JChem Choral History of Changes

    August 29th, 2023: JChem Choral 23.12.0

    Improvements

    July 12th, 2023: JChem Choral 23.9.0

    No changes.

    Long Term Supported Release - September 28th, 2023: JChem Choral 23.6.3 (Mercury.3)

    No changes.

    Long Term Supported Release - July 25th, 2023: JChem Choral 23.6.2 (Mercury.2)

    No changes.

    Long Term Supported Release - May 25th, 2023: JChem Choral 23.6.1 (Mercury.1)

    No changes.

    April 17th, 2023: JChem Choral 23.5.0

    Improvements

    • There were improvements implemented in chemical hashed fingerprint generation. The similarity values of some molecule pairs can be different causing different similarity search results compared to the former versions of JChem Choral.
    • JChem Choral runs in Java 17 Environment from now on.

    Bugfixes

    • Spring-boot framework has been upgraded to 3.0.5 fixing
      • CVE-2023-20860 Spring webmvc vulnerability
      • CVE-2022-1471 SnakeYaml vulnerability
      • CVE-2023-1436 Jettison vulnerability
      • CVE-2022-45143 Tomcat-embed vulnerability

    January 27th, 2023: JChem Choral 23.1.0

    Bugfixes

    • CVE-2022-0084 (xnio) vulnerability has been fixed.
    • CVE-2022-36437 (hazelcast) vulnerability has been fixed.
    • CVE-2022-40151 and CVE-2022-41966 (xstream) vulnerability has been fixed.
    • CVE-2022-40153 (woodstox) vulnerability has been fixed.
    • Install failed if dbsm_session.sleep call is forbidden for the Choral owner.

    December 1st, 2022: JChem Choral 22.21.0

    Improvements

    • Indexing of large molecules has been sped up especially in case of hybrid tautomerization strategy.

    Bugfixes

    • CVE-2022-40149 and CVE-2022-40150 (jettison) vulnerability has been fixed.
    • Full-fragment and duplicate search missed hits in case of hybrid tautomerization strategy if the query contained explicit Hydrogen.
    • Queries with feasible query properties didn't match corresponding target in tautomer type fullfragment search.

    October 28th, 2022: JChem Choral 22.19.0

    Bugfixes

    • CVE-2022-42004 jackson-databind vulnerability has been fixed.
    • CVE-2022-42889 commons-text vulnerability has been fixed.
    • CVE-2022-41853 hsqldb vulnerability has been fixed.
    • Aromatic query could match aliphatic target in canonic-generic hybrid tautomer mode during full-fragment and duplicate searches.

    Long Term Supported Release - September 25th, 2023: JChem Choral 22.17.7 (Lithium.7)

    No changes.

    Long Term Supported Release - June 16th, 2023: JChem Choral 22.17.6 (Lithium.6)

    Bugfixes

    • CVE-2022-1259 (undertow-core) vulnerability has been fixed.
    • CVE-2023-20883 (spring-boot) vulnerability has been fixed.

    Long Term Supported Release - April 6th, 2023: JChem Choral 22.17.5 (Lithium.5)

    Bugfixes

    • CVE-2023-20860 (spring-webmvc) vulnerability has been fixed.
    • CVE-2022-1471 (snakeyaml) vulnerability has been fixed.
    • CVE-2022-45143 (tomcat-embed-core) vulnerability has been fixed.

    Long Term Supported Release - January 19th, 2023: JChem Choral 22.17.4 (Lithium.4)

    Improvements

    • There is a 120 sec timeout set in the create index process for the tautomer calculation of each molecules.
    • Indexing of large molecules has been sped up especially in case of hybrid tautomerization strategy.

    Bugfixes

    • CVE-2022-0084 (xnio) vulnerability has been fixed.
    • CVE-2022-36437 (hazelcast) vulnerability has been fixed.
    • CVE-2022-40149 and CVE-2022-40150 (jettison) vulnerability has been fixed.
    • CVE-2022-40151 and CVE-2022-41966 (xstream) vulnerability has been fixed.
    • CVE-2022-40153 (woodstox) vulnerability has been fixed.

    Long Term Supported Release - November 29th, 2022: JChem Choral 22.17.3 (Lithium.3)

    No changes.

