkach in #1361
- #1330 Implicit H count is not added to the SMARTS file by @AliaksandrDziarkach in #1365
- #1355 Error appears when pressing 'Layout" by @AliaksandrDziarkach in #1364
- #1304 Indigo accepts [#6] notation in SMILES mode by @AliaksandrDziarkach in #1363
- #1360 Wrong ordering of atoms in atom list by @AliaksandrDziarkach in #1368
- #1337 List of atoms from custom query is converted into SMARTS filу without aliphatic attribute by @AliaksandrDziarkach in #1373
- #1332 Aromatic atom list is not recognized in SMARTS query by @AliaksandrDziarkach in #1370
- #1376 SMARTS file is paste into Ketcher as SMILES file by @AliaksandrDziarkach in #1375
- #1362 Valence is not added to the SMARTS file by @AliaksandrDziarkach in #1379
- #1371 Chirality symbol is added to the SMARTS when 'single up/down' or 'double cis/trans' bond type is set up by @AliaksandrDziarkach in #1382
- #1372 Wildcard symbol ('any') with logical operators at custom query for bond is missing at SMARTS by @AliaksandrDziarkach in #1386
Full Changelog: indigo-1.14.0-rc.1...indigo-1.15.0-rc.2
Contributors
AlexanderSavelyev, even1024, and 3 other contributors
Assets 2
Indigo 1.13.0
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: indigo-1.12.0...indigo-1.13.0
Indigo 1.12.0
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: indigo-1.11.0...indigo-1.12.0
Indigo-1.11.0
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: indigo-1.10.0...indigo-1.11.0
Indigo-1.10.0
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:release/1.9...release/1.10
Indigo-1.9.0
- 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: indigo-1.8.0...indigo-1.9.0
Contributors
MysterionRise, loimu, and 2 other contributors
Assets 2
Indigo-1.8.3
What's Changed
Full Changelog: indigo-1.8.2...indigo-1.8.3
Contributors
even1024
Assets 2
Indigo-1.8.2
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: indigo-1.8.0...indigo-1.8.2
Contributors
mkviatkovskii and even1024
Assets 2
Indigo 1.8.0
What's Changed
- 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
New Contributors
- @AStepaniuk made their first contribution in #803
- @loimu made their first contribution in #810
Full Changelog: indigo-1.7.0...indigo-1.8.0-rc.1
Contributors
AStepaniuk, loimu, and 6 other contributors
Assets 2
Indigo 1.7.0
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 144 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
Full Changelog: indigo-1.6.1...indigo-1.7.0
Contributors
SPKorhonen