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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 epam#741
  • Fixed mistypes by @SunFellow in epam#743
  • Rename indigo-ketcher.zip artifact to indigo-wasm.zip by @SunFellow in epam#744
  • api: added TPSA calculation by @mkviatkovskii in epam#745
  • api: added numRotatableBonds, numHydrogenBondAcceptors, numHydrogenBondDonors by @mkviatkovskii in epam#748
  • api: added logP and molarRefractivity, removed Python implementation by @mkviatkovskii in epam#750
  • Text cipfix by @even1024 in epam#739
  • api: added atom hybridization calculation by @mkviatkovskii in epam#751
  • api: renamed cLogP to logP by @mkviatkovskii in epam#752
  • api: bingo-nosql: fix partitioning in exact search by @mkviatkovskii in epam#754
  • api: c: another stage of abandoning self-written red-black tree collections by @mkviatkovskii in epam#756
  • api: cpp: replace multiple Indigo*Iterator classes to single template one; add Bingo.Part test by @mkviatkovskii in epam#757
  • metadata refactoring by @even1024 in epam#755
  • core: ket: text rendering support by @even1024 in epam#760
  • core: molecule auto loader: cdx enable; text for reaction fix (#706) by @even1024 in epam#763
  • core: base64 support for binary formats, uninitialized data and #764 fix by @even1024 in epam#766
  • #768: api: add hash() method for molecules and reactions, improve reaction hash to decrease number of collisions by @mkviatkovskii in epam#769
  • Bingo Elastic search by @AATDev21 in epam#772
  • #770: reduce list of exported symbols to avoid conflicts with other shared libraries by @mkviatkovskii in epam#793
  • #791: core: molecule: Lee-Crippen SMARTS pKa calculation method implemented by @mkviatkovskii in epam#792
  • #794: ci: add version changing script and update version to 1.8.0-dev by @mkviatkovskii in epam#795
  • core: render2d: text renderer fixes, UTF-8 support, subscript/superscript, all arrows styles, fix for #355 by @even1024 in epam#776
  • #777: utils: indigo-service: reorganize codebase, simplify docker compose, update ui by @mkviatkovskii in epam#796
  • #798: api: python: reorganize codebase by @mkviatkovskii in epam#799
  • #163: api: added test by @mkviatkovskii in epam#802
  • Issue #520: api: replace RedBlackMap in IndigoDeconvolution by @AStepaniuk in epam#803
  • #808: render2d: equilibrium arrows rendering supported by @even1024 in epam#801
  • Fix for Indigo-WASM build by @SPKorhonen in epam#828
  • Restore indigo service by @AlexanderSavelyev in epam#858
  • Issue #520: core: replace RedBlackMap and RedBlackSet implementation by @AStepaniuk in epam#804
  • Issue #520: core: replace RedBlackMap for GraphEmbeddingsStorage by @AStepaniuk in epam#805
  • Issue #520: core: replace RedBlackMap in SimpleCycleBasis by @AStepaniuk in epam#806
  • Issue #520: core: replace RedBlackMap for MangoPg by @AStepaniuk in epam#809
  • Issue #520: core: replace RedBlackMap in MoleculeRGroupsComposition class by @loimu in epam#810
  • Issue #520: core: replace RedBlackMap in CanonicalSmilesSaver by @AStepaniuk in epam#811
  • Issue #520: core: replace RedBlackMap in BaseMolecule class by @loimu in epam#812
  • Issue #520: core: replace RedBlackMap for Molecule3dConstraints by @AStepaniuk in epam#813
  • Issue #520: core: replace RedBlackMap in MoleculeGrossFormula class by @loimu in epam#814
  • Issue #520: core: replace RedBlackMap in MultipleCdxLoader class by @loimu in epam#816
  • Issue #520: core: replace RedBlackMap in MolfileSaver class by @loimu in epam#819
  • Issue #520: core: replace RedBlackMap in BaseReactionSubstructureMatcher class by @loimu in epam#820
  • #843 Make core List moveable by @AStepaniuk in epam#844
  • Fix indigo-service for config not found message issue by @AlexanderSavelyev in epam#873
  • CDXML agents and reactions support. #832, #836, #837, #835, #834, #832, #830, #853 by @even1024 in epam#872
  • S-Groups support for extended SMILES (#874) by @even1024 in epam#875

New Contributors

  • @AStepaniuk made their first contribution in epam#803
  • @loimu made their first contribution in epam#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: