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.

Known issues

• Upgrade of older versions than 17.24.0 can be executed only in two steps. 1st step: upgrade to 17.24.0 (or 17.25.0 or 17.26.0); 2nd step: upgrade to 17.29.0

Regeneration

Full regeneration is needed to use JChem 17.29.0. Please, regenerate all JChem tables after upgrade. The new table version is 17.29.0.0

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.

Known issues

• Invalid SYS_* indexes must be manually rebuilt on JCHEMPROPERTIES table in Oracle.

• Upgrade of older versions than 17.24.0 can be executed only in two steps. 1st step: upgrade to 17.24.0 (or 17.25.0 or 17.26.0); 2nd step: upgrade to 17.28.0

Improvements

• JChem Base - DB functionalities

  • In Oracle, the data type of the PROP_VALUE_EXT column in the JCHEMPROPERTIES table has been changed from LONG RAW to BLOB.

Bugfixes

• Search Engine

  • ArrayIndexOutOfBounds exception was thrown when an R-group-containing-molecule with polymers was searched with polymer matching option switched on.

Known issues

• Invalid SYS_* indexes must be manually rebuilt on JCHEMPROPERTIES table in Oracle.

• Upgrade of older versions than 17.24.0 can be executed only in two steps. 1st step: upgrade to 17.24.0 (or 17.25.0 or 17.26.0); 2nd step: upgrade to 17.27.0

Bugfixes

• Search Engine
  

  • Similarity search was slow when Chemical Terms filter was used.

  • Endless searches could happen with some homology groups in rare cases.

Bugfixes

• Search Engine
  

  • Tautomer duplicate search could give false results when aromatic rings were part of the tautomer region.

  • Stereo search could give false results in case of quaternary stereo centers where only one wedge bond was indicated.

Known issues

• Image generation in JChem Web Services might be very slow.

Regeneration

Full regeneration is needed to use JChem 17.24.0. Please, regenerate all JChem tables after upgrade. The new table version is 17.24.0.0

Bugfixes

• Search Engine
  

  • In tables where tautomerize standardizer action was set, tautomer search could result missing hits.

Regeneration

Full regeneration is needed to use JChem 17.23.0. Please, regenerate all JChem tables after upgrade. The new table version is 17.23.0.0

Bugfixes

• Search Engine
  

  • Duplicate / full fragment search combined with tautomer search could result failing hits.

Regeneration

Full regeneration is needed to use JChem 17.22.0. Please, regenerate all JChem tables after upgrade. The new table version is 17.22.0.0

Improvements

• Search Engine
  

  • New separate homology groups has been introduced: Aryl, Heteroaryl, Heteroalicyclyl, Fusedheteroaryl, Fusedheteroalicyclyl. Documentation

Bugfixes

• Search Engine
  

  • Additional text notes of HeterosubstitutedAlkyl, Hydroxyalkyl and Haloalkyl homology groups were not handled correctly.

Regeneration

Regeneration of "Markush" type tables is needed to use JChem 17.21.0. Please, regenerate the "Markush" type JChem tables after upgrade. Their new table version is 17.21.0.0.

Regeneration

Full regeneration is needed to use JChem 17.14.0. Please, regenerate all JChem tables after upgrade. The new table version is 17.14.0.0

Bugfixes

• Markush Search
  

  • Existence of haloAlkyl, hydroxyAlkyl, or heteroSubstitutedAlkyl in Markush target blocked finding substructure search hits if the matching substructure was outside the homology region.

Bugfixes

• Search Engine

  • Tautomer duplicate search missed hits in some rare cases. Versions 17.5.0 - 17.9.0 need manual regeneration in order to fix database searches influenced by this bug.

Bugfixes

• Search Engine
  

  • Filtered search with maximum hit count caused missing hit.

  • Superstructure search could give missing or additional hits when query properties were present.

