Epam Indigo Versions Save

Universal cheminformatics toolkit, utilities and database search tools

indigo-1.12.0

11 months ago

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: https://github.com/epam/Indigo/compare/indigo-1.11.0...indigo-1.12.0

indigo-1.11.0

11 months ago

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: https://github.com/epam/Indigo/compare/indigo-1.10.0...indigo-1.11.0

indigo-1.10.0

1 year ago

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

1 year ago
  • 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-1.8.3

1 year ago

What's Changed

Full Changelog: https://github.com/epam/Indigo/compare/indigo-1.8.2...indigo-1.8.3

indigo-1.8.2

1 year ago

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-rc.1

1 year ago

What's Changed

New Contributors

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

indigo-1.8.0

1 year ago

What's Changed

New Contributors

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

indigo-1.7.0

2 years ago

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: https://github.com/epam/Indigo/compare/indigo-1.6.1...indigo-1.7.0

indigo-1.6.1

2 years ago

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: https://github.com/epam/Indigo/compare/indigo-1.5.0...indigo-1.6.1