    Long Term Supported Release - November 9th, 2022: JChem Choral 22.17.2 (Lithium.2)

    Bugfixes

    • CVE-2022-42004 jackson-databind vulnerability has been fixed.
    • CVE-2022-42889 commons-text vulnerability has been fixed.
    • CVE-2022-41853 hsqldb vulnerability has been fixed.

    Long Term Supported Release - October 19th, 2022: JChem Choral 22.17.1 (Lithium.1)

    No changes.

    September 9th, 2022: JChem Choral 22.16.0

    Improvements

    • New upgrade method providing upgrade without downtime has been implemented. Documentation

    Bugfixes

    • Chemical terms returned the reference instead of the value for list of numbers.
    • Vulnerability CVE-2022-2053 has been fixed: spring-boot framework is updated to 2.7.3.
    • Vulnerability CVE-2022-25857 has been fixed: org.yaml:snakeyaml is updated to 1.31.

    August 11th, 2022: JChem Choral 22.15.0

    Improvements

    • There is a 120 sec timeout set in the create index process for the tautomer calculation of each molecules.
    • New function chemterm_clob has been implemented for cases when the chemterm returns more than 4000 characters.
    • Any atom doesn't match deuterium or tritium anymore. Speed-up of any atom - and no other query features - containing structures.

    Bugfixes

    • Reactions with empty reactant or product component didn't find themselves.
    • Spring-boot framework has been updated to 2.7.0.

    June 27th, 2022: JChem Choral 22.12.0

    Bugfixes

    • Function isvalidmolecule threw exception at some strange invalid structures.

    May 6th, 2022: JChem Choral 22.11.0

    Bugfixes

    • Vulnerability CVE-2020-36518 has been fixed: jackson-databind is updated to 2.12.6.1.
    • Vulnerability CVE-2022-22965 and CVE-2022-22968 has been fixed: spring-boot is updated to 2.5.13

    March 28th, 2022: JChem Choral 22.9.0

    No changes.

    Long Term Supported Release - November 9th: JChem Choral 22.6.5 (Krypton.5)

    Bugfixes

    • CVE-2022-42004 jackson-databind vulnerability has been fixed.
    • CVE-2022-42889 commons-text vulnerability has been fixed.
    • CVE-2022-41853 hsqldb vulnerability has been fixed.

    Long Term Supported Release - September 13th: JChem Choral 22.6.4 (Krypton.4)

    Bugfixes

    • Vulnerability CVE-2022-2053 has been fixed: spring-boot framework is updated to 2.7.3.
    • Vulnerability CVE-2022-25857 has been fixed: org.yaml:snakeyaml is updated to 1.31.

    Long Term Supported Release - June 23rd: JChem Choral 22.6.3 (Krypton.3)

    No changes.

    Long Term Supported Release - May 10th, 2022: JChem Choral 22.6.2 (Krypton.2)

    Bugfixes

    • Vulnerability CVE-2022-22965 and CVE-2022-22968 has been fixed: spring-boot is updated to 2.5.13

    Long Term Supported Release - April 11th, 2022: JChem Choral 22.6.1 (Krypton.1)

    Bugfixes

    • Vulnerability CVE-2020-36518 has been fixed: jackson-databind is updated to 2.12.6.1.
    • Vulnerability CVE-2022-22965 has been fixed: spring-boot is updated to 2.5.12

    March 16th, 2022: JChem Choral 22.6.0

    Bugfixes

    • Superatom sgroups caused IndexOutOfBoundsException in duplicate search.
    • Search could modify the target molecule in the case of duplicate search, if the target contained position variation feature.

    January 23rd, 2022: JChem Choral 22.2.0

    Bugfixes

    • Uncommitted structures were not sorted correctly when using index and order by together.

    January 18th, 2022: JChem Choral 22.1.0

    No changes.

    January 3rd, 2022: JChem Choral 21.20.0

    Bugfixes

    • Log4j vulnerability - CVE-2021-44228 - has been fixed. Log4j version 2.17.0 is applied. See announcement
    • Double bond stereo was not checked in reaction search.

    December 15th, 2021: JChem Choral 21.19.0

    Improvements

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

    Bugfixes

    • Log4j vulnerability - CVE-2021-44228 - has been fixed.See announcement
    • Generic tautomer mode of substructure search could result false hits in the case of some overlapping aromatic regions and tautomer regions.

