JChem PostgreSQL Cartridge History of Changes

    September 9th, 2022: JChem PostgreSQL Cartridge 22.16.0

    Bugfixes

    • Chemical terms returned the reference instead of the value for list of numbers.

    August 11th, 2022: JChem PostgreSQL Cartridge 22.15.0

    Improvements

    • There is a 120 sec timeout set in the insert process for the tautomer calculation of each molecules.
    • 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.

    June 27th, 2022: JChem PostgreSQL Cartridge 22.12.0

    No changes.

    March 28th, 2022: JChem PostgreSQL Cartridge 22.9.0

    No changes.

    Long Term Supported Release - September 13th 2022: JChem PostgreSQL Cartridge 22.6.4 (Krypton.4)

    No changes.

    Long Term Supported Release - June 23rd, 2022: JChem PostgreSQL Cartridge 22.6.3 (Krypton.3)

    No changes.

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

    No changes.

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

    Bugfixes

    • Vulnerability CVE-2020-36518 has been fixed: jackson-databind is updated to 2.12.6.1.

    March 16th, 2022: JChem PostgreSQL Cartridge 22.6.0

    Improvements

    • PostgreSQL jdbc driver has been upgraded to version 42.3.3.
    • Hazelcast has been upgraded to version 5.0.2.

    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.

    Upgrade level needed when upgrading from the previous version: Level 4

    January 23rd, 2022: JChem PostgreSQL Cartridge 22.2.0

    No changes.

    January 18th, 2022: JChem PostgreSQL Cartridge 22.1.0

    No changes.

    January 3rd, 2022: JChem PostgreSQL Cartridge 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.

    Upgrade level needed when upgrading from the previous version: Level 4

    December 15th, 2021: JChem PostgreSQL Cartridge 21.19.0

    Improvements

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

    Bugfixes

    • Log4j vulnerability - CVE-2021-44228 - has been fixed.See announcement
    • Similarity search fails with older versions of JPC when migrating to Postgres 12.9.See version compatibility matrix
    • Generic tautomer mode of substructure search could result false hits in the case of some overlapping aromatic regions and tautomer regions.

    Upgrade level needed when upgrading from the previous version: Level 4

    November 9th, 2021: JChem PostgreSQL Cartridge 21.18.0

    No changes.

    Upgrade level needed when upgrading from the previous version: Level 4

    October 28th, 2021: JChem PostgreSQL Cartridge 21.17.0

    Bugfixes

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

    Upgrade level needed when upgrading from the previous version:Level 4

    October 18th, 2021: JChem PostgreSQL Cartridge 21.16.0

    Bugfixes

    No changes.

    Upgrade level needed when upgrading from the previous version:Level 4

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

    No changes.

    Upgrade level needed when upgrading from the previous version:Level 4

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

    No changes.

    Upgrade level needed when upgrading from the previous version:Level 4

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

    Improvements

    • PostgreSQL jdbc driver has been upgraded to version 42.3.3.
    • Hazelcast has been upgraded to version 5.0.2.

    Upgrade level needed when upgrading from the previous version: Level 4

    Long Term Supported Release - January 14th, 2022: JChem PostgreSQL Cartridge 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.
    • Similarity search fails with older versions of JPC when migrating to Postgres 12.9.See version compatibility matrix
    • Double bond stereo was not checked in reaction search.

    Upgrade level needed when upgrading from the previous version: Level 4

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

    No changes.

    Upgrade level needed when upgrading from the previous version: Level 4

    September 28th, 2021: JChem PostgreSQL Cartridge 21.15.0

    Improvements

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

    Upgrade level needed when upgrading from the previous version:Level 3

    August 25th, 2021: JChem PostgreSQL Cartridge 21.14.0

    No changes.

    Upgrade level needed when upgrading from the previous version:Level 4

    August 3rd, 2021: JChem PostgreSQL Cartridge 21.13.0

    Improvements

    Upgrade level needed when upgrading from the previous version:Level 3

    July 16th, 2021: JChem PostgreSQL Cartridge 21.12.0

    No changes.

    Upgrade level needed when upgrading from the previous version:Level 3

    June 23rd, 2021: JChem PostgreSQL Cartridge 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.

    Upgrade level needed when upgrading from the previous version:Level 3

    June 9th, 2021: JChem PostgreSQL Cartridge 21.10.0

    No changes.

