JChem PostgreSQL Cartridge History of Changes

    October 29th, 2020: JChem PostgreSQL Cartridge 20.20.0

    Bugfixes

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

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

    September 17th, 2020: JChem PostgreSQL Cartridge 20.19.0

    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