Bugfixes

• Search Engine
  

  • The use of FilterQuery search option with FINE or more detailed logging failed with ArrayIndexOutOfBoundsException.

Improvements

• Installation

  • New version numbering system has been introduced. Blog

Bugfixes

• JChem Base - DB functionalities

  • UpdateHandler sometimes changed autoCommit mode of Postgres connections.

Regeneration

Full regeneration is needed to use JChem 17.5.0. Please, regenerate all JChem tables after upgrade. The new table version is 17.5.0.1

Improvements

• Installation

  • Bundled MySQL JDBC driver changed to MariaDB JDBC driver.

Bugfixes

• Search Engine

  • Double bond stereo was not always taken into account in tautomer duplicate search of molecules containing H atoms with stereo information.

  • Tautomer duplicate search could give false negative results when valence property was present on an atom within the tautomer region.

Bugfixes

• Search Engine
  

  • Tautomer duplicate search, tautomer full structure and tautomer full fragment search in database could result missing hits.

Regeneration

Full regeneration is needed to use JChem 17.1.2. Please, regenerate all JChem tables after upgrade. The new table version is 17.1.2.0.

Regeneration

Full regeneration is needed to use JChem 16.12.19. Please, regenerate all JChem tables after upgrade. The new table version is 16.12.19.0.

Improvements

• Search Engine
  

  • Speed of database search has been increased by improving the selectivity in the screening search phase, especially in case of query structures with Generic query atoms or with Any bonds.

Regeneration

Full regeneration is needed to use JChem 16.12.5. Please, regenerate all JChem tables after upgrade. The new table version is 16.12.5.0.

Bugfixes

• Search Engine

  • The tautomer duplicate and full structure search could have been very slow in case of large, highly symmetrical, and stereo configured molecules.

New features and Improvements

• Installation

  • New installers are provided which differ from the old installers (up to version 16.10.31).

    • The new installer does not upgrade JChem installations created by any old installer, they must be uninstalled manually.

    • New home directory of JChem is called JChemSuite, by default.

    • No desktop icons are created for the GUI applications.

    • JChem Manager GUI can be started by JChemSuite/bin/jcmanager.exe.

Bugfixes

• JChem Base - DB functionalities

  • Database import froze for molecules containing extreme number of rings.

Bugfixes

• Search Engine
  

  • Similarity search for reactions returned false results.

Regeneration

Full regeneration is needed to use JChem 16.9.26. Please, regenerate all JChem tables after upgrade. The new table version is 16.9.26.0.

Bugfixes

• Search Engine
  

  • Wedge bonds were not always recognized within the rings causing missing hits in search.

Regeneration

Full regeneration is needed to use JChem 16.8.29. Please, regenerate all JChem tables after upgrade. The new table version is 16.8.29.0.

Bugfixes

• R-group decomposition
  

  • Tetrahedral stereo information at the attachment points of the R-groups was lost.

Bugfixes

• JChem Base - DB functionalities

  • Reacting center query properties were not correctly persisted in the database.

Regeneration

Regeneration of "Query structures" and "Any structures" type tables is needed to use JChem 16.8.1. Please, regenerate the "Query structures" and "Any structures" type JChem tables after upgrade. Their new table version is 16.8.1.0.

Regeneration

Full regeneration is needed to use JChem 16.7.4. Please, regenerate all JChem tables after upgrade. The new table version is 16.7.4.0.

New features and Improvements

• Search Engine

  • Support of undefined R-atoms around tetrahedral stereo centers on query side is introduced.

Bugfixes

• JChem Base - DB functionalities

  • Cache registrations were not removed if multiple caches became invalid at the same time.

New features and Improvements

• JChem Web Services
  

  • Searching by JChem Oracle Cartridge is supported from now on.

Regeneration

Full regeneration is needed to use JChem 16.5.23. Please, regenerate all JChem tables after upgrade. The new table version is 16.5.23.0.