    Upgrade level needed when upgrading from the previous version:Level 4

    May 18th, 2021: JChem PostgreSQL Cartridge 21.9.0

    Bugfixes

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

    Upgrade level needed when upgrading from the previous version:Level 3

    April 27th, 2021: JChem PostgreSQL Cartridge 21.8.0

    Bugfixes

    • Critical vulnerability has been eliminated.

    Upgrade level needed when upgrading from the previous version:Level 3

    April 21st, 2021: JChem PostgreSQL Cartridge 21.7.0

    Improvements

    • Possible parallel execution has been set for more methods.
    • Health check endpoint has been implemented for checking the health status of jchem-psql service. Documentation

    Bugfixes

    • Structures with multicenter bonds - in tables with molecule types with tautomer handling mode GENERIC - throw java.lang.RuntimeException: contract violation!
    • Sequential scan 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.

    Upgrade level needed when upgrading from the previous version:Level 3

    JChem PostgreSQL Cartridge 21.6.0

    Not released.

    JChem PostgreSQL Cartridge 21.5.0

    Not released.

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

    Bugfixes

    • Log4j vulnerability - CVE-2021-44228 - has been fixed. Log4j version 2.17.0 is applied. See announcement
    • Similarity search fails with older versions of JPC when migrating to Postgres 12.9.See version compatibility matrix
    • Double bond stereo was not checked in reaction search.

    Upgrade level needed when upgrading from the previous version: Level 4

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

    No changes.

    Upgrade level needed when upgrading from the previous version:Level 4

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

    No changes.

    Upgrade level needed when upgrading from the previous version:Level 4

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

    No changes.

    Upgrade level needed when upgrading from the previous version: Level 4

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

    Bugfixes

    • Critical vulnerability has been eliminated.

    Upgrade level needed when upgrading from the previous version: Level 4

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

    No changes.

    Upgrade level needed when upgrading from the previous version: Level 4

    March 24th, 2021: JChem PostgreSQL Cartridge 21.4.0

    Improvements

    • Extension can be installed to a given schema, not only to the public schema. Documentation

    Bugfixes

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

    Upgrade level needed when upgrading from the previous version:Level 3

    February 23rd, 2021: JChem PostgreSQL Cartridge 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.

    Upgrade level needed when upgrading from the previous version:Level 3

    February 1st, 2021: JChem PostgreSQL Cartridge 21.2.0

    Improvements

    • First search after restarting service on each table with each search type was very slow on large databases.

    Upgrade level needed when upgrading from the previous version:Level 3

    January 21st, 2021: JChem PostgreSQL Cartridge 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.

    Upgrade level needed when upgrading from the previous version:Level 3

    December 3rd, 2020: JChem PostgreSQL Cartridge 20.21.0

    Bugfixes

    • Smarts atoms are not supported in generic tautomer substructure search exception was thrown when SMARTS queries were used.
    • Disturbing warning message Illegal reflective access by com.esotericsoftware.kryo.util.UnsafeUtil was thrown when initializing jchem-psql service.

    Upgrade level needed when upgrading from the previous version:Level 3

    October 29th, 2020: JChem PostgreSQL Cartridge 20.20.0 [not downloadable]

    Bugfixes

    • Sometimes hits were missing if the target had repeating units in rings.

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

    No changes.

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

    No changes.

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

    Bugfixes

    • Critical vulnerability has been eliminated.

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

    No changes.

    Long Term Supported Release - October 28th, 2020: JChem PostgreSQL Cartridge 20.19.1 (Gallium.1) [not downloadable]

    September 17th, 2020: JChem PostgreSQL Cartridge 20.19.0 [not downloadable]

    No changes.

    September 2nd, 2020: JChem PostgreSQL Cartridge 20.18.0

    Bugfixes

    • Double bond stereo information was sometimes ignored in case of ignoreTetrahedralStereo query transformation.

    August 12th, 2020: JChem PostgreSQL Cartridge 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 PostgreSQL Cartridge 20.16.0

    Bugfixes

    • Some ordered search threw the error "Ordered search is not supported in sequential scan." even though the searched column was indexed properly.

    June 30th, 2020: JChem PostgreSQL Cartridge 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 JPC.

    June 18th, 2020: JChem PostgreSQL Cartridge 20.14.0

    Bugfixes

    • jchem-psql service could not be restarted in some cases.

    • Molecule initialization at import or search for markush structures with a lot of enumerants was not stopped in the JChem Server when the query was cancelled.

