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JChem Suite Changelog

What's new in JChem Suite 24.1.2

Mar 22, 2024
  • Improvements:
  • Search Engine:
  • Performance of searching with isotope containing query structures has been improved in Reactions and AnyStructures type tables.
  • Regeneration:
  • Regeneration of "Reactions" and "AnyStructures" type tables is needed to use JChem 24.1.2. Please, regenerate the "Reactions" and "AnyStructures" type JChem tables after upgrade. Their new table version is 24.1.2.0.

New in JChem Suite 24.1.0 (Feb 19, 2024)

  • Alkenyl/Alkynyl homology groups with homology properties could have false hit on longer actual alkenyl chain.

New in JChem Suite 23.7.0 (May 4, 2023)

  • Regeneration of "Markush" type tables is needed to use JChem 23.7.0. Please, regenerate the "Markush" type JChem tables after upgrade. Their new table version is 23.7.0.0.

New in JChem Suite 23.5.0 (Apr 6, 2023)

  • Improvements:
  • Search Engine:
  • 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 Base.
  • Regeneration:
  • Full regeneration is needed to use JChem 23.5.0. Please, regenerate all JChem tables after upgrade. The new table version is 23.5.0.0
  • March 10th, 20

New in JChem Suite 23.3.0 (Feb 24, 2023)

  • Fixed:
  • JChem Base - DB functionalities:
  • Structure with R-groups and bicyclo stereo information failed with Exception at import into Markush table.

New in JChem Suite 23.1.0 (Jan 26, 2023)

  • Improvements: Java 17 runtime compatibility is supported

New in JChem Suite 22.20.0 (Nov 24, 2022)

  • Improvements:
  • New 'Additional Text Notes' homology group properties added: 'Number of single bonds - Z' and 'Number of aromatic bonds - A'.

New in JChem Suite 22.19.0 (Oct 28, 2022)

  • Bugfixes:
  • CVE-2022-42889 commons-text vulnerability has been fixed.
  • CVE-2022-41853 hsqldb vulnerability has been fixed.

New in JChem Suite 22.12.0 (Jun 17, 2022)

  • Improvements:
  • Installation
  • DB2 driver is no longer packed in the installer.
  • Bugfixes:
  • Search Engine
  • ArrayIndexOutOfBoundsException was thrown for specific Textnote homology group properties.

New in JChem Suite 22.6.0 (Feb 24, 2022)

  • Improvements:
  • JChem Base - DB functionalities
  • PostgreSQL jdbc driver has been upgraded to version 42.3.3.

New in JChem Suite 22.5.0 (Feb 15, 2022)

  • No changes.

New in JChem Suite 22.4.0 (Feb 12, 2022)

  • Improvements:
  • JChem Base - DB functionalities
  • PostgreSQL jdbc driver has been upgraded to version 42.3.2.

New in JChem Suite 21.30.0 (Feb 4, 2022)

  • Bugfixes:
  • Search Engine:
  • 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.

New in JChem Suite 21.20.0 (Dec 22, 2021)

  • Bugfixes:
  • Search Engine
  • Double bond stereo was not checked in reaction search.
  • Regeneration:
  • Full regeneration is needed to use JChem 21.20.0. Please, regenerate all JChem tables after upgrade. The new table version is 21.20.0.0

New in JChem Suite 21.19.0 (Dec 11, 2021)

  • Improvements:
  • JChem runs in Java 11 Environment from now on. Documentation [https://chemaxon.com/news/chemaxon-update-changes-to-java-net-and-ole-support]

New in JChem Suite 21.18.0 (Nov 10, 2021)

  • Bugfixes:
  • Search Engine:
  • False positive duplicate hits were received when homology groups were in the R-group definitions.
  • Index out of bounds exception could have been thrown in duplicate search.
  • User comparator was not called for homology equal translation matching.

New in JChem Suite 21.16.0 (Oct 18, 2021)

  • No changes.

New in JChem Suite 21.15.0 (Oct 4, 2021)

  • Regeneration:
  • Full regeneration is needed to use JChem 21.15.0. Please, regenerate all JChem tables after upgrade. The new table version is 21.15.0.0

New in JChem Suite 21.12.0 (Jul 19, 2021)

  • Regeneration:
  • Full regeneration is needed to use JChem 21.12.0. Please, regenerate all JChem tables after upgrade. The new table version is 21.12.0.0

New in JChem Suite 21.11.0 (Jun 23, 2021)

  • Improvements:
  • R-group decomposition:
  • Speeded-up r-group decomposition for cases where the specific part of the structure was simple, in certain cases with several orders of magnitude.
  • Regeneration:
  • Full regeneration is needed to use JChem 21.11.0. Please, regenerate all JChem tables after upgrade. The new table version is 21.11.0.0

New in JChem Suite 21.10.0 (Jun 9, 2021)

  • Improvements:
  • JChem Base - DB functionalities
  • Oracle JDBC driver was upgraded from 12.2.0.1 to 21.1.0.0.

New in JChem Suite 21.8.0 (Apr 27, 2021)

  • Bugfixes:
  • Security vulnerabilities at xml parsing were eliminated.

