JChem Microservices History of Changes

    January 25th 2022: JChem Microservices 22.2.0

    No changes.

    January 18th 2022: JChem Microservices 22.1.0

    No changes.

    January 3rd 2022: JChem Microservices 21.20.0

    • DB module
      • Double bond stereo was not checked in reaction search.

    December 15th 2021: JChem Microservices 21.19.0

    Improvements

    • JChem Microservices runs in Java 11 Environment from now on. Documentation

    Bugfixes

    • DB module
      • The export directory should have been created manually in order to run reindex successfully.
      • Generic tautomer mode of substructure search could result false hits in the case of some overlapping aromatic regions and tautomer regions.
      • Standardizer configuration could not be specified in xml file format.

    November 9th 2021: JChem Microservices 21.18.0

    No changes.

    October 28th 2021: JChem Microservices 21.17.0

    Improvements

    • IO module
      • The /rest-v1/molconvert/split-with-properties endpoint generated 0D output in some cases. These molecules are cleaned in 2D now.

    Bugfixes

    • DB module
      • Normal canonical tautomer search (full-fragment and duplicate) could miss hit in case of aromatic rings with different Kekule format.

    October 18th 2021: JChem Microservices 21.16.0

    Bugfixes

    • DB module
      • Extra "Markush Enumeration" license was necessary due to a bug.

    Long Term Supported Release - January 14th, 2022: JChem Microservices 21.15.2 (Iodine.2)

    Bugfixes

    • DB module
      • Double bond stereo was not checked in reaction search.

    Long Term Supported Release - November 3rd, 2021: JChem Microservices 21.15.1 (Iodine.1)

    No changes.

    September 28th 2021: JChem Microservices 21.15.0

    Improvements

    • DB module
      • Some invalid structures were stopped at inserting. Now it is fixed and the process progresses without errors.

    August 25th 2021: JChem Microservices 21.14.0

    No changes.

    August 3rd 2021: JChem Microservices 21.13.0

    Improvements

    • DB module
      • New search parameters implemented: ignoreCharge, ignoreIsotope

    July 16th 2021: JChem Microservices 21.12.0

    No changes.

    June 23rd 2021: JChem Microservices 21.11.0

    Improvements

    • DB module
      • /rest-v1/db/additional/upload endpoint:
        • Can now use import options from inputFormat
        • Does not add new line after one-line structures

    Bugfixes

    • DB module
      • Searching any bond on aromatic bond missed hit in substructure search in the case of molecule types with tautomerHandlingMode=GENERIC parameter.

    June 9th 2021: JChem Microservices 21.10.0

    No changes.

    May 18th 2021: JChem Microservices 21.9.0

    Bugfixes

    • False similarity search results were given in the case of molecule types with tautomerHandlingMode=GENERIC parameter.

    April 27th 2021: JChem Microservices 21.8.0

    Bugfixes

    • Critical vulnerability has been eliminated.

    April 21st 2021: JChem Microservices 21.7.0

    Bugfixes

    • DB module
      • The known issue relating the idProperty has been fixed.
      • Structures with multicenter bonds - in tables with molecule types with tautomer handling mode GENERIC - throw java.lang.RuntimeException: contract violation!
      • Standardized molecule search (rest-v1/db/substructure/ endpoint) could give false hits when the query structure contained specific combination of query bonds because query tetrahedral stereo configuration beside bondlists was not checked when matching on target tetrahedral configurations.

    JChem Microservices 21.6.0

    Not released.

    JChem Microservices 21.5.0

    Not released.

    Long Term Supported Release - January 19th, 2022: JChem Microservices 21.4.6 (Helium.6)

    Bugfixes

    • DB module
      • Double bond stereo was not checked in reaction search.

    Long Term Supported Release - November 2nd, 2021: JChem Microservices 21.4.5 (Helium.5)

    No changes.

    Long Term Supported Release - August 31st, 2021: JChem Microservices 21.4.4 (Helium.4)

    No changes.

    Long Term Supported Release - June 15th, 2021: JChem Microservices 21.4.3 (Helium.3)

    No changes.

    Long Term Supported Release - April 28th, 2021: JChem Microservices 21.4.2 (Helium.2)

    Bugfixes

    • Critical vulnerability has been eliminated.

    Long Term Supported Release - April 21st, 2021: JChem Microservices 21.4.1 (Helium.1)

    Bugfixes

    • DB module
      • The known issue relating the idProperty has been fixed.