    November 9th, 2021: JChem Choral 21.18.0

    Bugfixes

    • Choral install failed on some Oracle versions.

    October 28th, 2021: JChem Choral 21.17.0

    Bugfixes

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

    October 18th, 2021: JChem Choral 21.16.0

    Bugfixes

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

    Long Term Supported Release - October 27th, 2023: JChem Choral 21.15.9 (Iodine.9)

    No changes.

    Long Term Supported Release - July 3rd, 2023: JChem Choral 21.15.8 (Iodine.8)

    No changes.

    Long Term Supported Release - January 26th, 2023: JChem Choral 21.15.7 (Iodine.7)

    No changes.

    Long Term Supported Release - November 9th, 2022: JChem Choral 21.15.6 (Iodine.6)

    Bugfixes

    • CVE-2022-42889 commons-text vulnerability has been fixed.

    Long Term Supported Release - September 13th, 2022: JChem Choral 21.15.5 (Iodine.5)

    No changes.

    Long Term Supported Release - June 27th, 2022: JChem Choral 21.15.4 (Iodine.4)

    No changes.

    Long Term Supported Release - May 23th, 2022: JChem Choral 21.15.3 (Iodine.3)

    Improvements

    • Hazelcast has been upgraded to version 5.0.2.
    • H2 has been updated to version 2.1.210.

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

    Bugfixes

    • Log4j vulnerability - CVE-2021-44228 - has been fixed. Log4j version 2.17.0 is applied. See announcement
    • Normal canonical tautomer search (full-fragment and duplicate) could miss hit in case of aromatic rings with different Kekule format.
    • Double bond stereo was not checked in reaction search.

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

    No changes.

    September 28th, 2021: JChem Choral 21.15.0

    Improvements

    • Some invalid structures were stopped at importing or indexing. Now it is fixed and the process progresses without errors.Documentation

    August 25th, 2021: JChem Choral 21.14.0

    No changes.

    August 3rd, 2021: JChem Choral 21.13.0

    Improvements

    July 16th, 2021: JChem Choral 21.12.0

    No changes.

    June 23rd, 2021: JChem Choral 21.11.0

    Bugfixes

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

    June 9th, 2021: JChem Choral 21.10.0

    No changes.

    May 18th, 2021: JChem Choral 21.9.0

    Bugfixes

    • Search failed for molecule type names containing "_" symbol.
    • False similarity search results were given in the case of molecule types with tautomer=GENERIC parameter.

    April 27th, 2021: JChem Choral 21.8.0

    Bugfixes

    • Critical vulnerability has been eliminated.

    April 21st, 2021: JChem Choral 21.7.0

    Bugfixes

    • Structures with multicenter bonds - in tables indexed with molecule types with tautomer handling mode GENERIC - throw java.lang.RuntimeException: contract violation!
    • Function mode search 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 Choral 21.6.0

    Not released.

    JChem Choral 21.5.0

    Not released.

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

    Bugfixes

    • Log4j vulnerability - CVE-2021-44228 - has been fixed. Log4j version 2.17.0 is applied. See announcement
    • Double bond stereo was not checked in reaction search.

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

    No changes.

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

    No changes.

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

    No changes.

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

    Bugfixes

    • Critical vulnerability has been eliminated.

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

    No changes.

    March 24th, 2021: JChem Choral 21.4.0

    Improvements

    • Hit_highlight operator is implemented for highlighting hits of database search. Documentation
    • Added workaround to enable cost calculation for queries larger then the VARCHAR size limit.

    Bugfixes

    • Duplicate search could result missing hit in case of structures with repeating units.

    February 23rd, 2021: JChem Choral 21.3.0

    Improvements

    Bugfixes

    • 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.

    February 1st, 2021: JChem Choral 21.2.0

    No changes.

    January 21st, 2021: JChem Choral 21.1.0

    Improvements

    • 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.

    December 3rd, 2020: JChem Choral 20.21.0

    No changes.

    October 29th, 2020: JChem Choral 20.20.0

    No changes.

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

    No changes.

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

    No changes.

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

    Bugfixes

    • Critical vulnerability has been eliminated.

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

    No changes.

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

    September 17th, 2020: JChem Choral 20.19.0

    No changes.