Bugfixes

• Search Engine

  • Syn, anti, endo, exo information were calculated for ambiguous cases resulting inconsistent search results.

  • Chemical elements with valence 1 were handled incorrectly in searches on query side, resulting loss of hits.

Regeneration

Full regeneration is needed to use JChem 16.5.16. Please, regenerate all JChem tables after upgrade. The new table version is 16.5.9.0.

Bugfixes

• Search Engine
  

  • 'Duplicate keys in cache' error has been fixed. Affected versions are from 15.5.11.

Bugfixes

• Search Engine
  

  • Substitution count query property on atoms was not correctly handled causing missing hits in duplicate search.

Bugfixes

• Search Engine
  

  • Properties of homology groups were not checked during duplicate search.

Bugfixes

• JChem Base - DB functionalities

  • Import of chemical structures in InChI format could have been frozen in case of incorrect structures.

  • Due to a bugfix in the aromatization, full regeneration is needed.

Regeneration

Full regeneration is needed to use JChem 16.2.22. Please, regenerate all JChem tables after upgrade. The new table version is 16.2.22.0.

Bugfixes

• The Known issues of version 16.2.1 has been fixed.

Known issues

• Some slowdown in import and in searches can be experienced.

• Tables must be regenerated if tautomer duplicate and tautomer full structures searches are planned to be executed.

Bugfixes

• Search Engine

  • Duplicate search with ignoreCumuleneOrRingCisTransStereo:n or ignoreAxialStereo:n could have caused ArrayIndexOutOfBondsException if the query molecule contained an explicit hydrogen.

  • An ArrayIndexOutOfBoundsException could have been thrown for duplicate search with molecule containing a link node if this node had more than two ligands.

Bugfixes

• Markush Search
  

  • Homology aliases were not handled correctly in duplicate search.

Bugfixes

• Search Engine

  • Aromatic stereo bonds were not imported properly from SMARTS strings.

Regeneration

Full regeneration is needed to use JChem 15.11.23. Please, regenerate all JChem tables after upgrade. The new table version is 15.11.23.0.

Bugfixes

• Search Engine

  • Duplicate search did not consider link node outer atoms.

  • Some hits were missing when there was s<n> query property on explicit hydrogen atom.

  • False hits were resulted in duplicate and full structure search in the case of target structures with separated hydrogen ion/molecule fragments.

Regeneration

Regeneration of "Reactions" type tables is needed to use JChem 15.10.5. Please, regenerate the "Reactions" type JChem tables after upgrade. Their new table version is 15.10.5.0.

Regeneration

Regeneration of "Query structures" type tables is needed to use JChem 15.9.28. Please, regenerate the "Query structures" type JChem tables after upgrade. Their new table version is 15.9.28.0.

Improvements

• Search Engine

  • The default value of the search option vague bond level is modified. Its new default is half. Documentation

Bugfixes

• Search Engine

  • False positive polymer hits could be experienced when searching with particular ring structures.

  • IndexOutOfBoundsException was thrown by targets with attached data and monomer group.

Bugfixes

• Search Engine

  • Pseudo atom with UnknownGroup alias string was not recognized as homology group.

Bugfixes

• Search Engine

  • Query structures having atoms with explicit hydrogen and any atom (A) neighbours could result false positive hits.

Bugfixes

• JChem Base - DB functionalities

  • Date type data from an sdf file could not be imported into Date type column of a JChem table in Oracle.

• Search Engine

  • ClassCastException was thrown at search when a target reaction in an Any structures type table contained R-groups.

Improvements

• JChem Base - DB functionalities

  • Search speed up can be achieved in JChem tables filled with numerous structures having small, stereo-configured rings. To attain this speed-up, manual table regeneration is needed.

• Search Engine
  

  • R-group bridges are supported in Markush and query structures.