    March 24th 2021: JChem Microservices 21.4.0

    Bugfixes

    • DB module

      • Duplicate search could result missing hit in case of structures with repeating units.
      • The known issue relating the gcrdb schema has been fixed

    Known Issues

    • DB module
      • /rest-v1/db/additional/ upload endpoint can throw exception com.chemaxon.webservices.db.exception.BadChemicalDataInRequestException if idProperty is autogenerated in the case of tables with those molecule types which have tautomer handling mode different than OFF. The relevant parameter of the molecule type is specified in the application.properties file as com.chemaxon.zetor.types[n].tautomerHandlingMode.

    February 23rd 2021: JChem Microservices 21.3.0

    Bugfixes

    • DB module
      • Duplicate and full fragment search failed with some query structures if the molecule type had generic tautomerization method and some custom transformation set in its standaridzer configuration.

    Known Issues

    • DB module
      • If the default schema gcrdb is set in the application.properties file, the additional parameters - taken from JChem Engines cache and memory calculator like com.chemaxon.zetor.settings.molecule.cachedObjectCount are not taken into account. If you want to set these additional parameters, please set com.chemaxon.zetor.settings.scheme= mapdb
      • /rest-v1/db/additional/ upload endpoint can throw exception com.chemaxon.webservices.db.exception.BadChemicalDataInRequestException if idProperty is autogenerated in the case of tables with those molecule types which have tautomer handling mode different than OFF. The relevant parameter of the molecule type is specified in the application.properties file as com.chemaxon.zetor.types[n].tautomerHandlingMode.

    February 1st 2021: JChem Microservices 21.2.0

    Improvements

    • DB module

      • First search after restarting service on each table with each search type was very slow on large databases.
      • Significant speedup at similarity search with low or zero similarity threshold. Decreasing the threshold still slows down searches, but the effect on speed is decreased.

    Bugfixes

    • Structure checker module

      • StructureChecker custom name was not used when parsing from XML and checker was triggered.

    Known Issues

    • DB module

      • If the default schema gcrdb is set in the application.properties file, the additional parameters - taken from JChem Engines cache and memory calculator like com.chemaxon.zetor.settings.molecule.cachedObjectCount are not taken into account. If you want to set these additional parameters, please set com.chemaxon.zetor.settings.scheme= mapdb
      • /rest-v1/db/additional/ upload endpoint can throw exception com.chemaxon.webservices.db.exception.BadChemicalDataInRequestException if idProperty is autogenerated in the case of tables with those molecule types which have tautomer handling mode different than OFF. The relevant parameter of the molecule type is specified in the application.properties file as com.chemaxon.zetor.types[n].tautomerHandlingMode.

    JChem Microservices 21.1.0

    Not released.

    December 3rd 2020: JChem Microservices 20.21.0

    No changes.

    October 29th 2020: JChem Microservices 20.20.0

    Bugfixes

    • DB module

      • Fix known issue present since version 20.16.0.

    Long Term Supported Release - September 10th, 2021: JChem Microservices 20.19.5 (Gallium.5)

    No changes.

    Long Term Supported Release - June 11th, 2021: JChem Microservices 20.19.4 (Gallium.4)

    No changes.

    Long Term Supported Release - May 10th, 2021: JChem Microservices 20.19.3 (Gallium.3)

    Bugfixes

    • Critical vulnerability has been eliminated.

    Long Term Supported Release - February 18th, 2021: JChem Microservices 20.19.2 (Gallium.2)

    No changes.

    Long Term Supported Release - October 28th, 2020: JChem Microservices 20.19.1 (Gallium.1)

    September 17th 2020: JChem Microservices 20.19.0

    Bugfixes

    • Structure checker module

      • When using json as preset then exportFormat for final result did not work.

    Known Issues

    • DB module

      • Database cannot be reindexed if upgraded from version less than 20.16. In that case, export the data before the upgrade, and create new table(s) and import the data after the upgrade.

    September 2nd 2020: JChem Microservices 20.18.0

    Improvements

    • DB module

      • Autogenerated IDs are returned.

    Bugfixes

    • DB module

      • Double bond stereo information was sometimes also ignored in case of search parameter stereoSearchIgnoreTetrahedralStereo set to true .

    Known Issues

    • DB module

      • Database cannot be reindexed if upgraded from version less than 20.16. In that case, export the data before the upgrade, and create new table(s) and import the data after the upgrade.

