JChem PostgreSQL Cartridge History of Changes

May 22nd, 2020: JChem PostgreSQL Cartridge 20.13.0

No changes.

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