New in JChem Suite 21.7.0 (Apr 27, 2021)

  • Bugfixes:
  • Search Engine:
  • MolSearch 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.

New in JChem Suite 21.4.0 (Mar 24, 2021)

  • Regeneration:
  • Full regeneration is needed to use JChem 21.4.0. Please, regenerate all JChem tables after upgrade. The new table version is 21.4.0.0

New in JChem Suite 21.2.0 (Feb 1, 2021)

  • Bugfixes:
  • Search Engine:
  • Zero repetition number of repetition units caused missing hits in full structure search.
  • JChemSearch.setFilterIDList() method doesn't always set the filter if called on same object twice.

New in JChem Suite 20.21.0 (Dec 3, 2020)

  • Bugfixes:
  • Search Engine:
  • Tautomer search could give false results.
  • Regeneration:
  • Full regeneration is needed to use JChem 20.21.0. Please, regenerate all JChem tables after upgrade. The new table version is 20.21.0.0
  • October 29th, 2020: JChem Base 20.20.0
  • Improvements:
  • Search Engine:
  • New homology group 'Carbocyclyl' has been added.
  • Regeneration:
  • Regeneration of Query structures type tables is needed to use JChem 20.20.0. Please, regenerate Query structures JChem tables after upgrade. The new table version is 20.20.0.0.
  • The version number of the other types of JChem tables has not changed.
  • Long Term Supported Release - October 28th, 2020: JChem Base 20.19.1 (Gallium.1)

New in JChem Suite 20.20.0 (Nov 3, 2020)

  • Improvements:
  • Search Engine:
  • New homology group 'Carbocyclyl' has been added.
  • Regeneration:
  • Regeneration of Query structures type tables is needed to use JChem 20.20.0. Please, regenerate Query structures JChem tables after upgrade. The new table version is 20.20.0.0.
  • The version number of the other types of JChem tables has not changed.
  • Long Term Supported Release - October 28th, 2020: JChem Base 20.19.1 (Gallium.1)
  • September 17th, 2020: JChem Base 20.19.0
  • Bugfixes:
  • Search Engine:
  • Hetero atom count property on heterocyclyl homology group caused missing hit.

New in JChem Suite 20.19.0 (Sep 21, 2020)

  • Bugfixes:
  • Search Engine:
  • Hetero atom count property on heterocyclyl homology group caused missing hit.

New in JChem Suite 20.18.0 (Sep 7, 2020)

  • Bugfixes:
  • JChem Base - DB functionalities:
  • JChem Base upgrade with PostgreSQL database failed if pg schema prefixes were missing in the JChemProperties file.

New in JChem Suite 20.17.0 (Aug 13, 2020)

  • No changes.

New in JChem Suite 20.14.0 (Jun 23, 2020)

  • Bug fixes:
  • Search Engine:
  • Hitdisplay with rotation alignment could be very long for structures that have many graph invariants (they are symmetric).
  • AIOBE could have been thrown in R-group search when an R-group ID was 0.
  • Searching queries containing homolgy structures on any-type tables containing unhandled markush structures required markush license.
  • Enumerable queries reaching timeout during many enumerate didn't check timeout. All enumerates of enumerable queries were stored which could fill heap space.

New in JChem Suite 20.13.0 (May 25, 2020)

  • Improvements:
  • Search Engine
  • Configurable timeout introduced in reaction mapping, default value is 3000ms, it can be set with the reaction.mapping.timeout.ms system property.
  • Bugfixes:
  • Search Engine
  • Searching aromatic or ambiguous aromatic rings with single or double bond single ligand and vagueBondLevel 1 could throw exception.

New in JChem Suite 20.12.0 (May 11, 2020)

  • Regeneration:
  • Full regeneration is needed to use JChem 20.12.0. Please, regenerate all JChem tables after upgrade. The new table version is 20.12.0.0

New in JChem Suite 20.11.0 (Apr 20, 2020)

  • No changes.

New in JChem Suite 20.10.0 (Apr 6, 2020)

  • Improvements:
  • Search Engine
  • Reactions of null cd_smiles entries are mapped parallel if the cache load system proprty is set.

New in JChem Suite 20.4.0 (Feb 7, 2020)

  • JChem Base - DB functionalities
  • Oracle 19c is supported from now on.

New in JChem Suite 20.3.0 (Jan 25, 2020)

  • No changes.

New in JChem Suite 20.2.0 (Jan 21, 2020)

  • No changes.

New in JChem Suite 20.1.0 (Jan 14, 2020)

  • Improvements:
  • Search Engine: Technical improvements were made on the search process.
  • Regeneration:
  • Full regeneration is needed to use JChem 20.1.0. Please, regenerate all JChem tables after upgrade. The new table version is 19.29.0.0

New in JChem Suite 19.26.0 (Dec 13, 2019)

  • No changes.

New in JChem Suite 19.25.0 (Dec 2, 2019)

  • No changes.