    August 12th 2020: JChem Microservices 20.17.0

    Improvements

    • DB module

      • Import from and export to Amazone S3 buckets is supported from now on.

      • Highlight endpoint has been improved. It is able to export to different formats including images with all image options.

      • Version of Hazelcast backend has been increased to 4.

    Bugfixes

    • DB module

      • Queries with explicit H and any or notlist atoms didn't match the appropriate target in generic tautomer substructure search.

    • IO module

      • Arrow and structures were mispositioned at image generation for reactions.

    Known Issues

    • DB module

      • Database cannot be reindexed if upgraded from version less than 20.16. In that case, export the data before the upgrade, and create new table(s) and import the data after the upgrade.

    July 20th 2020: JChem Microservices 20.16.0

    Improvements

    • All modules

      • The configuration parameters specified in the jws-config/common-config/application.properties file can also be received from a table. Documentation

    • Structure manipulation module

      • CIP Stereo Calculator endpoint is added

      • Reaction Converter endpoint is added

    • DB module

      • Tautomer hits are also displayed at Hit highlight

      • Endpoints added for Standardized molecule search

    Bugfixes

    • Structure checker module

      • SubstructureChecker could throw AIOOBE in case of structures with explicit Hydrogen atoms.

    Known Issues

    • DB module

      • Database cannot be reindexed. Export the data before the upgrade, and create new table(s) and import the data after the upgrade.

    June 30th 2020: JChem Microservices 20.15.0

    Improvements

    • Structure manipulation module

      • Automapper endpoint is added.

      • Aromatization/Dearomatization endpoints are added.

    • DB module

      • Hit highlight endpoint is added.

      • Query transformations stereoSearchIgnoreTetrahedralStereo and stereoSearchOnMarkedDoubleBondOnly are available for refining stereo searches.

    June 18th 2020: JChem Microservices 20.14.0

    Improvements

    • Calculation module

      • New operations are added to TopologyAnalyser: possibleCTBondCount and possibleCTBonds

    Bugfixes

    • Calculation module

      • IllegalArgumentException was thrown in BatchCalculations because of missing pH property.

    May 22nd 2020: JChem Microservices 20.13.0

    Improvements

    • Calculation module

      • Properties can be separately requested in Topology analyzer..

    • DB module

      • Standard reindex process does not work when upgrading from previous version to this version. The stored data must be exported and re-imported.

    May 4th 2020: JChem Microservices 20.12.0

    Improvements

    • DB module

      • Consideration of chiral flag can be set by com.chemaxon.zetor.types[n].stereoAssumption=RELATIVE in the application.properties file of jws-config and of jws-db.

    April 16th 2020: JChem Microservices 20.11.0

    Bugfixes

    • DB module

      • AIOBE could have been thrown in case of some standardizer configuration.

    April 6th 2020: JChem Microservices 20.10.0

    No changes.

    March 23th 2020: JChem Microservices 20.9.0

    No changes.

    Long Term Supported Release - September 17th, 2020: JChem Microservices 20.8.5 (Fermium.5)

    No changes.

    Long Term Supported Release - August 12th, 2020: JChem Microservices 20.8.4 (Fermium.4)

    No changes.

    Long Term Supported Release - June 5th, 2020: JChem Microservices 20.8.3 (Fermium.3)

    Bugfixes

    • DB module

      • Database export/import did not work.

      Long Term Supported Release - May 14th, 2020: JChem Microservices 20.8.2 (Fermium.2)

    No changes.

    Long Term Supported Release - March 30th, 2020: JChem Microservices 20.8.1 (Fermium.1)

    March 13th 2020: JChem Microservices 20.8.0

    Bugfixes

    • DB module

      • Duplicate search in tables of molecule type with tautomerHandlingMode = GENERIC parameter didn't find hits for some structures with tetrahedral stereo information.

    March 3rd 2020: JChem Microservices 20.7.0

    No changes.

    February 26th 2020: JChem Microservices 20.6.0

    Improvements

    • Calculation module

      • Atom count and isotope count is added to elemental analysis.

    Bugfixes

    • DB module

      • Non-polymer query was not found in polymer targets if it was matching on end groups.

    February 21st 2020: JChem Microservices 20.5.0

    No changes.

    February 7th 2020: JChem Microservices 20.4.0

    Bugfixes

    • DB module

      • Large structures with stereo configuration could be incorrectly handled.