  • Reserved memory of database search engine have been increased from 10 - 100 MB to 250 - 1000 MB. API documentation

Improvements

• Search Engine
  

  • New homology group - Heterocyclyl - is introduced. Documentation

Bugfixes

• Markush Search
  

  • Search hit coloring was inaccurate in case of Markush targets with position variation bonds.

• Search Engine
  

  • JChemSearch could block for searches throwing exception.

Deprecations

• Removals
  

  • Function UpdateHandler#getPreferredTableType(Molecule) is removed. Please read our documentation in order to select the table type to use.

Bugfixes

• JChem Base - DB functionalities

  • NumberFormat exception was thrown during import in case of molecule with large coordinate value.

• Search Engine
  

  • Query atom property '(A)' was removed by default standardizer action 'aromatize:g' causing false search results.

  • Searches reaching their timeout limits could run into deadlock situation.

Deprecations

• Search Engine
  

  • JChemSearch#setTimeout(int seconds) has been deprecated. JChemSearchOptions#setTotalSearchTimeoutLimitMilliseconds(int milliseconds) should be used instead. Note: the new method handles its parameter as milliseconds.

  • JChemSearch#getTimeout() has been deprecated. JChemSearchOptions#getTotalSearchTimeoutLimitMilliseconds() should be used instead. Note: the new method returns milliseconds instead of seconds.

  • Previously deprecated method JChemSearchOptions#setMaxTime() should be replaced by JChemSearchOptions#setTotalSearchTimeoutLimitMilliseconds() in order to limit the total timeout on multiple targets. The timeout limit for a search on a single target should be set via SearchOptions#setTimeoutLimitMilliseconds().

  • Previously deprecated method JChemSearchOptions#getMaxTime() should be replaced by JChemSearchOptions#getTotalSearchTimeoutLimitMilliseconds() in order to retrieve the total timeout limit on multiple targets. The timeout limit for a search on a single target should be retrieved via SearchOptions#getTimeoutLimitMilliseconds().

Upgrade

• IKVM.NET version has been upgraded to 7.4.

Bugfixes

• JChem Base - DB functionalities

  • Import with duplicate filtering or duplicate search may have frozen for big tables.

Known issues

• JChem Base - DB functionalities

  • Import with duplicate filtering or duplicate search might be frozen for big tables.

Known issues

• JChem Base - DB functionalities

  • Import with duplicate filtering or duplicate search might be frozen for big tables.

Bugfixes

• JChem Base - DB functionalities

  • Cache load was slow on big tables in some cases.

Known issues

• JChem Base - DB functionalities

  • Import with duplicate filtering or duplicate search might be frozen for big tables.

Known issues

• JChem Base - DB functionalities

  • Import with duplicate filtering or duplicate search might be frozen for big tables.

Bugfixes

• JChem Base - DB functionalities

  • JChem now accepts yyyy-mm-dd date format too during import and not only mm/dd/yyyy.

• Search Engine

  • ArrayIndexOutOfBoundsException may have occurred when handling molecules containing multiple groups.

Known issues

• JChem Base - DB functionalities

  • Import with duplicate filtering or duplicate search might be frozen for big tables.

Known issues

• JChem Base - DB functionalities

  • Import with duplicate filtering or duplicate search might be frozen for big tables.

Bugfixes

• Search Engine

  • Parallel execution of StandardizerMolSearch with the same query instance could cause NullPointerException.

Known issues

• Installation

  • Four needless jar files are included in the installers: hamcrest-core-1.3.jar, jackson-core-asl-1.9.13.jar, jackson-mapper-asl-1.9.13.jar, and junit-4.11.jar.

• JChem Base - DB functionalities

  • Import with duplicate filtering or duplicate search might be frozen for big tables.

Improvements

• Search Engine

  • Molecular descriptor caching can be switched on resulting in a 1-2 orders of magnitude speed-up of similarity search with molecular descriptors. Documentation

Bugfixes

• Search Engine

  • HitDisplayTool.getHitIndexes() method returned null instead of correct atom indexes.

