Epam.indigo

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

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

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

Released 2022-10-14

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

New Contributors
* AStepaniuk made their first contribution in https://github.com/epam/Indigo/pull/803
* loimu made their first contribution in https://github.com/epam/Indigo/pull/810

**Full Changelog**: https://github.com/epam/Indigo/compare/indigo-1.7.0...indigo-1.8.0-rc.1

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

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.