    September 2nd, 2020: JChem Choral 20.18.0

    Bugfixes

    • Double bond stereo information was sometimes also ignored in case of IGNORETETRAHEDRALSTEREO option.

    August 12th, 2020: JChem Choral 20.17.0

    Bugfixes

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

    July 20th, 2020: JChem Choral 20.16.0

    No changes.

    June 30th, 2020: JChem Choral 20.15.0

    Improvements

    • New, simpler syntax is available for full fragment search. Documentation

    • The use of normal canonical tautomers in full fragment search is also available . Documentation

    Dropping index is necessary before upgrade in Choral.

    June 18th, 2020: JChem Choral 20.14.0

    No changes.

    May 22nd, 2020: JChem Choral 20.13.0

    No changes.

    May 4th, 2020: JChem Choral 20.12.0

    Improvements

    • Consideration of chiral flag can be set by stereoAssumption = RELATIVE parameter in the type files. Documentation

    April 16th, 2020: JChem Choral 20.11.0

    Bugfixes

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

    April 6th, 2020: JChem Choral 20.10.0

    Improvements

    • Non-valid structures can be imported and indexed However, they won't hit any structure, including themselves.

    • New tautomerization method added to the molecule type definitions called CANONIC_GENERIC_HYBRID. Documentation

    March 23th, 2020: JChem Choral 20.9.0

    No changes.

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

    No changes.

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

    No changes.

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

    No changes.

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

    No changes.

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

    March 13th, 2020: JChem Choral 20.8.0

    Bugfixes

    • Tautomer duplicate search didn't find hits for some structures with tetrahedral stereo information.

    March 3rd, 2020: JChem Choral 20.7.0

    No changes.

    February 26th, 2020: JChem Choral 20.6.0

    Bugfixes

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

    February 21st, 2020: JChem Choral 20.5.0

    No changes.

    February 7th, 2020: JChem Choral 20.4.0

    Bugfixes

    • Large structures with stereo configuration could be incorrectly handled.

    January 24th, 2020: JChem Choral 20.3.0

    Improvements

    • Searching with ignored tetrahedral stereo information has been introduced. Documentation

    Bugfixes

    • Tautomer search could give false hits with queries containing explicit Hydrogen atoms.

    January 21st, 2020: JChem Choral 20.2.0

    No changes.

    January 13th, 2020: JChem Choral 20.1.0

    Improvements

    • Technical improvements were made on the search process.

    Reindex of tables is needed.

    December 19th, 2019: JChem Choral 19.27.0

    Improvements

    • Searching compounds in materialized views with fast sync are supported by Choral.

    December 12th, 2019: JChem Choral 19.26.0

    No changes.

    November 29th, 2019: JChem Choral 19.25.0

    Improvements

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

    Bugfixes

    • Performing joined queries including search on multiple molecular column could miss hits.

    November 15th, 2019: JChem Choral 19.24.0

    No changes.

    November 8th, 2019: JChem Choral 19.23.0

    No changes.

    October 21th, 2019: JChem Choral 19.22.0

    Improvements

    • Cache size decreased by 20% for target-type datasets.

    • 15% indexing speed improvement.

    • 20-50% search speedup for frequent queries

    Bugfixes

    October 7th, 2019: JChem Choral 19.21.0

    No changes..

    September 18th, 2019: JChem Choral 19.20.0

    Bugfixes

    • Search Engine

      • Nitrogen in marked tetrahedral stereo chiral center matched Nitrogen in unmarked chiral center.

    September 2nd, 2019: JChem Choral 19.19.0

    No changes.

    August 3rd, 2019: JChem Choral 19.18.0

    No changes.

    July 6th, 2019: JChem Choral 19.17.0

    Bugfixes

    • Create index failed on materialized views.

    July 4th, 2019: JChem Choral 19.16.0

    No changes.

    June 27th, 2019: JChem Choral 19.15.0

    No changes.

    June 24th, 2019: JChem Choral 19.14.0

    No changes.

    June 17th, 2019: JChem Choral 19.13.0

    No changes.

    June 3rd, 2019: JChem Choral 19.12.0

    No changes.

    May 21st, 2019: JChem Choral 19.11.0

    No changes.

    April 8th, 2019: JChem Choral 19.9.0

    No changes.