    January 24th 2020: JChem Microservices 20.3.0

    Improvements

    • DB module

      • Searching with ignored tetrahedral stereo information has been introduced.

    January 21st 2020: JChem Microservices 20.2.0

    No changes.

    January 13th 2020: JChem Microservices 20.1.0

    Improvements

    • DB module

      • Technical improvements were made on the search process. Reindex is needed; see updateMode.

      • New endpoint /rest-v1/db/additional/upload added for importing molecule files.

    December 19th 2019: JChem Microservices 19.27.0

    No changes.

    December 12th 2019: JChem Microservices 19.26.0

    No changes.

    November 29th 2019: JChem Microservices 19.25.0

    Improvements

    • DB module

      • Duplicate search takes also higher order stereo information (like axial stereo information) into account.

    November 15th 2019: JChem Microservices 19.24.0

    No changes.

    November 8th 2019: JChem Microservices 19.23.0

    Improvements

    • New module - Structure Checker - has been implemented providing structure checker and fixer functionalities.

    October 21th 2019: JChem Microservices 19.22.0

    Improvements

    • DB module

      • Cache size decreased by 20%.

      • 15% import speed improvement.

      • 20-50% search speedup for frequent queries

    Bugfixes

    October 7th 2019: JChem Microservices 19.21.0

    Improvements

    • DB module

      • Memory need decreases in case of datasets with explicit Hydrogens.

    Bugfixes

    • DB module

      • Sometimes searches did not stop if search wall time limit was reached.

    September 18th 2019: JChem Microservices 19.20.0

    No changes.

    September 2nd 2019: JChem Microservices 19.19.0

    Improvements

    • DB module

      • Double bond stereo information can be ignored during substructure search.

    August 3rd, 2019: JChem Microservices 19.18.0

    No changes.

    July 16th, 2019: JChem Microservices 19.17.0

    No changes.

    July 4th, 2019: JChem Microservices 19.16.0

    No changes.

    June 27th, 2019: JChem Microservices 19.15.0

    Improvements

    • Default timeout is lowered to 30 seconds.

    June 24th, 2019: JChem Microservices 19.14.0

    No changes.

    June 17th, 2019: JChem Microservices 19.13.0

    No changes.

    June 3rd, 2019: JChem Microservices 19.12.0

    Improvements

    • DB module

      • New endpoint added: substructureHitCountEstimate

    May 21st, 2019: JChem Microservices 19.11.0

    Bugfixes

    • Config server was not visible in Eureka.

    • Calculations module

      • API provided superfluous fields for structure input.

    May 7th, 2019: JChem Microservices 19.10.0

    Improvements

    • Calculations module has been extended by

      • Batch calculations

    March 18th, 2019: JChem Microservices 19.8.0 (removed from the downloadables)

    No changes.

    Long Term Supported Release - July 30th, 2019: JChem Microservices 19.7.3 (Deuterium.3)

    Long Term Supported Release - June 3rd, 2019: JChem Microservices 19.7.2 (Deuterium.2)

    Long Term Supported Release - April 11th, 2019: JChem Microservices 19.7.1 (Deuterium.1)

    March 8th, 2019: JChem Microservices 19.7.0

    No changes.

    February 28th, 2019: JChem Microservices 19.6.0

    Improvements

    • New module - Markush (Markush Enumeration) - has been implemented.

    • Structure manipulation module has been extended by

      • Extractor

      • Fragmenter

      • Molecule cleaner

    Bugfixes

    • Substructure search returned NaN if similarity value was requested but could not be calculated. From now on, fingerprint bit distance is returned instead of similarity value.

    February 13th, 2019: JChem Microservices 19.4.0

    Improvements

    • Calculations module has been extended by

      • Topology analyser

      • Polar surface area

      • Major microspecies

    February 4th, 2019: JChem Microservices 19.3.0

    Improvements

    • Calculations module has been extended by

      • HBDA

      • logD

      • pKa distribution

      • Canonical tautomerization

      • Dominant tautomerization

    January 23rd, 2019: JChem Microservices 19.2.0

    No changes.

    January 11th, 2019: JChem Microservices 19.1.0

    Improvements

    • Calculations module has been extended by

      • Elemental analysis

      • HLB

      • Isoelectric point

      • logP

      • pKa

      • Solubitility

      • Stereoisomer

    December 14th, 2018: JChem Microservices 18.30.0

    Improvements.

    • New module - Calculations - has been implemented