    May 22nd, 2020: JChem PostgreSQL Cartridge 20.13.0

    Known issue

    • It is not possible to upgrade from version 20.12.0 to version 20.13.0.

    May 4th, 2020: JChem PostgreSQL Cartridge 20.12.0

    Improvements

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

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

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

    • JPC is put to frequent release its version equals other projects'. Documentation is not bundled.

    Bugfixes

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

    • Large structures with stereo configuration could be incorrectly handled.

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

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

    January 23rd, 2020: JChem PostgreSQL Cartridge 5.1

    Improvements

    • JPC can run in highly available mode. Documentation

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

    • The speed of stereo search has been increased by approximately 90%.

    Bugfixes

    • Unlogged index creation failed.

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

    • Tautomerization of structures with valence error could be erroneous.

    October 29th, 2019: JChem PostgreSQL Cartridge 5.0

    Improvements

    • PostgreSQL 12 is the only supported PostgeSQL version from now on.

    • Monitoring of index creation progress is enabled. Documentation

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

    • 15% indexing speed improvement.

    • 20-50% search speedup for frequent queries

    • Vacuum speed up for large tables.

    • Cost estimation has been improved, joined queries run faster.

    Bugfixes

    • Nitrogen in marked stereo configuration matched unmarked chiral center.

    • Small ring cis double bond stereo configurations were recognized as trans in case of trans perspective drawing in 3D.

    September 23rd, 2019: JChem PostgreSQL Cartridge 4.4

    Improvements

    • JChem Service can be installed on other instance than the PostgreSQL database.

    • Pseudo formula handling has been added to chemical terms .

    • Allow NULL values in queries and molecular columns of tables.

    • Standardize method added.

    August 13th, 2019: JChem PostgreSQL Cartridge 4.3

    No changes.

    March 11th, 2019: JChem PostgreSQL Cartridge 4.2

    Bugfixes

    • Chemical term evaluation could cause OperationAbortedException because of concurrency problems.

    • Initializing jchem-psql service sometimes failed because of missing log folder.

    October 2nd, 2018: JChem PostgreSQL Cartridge 4.1

    Improvements

    • Enabled logical replication of indexed chemical data.

    Bugfixes

    • A memory leak during indexing is fixed.

    May 10th, 2018: JChem PostgreSQL Cartridge 4.0

    Improvements

    • Default fingerprint size is reduced from 1024 to 512.

    • Upgrade of Thrift to 0.11.0.

    Bugfixes

    • Copy of binary data was erroneous.

    • Chemical terms returning a list of values (e.g. logD) did not return the values.

    • Polymers with ambiguous aromatic rings in end groups could not be indexed.

    December 7th, 2017: JChem PostgreSQL Cartridge 3.0

    Improvements

    • PostgreSQL 10 is supported from now on.

    • Parallel sequential scan mode is supported.

    • Indexing speed has been increased.

    • Log4j logging is implemented. Documentation

    • New cache parameters are provided for performance tuning of searches. Documentation

    Bugfixes

    • Peptide sequence file format was not handled correctly in the searches. From now on the 3-letter peptide format works in searches.

    • Duplicate search could be slow when the target structure contained charged hydrogen atom.

    September 20th, 2017: JChem PostgreSQL Cartridge 2.10

    Improvements

    • Speedup when query contains 5-membered ring with ambiguous aromaticity.

    Bugfixes

    • Wrong fingerprints were used after copying columns from one molecule subtype to another.

    June 9th, 2017: JChem PostgreSQL Cartridge 2.9

    Bugfixes

    • Similarity search did not always return hits in the order of similarity.

    • Molfiles with sgroups embedded in SRU groups were not handled.

    • Missing hits could have been experienced in tautomer duplicate search in case of InChi files.

    • jchem-psql service could crash if erroneous query structure was applied in a query.

    • Service jchem-psql stop did not work on some new Ubuntu versions.

    • Known issue present in version 2.8 has been solved.

    May 17th, 2017: JChem PostgreSQL Cartridge 2.8 (version withdrawn)

    Improvements

    • Changing MapDB backend to MVStore approximately doubles the speed of the CREATE INDEX processes.

    Bugfixes

    • Similarity search did not always return hits in the order of similarity.

    • Molfiles with sgroups embedded in SRU groups were not handled.

    • Missing hits could have been experienced in tautomer duplicate search in case of InChi files.

    • jchem-psql service could crash if erroneous query structure was applied in a query.

    • Service jchem-psql stop did not work on some new Ubuntu versions.