New in JChem Suite 19.23.0 (Nov 11, 2019)

  • No changes

New in JChem Suite 19.22.0 (Oct 22, 2019)

  • BUG FIXES:
  • Search Engine:
  • Order sensitive search of reaction structures did not retrieve all hits.
  • 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.
  • Regeneration:
  • Regeneration of Markush structures type tables is needed to use JChem 19.22.0. Please, regenerate Markush structures JChem tables after upgrade. The new table version is 19.22.0.0.
  • The version number of the other types of JChem tables has not changed.

New in JChem Suite 19.21.0 (Oct 7, 2019)

  • Regeneration:
  • Full regeneration is needed to use JChem 19.21.0. Please, regenerate all JChem tables after upgrade. The new table version is 19.21.0.0

New in JChem Suite 19.20.0 (Sep 18, 2019)

  • Search Engine:
  • Nitrogen in marked tetrahedral stereo chiral center matched Nitrogen in unmarked chiral center.

New in JChem Suite 19.18.0 (Aug 12, 2019)

  • No changes.

New in JChem Suite 19.17.0 (Jul 17, 2019)

  • Full regeneration is needed to use JChem 19.17.0. Please, regenerate all JChem tables after upgrade. The new table version is 19.17.0.0

New in JChem Suite 19.8.0 (Mar 19, 2019)

  • No changes.

New in JChem Suite 19.7.0 (Mar 11, 2019)

  • Improvements:
  • Installation:
  • com.fasterxml.jackson.core:jackson-databind:2.9.8 dependency was removed from JChem Base

New in JChem Suite 19.1.0 (Jan 11, 2019)

  • Bugfixes:
  • JChem Base - DB functionalities
  • Reaction fingerprint parameters at database import were not cached and caused slowdown

New in JChem Suite 18.30.0 (Dec 17, 2018)

  • JChem Base - DB functionalities:
  • Reactions that can't be mapped upon database import were repeatedly mapped during searching.

New in JChem Suite 18.18.0 (Aug 3, 2018)

  • Regeneration:
  • Full regeneration is needed to use JChem 18.18.0. Please, regenerate all JChem tables after upgrade. The new table version is 18.18.0.0

New in JChem Suite 18.17.0 (Jul 30, 2018)

  • No changes

New in JChem Suite 18.16.0 (Jul 9, 2018)

  • No changes.

New in JChem Suite 18.15.0 (Jun 28, 2018)

  • Bugfixes:
  • Search Engine:
  • False hits could be received when searching molecules with axial stereo information.

New in JChem Suite 18.14.0 (Jun 22, 2018)

  • Structural keys with explicit hydrogens and a single heavy atom caused missing hits when searching with queries with atom/bond list.

New in JChem Suite 18.13.0 (Jun 12, 2018)

  • No changes.

New in JChem Suite 18.12.0 (Jun 1, 2018)

  • Bugfixes:
  • Search Engine:
  • Searching with alkenyl query homology atom could throw StackOverflowError.

New in JChem Suite 18.11.0 (May 23, 2018)

  • Bugfixes:
  • Search Engine:
  • The hit display of a similarity search showed the query instead the target in some cases.
  • Queries with explicit H were searched far longer in isMatching than in findFirstHit.

New in JChem Suite 18.10.0 (Apr 16, 2018)

  • Bugfixes:
  • Search Engine:
  • Search did not stop if totalSearchTimeoutLimit was reached.

New in JChem Suite 18.8.0 (Apr 4, 2018)

  • Full regeneration is needed to use JChem 18.8.0. Please, regenerate all JChem tables after upgrade. The new table version is 18.8.0.0

New in JChem Suite 18.5.0 (Mar 14, 2018)

  • Regeneration:
  • Full regeneration is needed to use JChem 18.5.0. Please, regenerate all JChem tables after upgrade. The new table version is 18.5.0.0

New in JChem Suite 18.4.0 (Feb 14, 2018)

  • Search Engine:
  • Structural keys were useless in screening as the structural fingerprint was always zero.

New in JChem Suite 17.29.0 (Dec 22, 2017)

  • Improvements:
  • Installation:
  • JChem runs in Java 8 Environment from now on. Documentation
  • Bugfixes:
  • Search Engine:
  • Duplicate structures could be inserted into tables with duplicate filtering true option if there were too many structures with the same hash code already in the database.
  • JChem Base - DB functionalities
  • Known issue relating invalid SYS_* indexes on JCHEMPROPERTIES table in Oracle has been fixed.

New in JChem Suite 17.28.0 (Dec 22, 2017)

  • Bugfixes:
  • Search Engine:
  • Peptide sequence file format was not handled correctly in the searches. From now on the 3-letter peptide format works in searches.
  • Duplicate search was extremely slow when the target structure contained charged hydrogen atom.

New in JChem Suite 17.27.0 (Oct 26, 2017)

  • Bug fixes (search engine):
  • ArrayIndexOutOfBounds exception was thrown when an R-group-containing-molecule with polymers was searched with polymer matching option switched on.

New in JChem Suite 17.25.0 (Oct 14, 2017)

  • Bugfixes (search engine):
  • Similarity search was slow when Chemical Terms filter was used.
  • Endless searches could happen with some homology groups in rare cases.