JChem 5.9.0 beta available for testing

Dear users,

JChem 5.9.0 beta is available for testing. For a full list of changes, please see below.

Download: https://www.chemaxon.com/download.php?d=/data/download/jchem/5.9.0beta2

Bug reports: if you found a bug in this beta release, please let us know through the regular support channels.

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March 2nd, 2012: JChem 5.9.0 Beta

Marvin 5.9.0 is included

New features and Improvements

• JChem Cartridge
  
  
  
  • Function is implemented to check compliance of molecule with index "structureType". Forum topic
  
  
  • JChem Cartridge Owner can view the license information via table function. Forum topic, Documentation
  
  
  • Creating index and rebuilding index can also be tracked via the v$session_longops table. See the documentation.
  
  
  • Provide SQL interface to administratively kill (runaway) searches. Documentation
  
  
  
  


• JChem Base - jcman
  
  
  
  • New connection window has been developed for JChem Manager. Documentation
  
  
  
  


• JChem Base - DB functionalities
  
  
  
  • JTF format now stores the structure in the original format with base64 encoding instead of always using mol; ExportFileHandler has been renamed to JTFExporter as it now only deals with the JTF format.
  
  
  
  


• Search Engine
  
  
  
  • Speed up molecule tables for several query features (charge, isotope, radical, tautomer, atom list, (R) and (rb) query properties).
  
  
  
  


• Standardizer
  
  
  
  • Tautomer generation for large molecules has become notably faster than in 5.8.x and earlier versions.
  
  
  
  


• Reaction Library has been expanded with the following reactions:
  
  
  
  • Acylation of nucleophiles with carboxylic acids
  
  
  • Hell-Volhard-Zelinsky bromination
  
  
  • Reduction of oxocompounds with NaBH4
  
  
  • Hydrolysis of carboxylic acid halides and anhydrides
  
  
  • Acylation of nucleophiles with carboxylic acid anhydrides
  
  
  • 2+2*1+1 Imidazole synthesis
  
  
  • Hydrolysis of amides
  
  
  • Knorr pyrrole synthesis
  
  
  • 3+2 Dihydroimidazole thione synthesis
  
  
  • Transesterification reaction
  
  
  • 2+3 Imidazole synthesis
  
  
  • Cross-Claisen condensation
  
  
  • 3+2 Pyrazole synthesis
  
  
  • Hinsberg thiophene synthesis
  
  
  • Reduction of esters
  
  
  • Hantzsch pyrrole synthesis
  
  
  • 3+2 Furan synthesis
  
  
  • Pinner reaction
  
  
  • Reduction of nitriles
  
  
  • Paal-Knorr thiophene synthesis
  
  
  • Paal-Knorr pyrrole synthesis
  
  
  • 3+2 Pyrazole synthesis
  
  
  • Pictet-Spengler isoquinoline synthesis
  
  
  • Benzimidazole synthesis
  
  
  • 2,3-Dihydro-1H-benzimidazole synthesis
  
  
  • Benzothiazole synthesis
  
  
  • Benzoxazole synthesis from aldehyde
  
  
  • Hantzsch thiazole synthesis
  
  
  • Tetrazole synthesis
  
  
  • Huisgen triazole synthesis
  
  
  • 1,2,4-Triazole synthesis
  
  
  • Guareschy-Thorpe pyridone synthesis
  
  
  • Hantzsch pyridine synthesis
  
  
  
  

Bugfixes

• JChem Cartridge
  
  
  
  • jc_matchcount was not working correctly in domain index scan.
  
  
  • Cost estimation was not generated for searches in other users' schema.
  
  
  
  


• WS-AJAX example
  
  
  
  • Removed an erroneous security warning message in Ajax Example.
  
  
  
  


• JChem Base - general
  
  
  
  • VMN format sometimes was recognized as cdxml.
  
  
  
  


• JChem Base - DB functionalities
  
  
  
  • Searches on HSQLDB database threw DatabaseSearchException: "ERROR: Table "TEST_TABLE" could not fit into structure cache (out of memory)."
  
  
  • Update log purge blocked other searches for long time.
  
  
  
  


• Search Engine
  
  
  
  • Using implicitHMatching ignore option, special hydrogens are still taken into account. Special hydrogens are: 0 or multiple bonds, isotope, radical, or charge information.
  
  
  • Inserting polymers with H endgroups into tautomer duplicate filtered tables threw exception.
  
  
  • R-group decomposition refused targets with position variation bonds.
  
  
  
  


• Reactor
  
  
  
  • Achiral reaction product "remembered" the stereo information of the reactant.
  
  
  • Pressing "Apply" button in reaction editor did not save the modification of the reaction.
  
  
  
  


• Standardizer
  
  
  
  • Stereo information was lost after tautomerize action.
  
  
  
  


• Structure Checker
  
  
  
  • Structure checker still had problem after all errors were cleaned in "Manual" or "Fix" mode.
  
  
  
  

Known issue

• Structure Checker
  
  
  
  • R-group Reference Error Checker cannot find circular and selfreferring R-atoms and R-groups.
  
  
  
  

Regeneration

No table regeneration is needed to use JChem 5.9.
New table version of "Markush library" and "Query structures" type tables, and tables with "Duplicate search uses tautomers" option is 5080000, while in case of other table types table version is 5070000. All the new tables get CT version 5070000 and MD version 5080100.