  • Descriptor similarity search always used the first metric of the descriptor. Now the dissimilarity metric option is considered.

Deprecations

• Removals

  • Public constants in chemaxon.jchem.version.VersionInfo were removed; use public functions of the same class instead.

Known issues

• JChem Base - DB functionalities

  • Import with duplicate filtering or duplicate search might be frozen for big tables.

Deprecations

• Search Engine

  • JChemSearchOptions#setMaxTime() and JChemSearchOptions#getMaxTime() has been deprecated.

Known issues

• JChem Base - DB functionalities

  • Import with duplicate filtering or duplicate search might be frozen for big tables.

Bugfixes

• Search Engine

  • The known slow-down in similarity search from previous week has been eliminated.

Known issues

• JChem Base - DB functionalities

  • Import with duplicate filtering or duplicate search might be frozen for big tables.

Known issues

• Search Engine

  • Similarity search has a slow-down of about 50-60% compared to the previous releases.

Regeneration

Full regeneration is needed to use JChem 15.3.9. Please, regenerate all JChem tables after upgrade. The new table version is 15.3.9.0.

Regeneration

Full regeneration is needed to use JChem 15.3.2. Please, regenerate all JChem tables after upgrade. The new table version is 15.3.2.0.

Bugfixes

• Search Engine

  • Mapped reactions did not hit unmapped ones in case of memory searches.

Bugfixes

• Markush Search

  • Coloring of bonds in R-groups of Markush hits was not correct.

Bugfixes

• Search Engine
  

  • Mapped reactions did not hit unmapped ones in case of memory searches.

  • Query structure having double bond in symmetric ring system and explicit Hydrogen atom on the ring system failed to match to the corresponding structure without the explicit Hydrogen atom using FULL match, stereo search type set to STEREO_SPECIFIC, double bond stereo matching set to DBS_ALL, and stereo model set to STEREO_MODEL_GLOBAL.

Improvements

• Search Engine
  

  • Combined searches have been speed-up. Blog

Bugfixes

• JChem Base - DB functionalities

  • UnsupportedOperationException was thrown in database import of peptide sequences containing amino acids with three attachment points.

• Search Engine
  

  • Reaction search on reaction tables caused missing hits in case of basic aromatization.

• JChem API

  • The accidental API change of the previous release which rendered the constants of chemaxon.jchem.db.TableTypeConstants unusable in switch statements (since they became non-compile time constants) has been reverted.

Bugfixes

• JChem Base - DB functionalities

  • Targets that have list atoms or not-list atoms with empty definition lists caused errors during search. These structures won't be allowed to be imported/indexed.

• Search Engine
  

  • [!#1;!#6] smarts atom matched isotopic hydrogens.

  • NullPointerException was thrown during search when disconnected R-group definitions were found in a target structure.

Known issues

• JChem API

  • An accidental API breaking change has been introduced in chemaxon.jchem.db.TableTypeConstants which may cause compile error if table type constants are used in the case clause of switch statements. This change will be reverted in the next release.

Bugfixes

• Search Engine
  

  • JChemSearch.getHitsAsMolecules() returned standardized structures for Superstructure search.

Bugfixes

• Search Engine
  

  • NullPointerException was thrown when search contained Markush structure with R-atom in a ring system with bicyclo stereo information.

Bugfixes

• JChem Base - DB functionalities

  • Molfiles with brackets in their first line could be erroneously imported into JChem tables.

Bugfixes

• Search Engine
  

  • Some structures with multiple syn-anti stereo configurations didn't match themselves.

Deprecations

• Removals from the public API
  

  • Methods with NOV_01_2014 RemovalDate were removed. The following classes are affected:

    • chemaxon.jchem.db.Exporter

    • chemaxon.jchem.db.StructureTableOptions

    • chemaxon.jchem.db.TableInfo

Bugfixes

• Markush search
  

  • Hydrogen atoms in nested R-group definitions were not correctly handled in full searches and searches with queries having s* property.

