JChem 5.8.0 beta available for testing

Dear users,

JChem 5.8.0 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/5.8.0beta

Known issues:

• jcman doesn't work. Workaround: please restart your desktop after installing JChem 5.8.0 beta

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

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JChem 5.8.0 beta changes:

Marvin 5.8 is included

New features and Improvements

• JChem Cartridge
  
  
  
  
  • Selectivity and cost estimations for JC_TANIMOTO.
  
  
  • Option to defer error handling for index rebuild. Documentation
  
  
  • Allow indexing of structures with formula as long as 4000 characters (from the previous 100 characters) in regular structure tables.
  
  
  • Oracle client is no more required for installation/upgrade.
  
  
  
  


• Search Engine
  
  
  
  
  • Markush descriptors are loaded into structure cache, resulting in better screening performance.
  
  
  • Use fingerprint for Markush structures in case of homology translation off.
  
  
  • Added search option to specify what kind of set of smallest rings (SSSR vs. CSSR) to use for atom property calculations. Forum topic
  
  
  • Explicit hydrogen is now allowed to be used in structural key molecules. Documentation
  
  
  • Added search option for disabling or enabling fingerprint based screening in case of Markush table search.
  
  
  • Added the possibility of fine tuning Markush database searches by enabling or disabling the available screening methods.
  
  
  
  


• Markush Viewer
  
  
  
  
  • R-group tree is colored if the displayed Markush structure is a colored searching result.
  
  
  • The loaded file opens with expanded R-group tree on the first level.
  
  
  • The Nesting View highlights the appropriate tree node.
  
  
  
  


• Reaction Library
  has been expanded with the following reactions:
  
  
  
  
  • Fischer esterification;
  
  
  • Synthesis of acid chlorides;
  
  
  • Synthesis of acid bromides
  
  
  • Reduction of carboxylic acids to primary alcohols;
  
  
  • Synthesis of carboxylic acid anhydrides;
  
  
  • Alpha halogenation of carboxylic acids;
  
  
  • Synthesis of cyclic anhydrides;
  
  
  • Acylation of nucleophiles with acid chlorides;
  
  
  • Schotten-Baumann reaction;
  
  
  • N-acylation of azides.
  
  
  
  

Bugfixes

• JChem Cartridge
  
  
  
  
  • Upgrader ignored user's instruction not to recalculate CT columns.
  
  
  • jc_insert with the userDefColMap option aborted with error when SELECT was specified as target.
  
  
  • Non-ASCII character output of jc_molconvert was incorrectly encoded. (In particular conversion to SVG resulted in partial garbage.)
  
  
  • Similarity search returned inconsistent results with multiple query structures.
  
  
  • Searches with filterQuery aborted with ORA-20102, when executed in functional/filter mode.
  
  
  • ALTER INDEX REBUILD on compressed tables failed with ORA-39726.
  
  
  • jc_evaluate_x returned SMILES with "\n" appended.
  
  
  • Dependency on the JCC server's locale of country/language settings of database sessions removed.
  
  
  
  


• JChemBase-DB functionalities
  
  
  
  
  • Missing tableType properties are added to the JChemProperties table during database upgrade process.
  
  
  
  


• Search Engine
  
  
  
  
  • Possible false hits of a SMARTS search in case the query structure contains an atom that can be part of an aromatic ring and is connected to an aromatic ring by a single bond.
    Forum topic
  
  
  • Fixed query pseudo atom matching to undefined R atoms in target.
  
  
  • Fixed similarity result coloring in case of exchanged atom orders.
  
  
  • Queries containing R-group definitions could miss hits when an R-group member's attachment points were not added last.
  
  
  
  


• Markush Viewer
  
  
  
  
  • Ctrl + o didn't open Markush Viewer file chooser unless the file menu has been clicked previously.
  
  
  
  


• Fingerprints
  
  
  
  
  • Reaction fingerprint generation threw AIOOBE if the reactant was empty molecule.
  
  
  
  


• Standardizer
  
  
  
  
  • Neutralize action: Hydrogen was not removed from aromatic nitrogen during neutralization.
  
  
  
  

Regeneration

Table regeneration is needed to use JChem 5.8, please regenerate 'Markush libraries' and 'Query structures' type JChem tables and indexes after upgrade.

The new table version is 5080000.