JChem 5.10.0 beta available for testing

 

Dear users,

JChem 5.10.0 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/5.10.0beta2

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

 

 

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June 8th, 2012: JChem 5.10.0

Marvin 5.10.0 is included

New features and Improvements

• Installation/deployment
  
  
  
  • Customize isotope and element data: If isotopes.zip or elements.zip are present on the user's machine in the chemaxon folder in user home, Marvin prefers it instead of default one.
  
  
  
  


• JChem Cartridge
  
  
  
  • Readmol and writemol functions have been added to read and write molecules from/in files.
  
  
  • Index parameter is provided to store errors in a database table.Documentation
  
  
  • Oracle log entries are available on server side (no need for DBA).
  
  
  • Molecule converting function and parameter types have been extended: conversion between VARCHAR2/BLOB/CLOB types is possible in all directions. See more in the documentation about jc_molconvert, jc_molconvertv, jc_molconvertb and jc_molconvertc functions.
  
  
  • Connections opened from JCC server maintain the CLIENT_INFO, MODULE and ACTION columns in the V$SESSION data dictionary view.
  
  
  • The use of service names and full connection strings are allowed instead of only service ids during installation/upgrade.
  
  
  • Size of cd_smiles column in the index tables has been increased to 4000 characters.
  
  
  • haltOnError parameter has been added for jc_evaluate.
  
  
  • Global option for configuring Marvin Services to be accessed in jc_evaluate. Documentation
  
  
  
  


• JChem Base - DB functionalities
  
  
  
  • API changes:
    
    
    
    • Deprecated constructor ConnectionHandler(Connection) has been removed from the public API.
    
    
    • The first parameter of FingerprintHandler.save() function has been changed from ConnectionHandler to DatabaseProperties; old function has been deprecated.
    
    
    
    
  
  
  
  


• Search Engine
  
  
  
  • API changes:
    
    
    
    • RgDecompResults returns the Decomposition objects in RgDecompResults.getDecompositions(). Forum topic
    
    
    • RGroupDecomposition.setQuery(Molecule, int) has been deprecated. setQuery(Molecule) and getSearchOptions().setUndefinedRAtom(int) can now be called separately in the same way as in case of MolSearch.
    
    
    
    
  
  
  
  


• Reaction Library has been expanded with the following reactions:
  
  
  
  • Sonogashira coupling;
  
  
  • Negishi coupling;
  
  
  • Suzuki coupling;
  
  
  • Friedlander quinoline synthesis;
  
  
  • Fischer indole synthesis;
  
  
  • Huisgen 1,5-disubstituted triazole synthesis;
  
  
  • Huisgen 1,4 disubstituted triazole synthesis;
  
  
  • Synthesis of spirochromanone;
  
  
  • Heck coupling;
  
  
  • Buchwals-Hartwig cross coupling;
  
  
  • 2+3 imidazole synthesis;
  
  
  • Williamson ether synthesis.
  
  
  
  


• Standardizer
  
  
  
  • New Standardizer action: Create group. User defined abbreviated groups can be specified. The create group standardization process consists of three steps: substructure match, grouping, and contracting group.
  
  
  
  


• Documentation
  
  
  
  • User documentation of Hit display/coloring has been prepared. Documentation
  
  
  
  

Bugfixes

• JChem Cartridge
  
  
  
  • Inserting large structures into duplicate filtering index failed with ORA-04091. Forum topic
  
  
  • jc_delete failed with IllegalStateException when the table was not JChem-indexed.
  
  
  • Highlight superstructure & similarity search failed without informative error message when rowid parameter is wrong. Forum topic
  
  
  • jc_compare failed with "ORA-29532: [...] Exhausted Resultset" was in case of some queries, when the index was created with haltOnError=nf parameter.
  
  
  • Session longops showed only the first half of the index creation when creating index on Markush table.
  
  
  • Creating index with haltOnError=nf failed with error on Markush tables in some cases.
  
  
  • Some structures may have remained unindexed with duplicateFiltering=y and haltOnError=nf index parameters.
  
  
  • Installer and upgrader command line user interface may have been garbled (due to excessive delay in JChem Server start-up).
  
  
  • Misleading error message was appeared in the case of jc_evaluate errors in domain index scan mode.
  
  
  • Search had the potential to hang due to connection problems in JChem server.
  
  
  • CREATE INDEX failed with ORA-06502 ... character string buffer too small (other SQLs failing with error messages might be affected).
  
  
  • jc_react(4) didn't abort on some errors.
  
  
  • Creating and rebuilding Markush tables with haltOnError=nf option failed when there was an error during molecular descriptor creation. The information in v$session_longops table shows more precise values during these operations.
  
  
  
  


• JChem Base - general
  
  
  
  • ArrayIndexOutOfBoundsException was thrown when filter ID list was set and query could be enumerated or had tautomers (in case of tautomer search).
  
  
  
  


• Search Engine
  
  
  
  • Hits in ambiguous aromatic rings with adjacent R-groups were not found by aromatic queries.
  
  
  • Hit display and coloring of R-group queries in Markush search did not work correctly.
  
  
  • jcunique command line utility didn't work if the user didn't have a database connection.
  
  
  • Query structure having R-groups did not match its enumerate as target during database substructure search.
  
  
  • Structures with double bond stereochemistry difference due to explicit/implicit hydrogen representation could not be found in duplicate search.
  
  
  • Markush reduction incorrectly removed R-group definitions.
  
  
  • Full structure search error involving explicit and implicit hydrogens with exact radical matching.
  
  
  
  

Regeneration

Full table regeneration is needed to use JChem 5.10, please regenerate all JChem tables and indexes after upgrade. The new table version is 5100000.