  • False hits could be resulted in Markush searches when atoms of the query structure had s* query atom property and position variation bonds were present in the target structures. The previous solution was further improved.

Regeneration

Full regeneration will be required in case of "Any structures" and "Query structures" type JChem tables after upgrade. Their new table version will be 14.10.20.0.

Bugfixes

• Search Engine
  

  • Hydrogen query properties of atoms within tetrahedral stereo configuration were not exported correctly to SMARTS causing false hits.

Regeneration

Full regeneration is needed in case of specific tables to use JChem 14.10.13. Please, regenerate "Any structures" and "Query structures" type JChem tables after upgrade.

Bugfixes

• Installation/deployment

  • JChem Manager could not be launched by 'jcman.bat' on Windows Prompt.

• Markush search

  • False hits could be resulted when atoms of the query structure had s* query property and position variation bonds were present in the target structures.

Bugfixes

• Installation/deployment

  • Command line options (switches) of 'jcman.bat' did not work correctly on Windows Prompt.

Known issues

• Installation/deployment

  • JChem Manager cannot be launched by 'jcman.bat' on Windows Prompt. Recommended workaround: apply the desktop icon of JChem Manager or start by JChemManager.exe.

New features and Improvements

• Search Engine

  • The performance of tautomer search has been increased resulting even 100% speed-up in some cases of tautomer substructure search.

Bugfixes

• JChem Base - DB functionalities

  • ConnectionHandler incorrectly stated that it closes open connection in its finalize() method - warning message has been changed.

Bugfixes

• Search Engine

  • Matching of structures with ring cis/trans stereo configuration could fail. Forum topic

  • Searching with query side homology groups could cause ClassCastException in version 14.9.1

Bugfixes

• JChem Base - DB functionalities

  • Oracle locking exception during database modification in JChem version 14.8.25 fixed.

Regeneration

Full table regeneration is needed to use JChem 14.9.1. Please, regenerate all JChem tables after upgrade. The new table version is 14.9.1.0.

Bugfixes

• JChem Base - DB functionalities

  • Not fully mapped reactions could be imported incorrectly.

New features and Improvements

• JChem Base - DB functionalities

  • Oracle 9i is not supported anymore.

• Search Engine

  • The accuracy of Maximum Common Substructure (MCS) search was improved in case of connected mode.

Bugfixes

• Search Engine

  • Reaction center bond query properties were not correctly handled during the evaluation of exact bond matching.

  • Stereo marking "marked" of double bonds was not checked during searching with exact bond matching option.

Bugfixes

• Search Engine

  • Some structures could not find an identical structure if axial stereo search option was switched on. Forum topic

New features and Improvements

• JChem Base - DB functionalities

  • Support of VMN format of Markush structures is disabled.

  • JTF format is not supported anymore.

• Search Engine

  • New homology groups - heterosubstitutedAlkyl, haloalkyl, and hydroxyalkyl - are introduced. Documentation

  • Allene stereo search option is renamed to cumulene or ring cis-trans stereo as this describes the behavior of the option better. Documentation

  • Full structure and full fragment structure search is not allowed on query table type.

  • Markush MCS search type has been removed from JChem Base search types.

Bugfixes

• JChem Base - DB functionalities

  • Export from big JChem tables threw out of memory exception on PostgreSQL database.

  • NullpointerException was thrown during chemical terms calculation in database.

  • Any (A) and hetero (Q) atoms could not be saved in Markush tables.

• Search Engine

  • Explicit H sometimes did not match AH, MH, QH in case of markush searches.

  • Any (A) and hetero (Q) atoms could not be used on the target side in memory Markush searches.

  • Structures with explicit hydrogen could throw exception for allene and axial searches

Regeneration

Full table regeneration is needed to use JChem 14.7.7. Please, regenerate all JChem tables after upgrade. The new table version is 14.7.7.0.