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

Indigo 1.6.1

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.
• Enhanced stereochemistry support for KET-format.
• Atom's aliases and functional groups' attributes support for KET-format.
• Indigo-Python: initial version of inorganic salt checker added.
• Implemented checkSalt() #539

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.

Full Changelog: indigo-1.5.0...indigo-1.6.1

indigo-1.5.0

Indigo 1.5.0

18 Aug 2021

New features and improvements

• Added WebAssembly support to run Indigo in a web browser. See how to build. [milestone].
• Implemented NodeJS API for Indigo [implemented].
• Added Java API for Bingo Elasticsearch cartridge [feature].
• Implemented reactions in Python API of Bingo Elasticsearch cartridge [feature].
• Added support for JSON-based interaction with Ketcher for supporting enhanced stereochemistry, simple graphics, etc. [feature]
• Supported reactions in JSON-based format [feature].
• Supported r-groups in JSON-based format [feature].
• Added C++ unittests [feature].
• Added multiple integration tests [feature].
• Now Indigo uses CMake build system. See how to build
• Migrated to standard C++11 smart pointers. Changed AutoPtr to std::unique_ptr and std::shared_ptr.
• Unified molecule check function and changed the result format [improvement].
• Miscelaneous C++11 related refactorings: added 'override', replaced plain C functions with corresponding from std:: ) [improvement].
• Optimized the adding of elements to atoms and bonds arrays [improvement].
• Exposed oneBitsList in .NET API [fix].
• Implemented context manager and iterator for Bingo object [improvement].
• Added Bingo CI for Postgres 9.6 [improvement].

Bug fixes

• Incorrect calculation and check on partially selected structure [fix].
• PNG rendering crash [fix].
• .NET Indigo nuget error: Unable to load DLL 'indigo' [fix].
• Bingo-MSSQL compilation fails [fix].
• Ionize segfault for deuterated molecule (if pKa-model-level >= 1) [fix].
• SDF decomposition test fail [fix].
• Fingerprints differ between mac os x and other platforms [fix].
• Unstable behavior of Indigo on different platforms [fix].
• CDX parser failure [fix].
• Java API: native libs loading fail [fix].

Indigo 1.4.3

This release also includes all improvements and fixes from intemediate version 1.4.2.

New features and improvements:

• bingo-elastic: python:
  • catch and log Indigo exceptions on iterate_file added
  • PyLint checking added
• bingo-nosql: python:
  • added context manager and iterator for BingoObject

Bugfixes

• api: build: reduce list of exported symbols for Indigo shared library on Linux to hide libstdc++ symbols (#276)
• api: java: fix load native libs on Windows (#261) (Thanks to @00Green27 for pull request)
• api: data S-groups strings were not properly terminated (#231)

Indigo 1.4.1

New features and improvements:

• License changed to Apache 2.0
• Initial version of Bingo ElasticSearch plugin for Java and Python was added. See details:
  • https://github.com/epam/Indigo/blob/master/api/plugins/bingo-elastic/java/README.md
  • https://github.com/epam/Indigo/blob/master/api/plugins/bingo-elastic/python/README.md
• Indigo.NET switched to .NET Standard 2.0 format and became truly cross-platform, supporting Windows, Linux and macOS on all .NET
  runtimes supporting .NET Standard 2.0.
• Indigo REST API service sources published
• Support of ECFP, FCFP fingerprints added
• Python wheels added to PyPI as epam.indigo
• Preliminary support of new molecules and reactions JSON format added
• Method check for validating molecules and reactions added
• CI for native libraries and wrappers for Python, Java and .NET moved to Github Actions engine
• iterateSDF with files over 4GB support added
• 32-bit x86 libraries were removed from binary packages, although you can still build the manually.
• Python 2 support dropped, but you can still build Indigo Python 2 wrapper manually
• API functional tests added
• Java API cleanup
• Support for building in Visual Studio 2019, macOS 10.14 and 10.15 added
• Added support for isotopic information in Gross formula

Bugfixes

• Python renderer usage (#136)
• Molecule corruption after atom.remove (#177)
• indigo.loadMolecule("ARS") crashes (#162)
• Python iterateTautomers bug (#143)
• Fixes for tautomer fingerprints calculation
• Fixes in SMARTS rendering
• Added saving chirality flag