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 calculatedhas 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
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