    Known issue

    • The size of the index files under /var/lib/jchem-psql/store/ have been hugely increased.

    March 10th, 2017: JChem PostgreSQL Cartridge 2.7

    Improvements

    • Performance of select statements containing conditions for several rows or tables and including substructure search is improved by up to 20 times. Documentation

    Bugfixes

    • Missing hits could have been experienced in tautomer duplicate search in the case of molecules with aromatic rings.

    February 1st, 2017: JChem PostgreSQL Cartridge 2.6

    Improvements

    • Quick relevance sorting of substructure search hits is provided by using a new chemical indextype SORTEDCHEMINDEX. Documentation

    Bugfixes

    • Querying with R-group structures did not work without Markush Enumeration license.

    November 7th, 2016: JChem PostgreSQL Cartridge 2.5

    Improvements

    • New method providing fast similarity search has been implemented. Documentation

    Bugfixes

    • Molecules with small rings containing double bonds could miss duplicates when duplicate search was performed.

    • Tautomer duplicate search could result false negative hits.

    August 30th, 2016: JChem PostgreSQL Cartridge 2.4

    Improvements

    • Speed of insert into indexed table has been increased.

    Bugfixes

    • Index creation threw exception in case of molecules having deuterium atom.

    • Tautomer duplicate search could result false positive hits.

    August 2nd, 2016: JChem PostgreSQL Cartridge 2.3

    Improvements

    • Reaction search is supported from now on. Documentation

    • Searching structures containing rings is sped-up.

    June 28th, 2016: JChem PostgreSQL Cartridge 2.2

    Improvements

    • JChem PostgreSQL Cartridge is supported on a distributed PostgreSQL Citus database. Documentation

    Bugfixes

    • Duplicate search could result failing hits in tables indexed with chemindex.

    • Misleading warning: WARNING: molecule_ops.cpp:205 Cost estimation values were not calculated has been fixed.

    June 20th, 2016: JChem PostgreSQL Cartridge 2.1

    Improvements

    • PostgreSQL 9.5 is the only supported PostgeSQL version from now on. PostgreSQL 9.4 is only supported in JChem PostgreSQL Cartridge versions up to 2.0. Documentation

    Bugfixes

    • Tetrahedral stereo properties were incorrectly evaluated in case of structures where a substituent on the chiral center - e.g., on phosphorus - was connected by double bond.

    May 26th, 2016: JChem PostgreSQL Cartridge 2.0

    Improvements

    • Searches with joined queries and with limit <n> conditions has been improved due to cost estimation and function mode search enhancements.

    • Limitation of the number of jchem-psql service sessions is configurable by the administrator. Documentation

    Bugfixes

    • Searches combining more than three SELECT statements with logical operators could run into dead lock state.

    • Relevance calculation threw exception in case of polymer and query structures.

    • Relevance calculation could throw license exception even if the postgresql license was present.

    • Custom standardizer.xml applied in type definition generated exception when more than one molecules were inserted in one statement.

    February 10th, 2016: JChem PostgreSQL Cartridge 1.8

    Improvements

    • Relevance sorting possibility of the search hits is provided. Documentation

    • Collecting invalid molecules during sdf import and (cx)smiles/(cx)smarts import is available.

    • New function, is_valid_molecule, is introduced.

    • Memory size requirement of searches in big tables has been decreased, and further performance tuning possibilities are provided. Documentation

    October 20th, 2015: JChem PostgreSQL Cartridge 1.7

    Improvements

    • Speed of searches - compared to version 1.6 - has been increased.

    Bugfixes

    • Specified requirement regarding glibc version for running JChem PostgreSQL Cartridge is canceled.

    October 7th, 2015: JChem PostgreSQL Cartridge 1.6

    Improvements

    • From now on, search engine in JChem PostgreSQL Cartridge works on vague bond level half. Previously, it worked on vague bond level 0.

    Known issue

    • glibc version 2.14 is needed to run JChem PostgreSQL Cartridge.

    Bugfixes

    • Tautomer substructure search could result false negative hits in case of aromatic structures.

    • Index entries were overridden by each other in some cases resulting loss of hits.

    August 14th, 2015: JChem PostgreSQL Cartridge 1.5 (version withdrawn)

    July 27th, 2015: JChem PostgreSQL Cartridge 1.4

    Improvements

    • The use of chemical terms is implemented. Documentation

    • The performance of searching with combined queries can be tuned by calibration. Documentation