JChem Base & Cartridge II: Structure searching in database - Developer Training

Posted by
Tamás Csizmazia
on 12 09 2013

In this webinar we would like to concentrate on the Java API and JChem Cartridge. The main focus will be on using Java API to connect to JChem databases, and Cartridge examples are also given where relevant. Below we outline the main search tasks in a JChem chemical database system:

Search in the database Main steps of chemical database search (from the viewpoint of a Java programmer) are:

  • creating a JChemSearchOptions object of appropriate search type and setting search options:
    • chemical matching behaviour (stereo features, isotopes, radicals, charges, …)
    • other search behaviour (maximum number of returned results, maximum running time of search, returning non-hits, …)
  • creating a JChemSearch object with appropriate attributes (database connection handler, query structure, target database table and a JChemSearchOptions object containing search options)
  • running search (can be run in separate thread)
  • retrieving results

Manipulating search results Beyond these common tasks one can reduce the scope of the search or change appearance of result molecules for better visualization.

  • pre-filtering molecules in database before search (search time can also be reduced using this technique)
  • ordering results

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