ChemAxon launches JChem 3.0 and Marvin 3.5.

news · 14 years ago
The new JChem 3.0 includes the Marvin 3.5. Please run through the list of the most important changes:
  • Marvin 3.5.1 is included.
  • JChem Base
    • The structure of JChem tables changed, 3 more columns were added:
      • cd_hash : hash code for speeding up duplicate filtering during import (registration). With this column there's no need for a composite index on the fingerprint columns, therefore the length of the fingerprint is no longer limited by the maximum length of composite fingerprints in the database.
      • cd_flags : for storing molecule-specific tags. Currently only indicates if the missing chiral flag should be overridden in imported structures. This means there's no need to change the chiral flag field in the original molecule string when the import option "Set chiral flag for MDL formats" is enabled.
      • cd_timestamp: the timestamp of the insertion of the structure.
    • The old tables are transformed automatically into the new format on the first start of the jcman GUI.
    • JChemSearch
      • Multiple search threads for increased performance on multi-processor systems. Currently only for searches that use structure cache.
      • Timeout option to abort searches which the client stopped checking.
      • New search options:
        • Stereo search can be turned off
        • Double bond stereo matching mode
        • Exact charge matching
        • Exact isotope matching
        • Exact query atom matching
        • Exact radical matching
        • Exact stereo matching
        • Hydrogen count matching
        • Match count with boundaries
        • Match count in relation
    • Structure Cache improvements:
      • Incremental cache update: the cache won't be reloaded after every change to the table, only the changed rows are updated if possible.
      • Improved memory control:
      • maximum cache size may be specified with setMaxCacheSize
      • auto detection of available memory
      • minimum non-cached memory size may be specified with setMinNonCachedMemory. This amount will be reserved for other allocations.
      • least recently used tables are dropped from the cache if necessary. (Note: StructureCache is no longer a public API, and direct use of the class is not recommended any more, since some incompatible changes had to be made for the new features.)
    • Rxnfile import / export
    • Structure search speedup
    • Import speedup
    • JSP example web application
      • Chemical Terms expression can be specified for the query
      • Structure caching can be turned on / off using the configuration file. Please make sure you have set the appropriate cache setting after upgrading your JChem version. For more information see the JSP setup guide.
      • The status of the Structure Cache can be monitored from the "About" dialog
    • Evaluator
      • Added Language Reference.
      • Added Working Examples.
      • Added topology analyser plugin references (see the Short Reference).
    • Bugfixes
      • MySQL 4.x compatibility issue fixed
      • Compatibility issue fixed when upgrading early versions of JChem
      • JSP example : problem with deleted structures fixed
      • Other minor bugfixes
  • Search
    • New search mode: SUPERSTRUCTURE search.
    • Double bond stereo: adjoining wiggly bond means "cis or trans"
    • new jcsearch options: --stereoSearch, --exactStereoSearch, -t:c (count hits), --maxResults:
  • Standardizer
    • New actions: clear stereo and set/clear absolute stereo (chiral) flag
  • Synthesizer
    • New algorithm: ExhaustiveAlgorithm.
  • JChem Cartridge
    • New options to jc_compare.
    • jc_evaluate for calculation based on chemical terms.
    • Dramatically improved performance and stability.
  • Maximum Common Structures of a compound set
    • Small/medium sized compound sets, libraries (100-10000 structures) can be analyzed
    • finds all scaffolds (molecular backbones), hierarchically clusters structures around these scaffolds
    • fast: 100 structures/s
    • experimental viewer