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Indigo 1.10.0

Released 2023-03-22

What's Changed

Features

  • #941 CDX export

Bugfixes

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

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

Indigo 1.9.0

Released 2023-01-31

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

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

Indigo 1.8.2

Released 2022-11-28

What's Changed

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

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

Indigo 1.8.0

Released 2022-10-14

What's Changed

  • ci: fix npm versioning according to semver by @mkviatkovskii in #741
  • Fixed mistypes by @SunFellow in #743
  • Rename indigo-ketcher.zip artifact to indigo-wasm.zip by @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: https://github.com/epam/Indigo/compare/indigo-1.7.0...indigo-1.8.0-rc.1

Indigo 1.7.0

Released 2022-05-26

Features

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

Improvements

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

Bugfixes

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

Indigo 1.6.1

Released 2021-12-28

Features

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

Improvements

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

Bugfixes

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

Indigo 1.5.0

Released 2021-09-06.

Features

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

Improvements

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

Bugfixes

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

Previous versions: