gistfile1.rb

require 'java'
require 'jchem_connection'

require 'lib/jchem/lib/jchem.jar'

java_package 'search.db'

java_import 'chemaxon.jchem.db.JChemSearch'
java_import 'chemaxon.sss.SearchConstants'
java_import 'chemaxon.sss.search.JChemSearchOptions'
java_import 'chemaxon.sss.search.options.HomologyTranslationOption'

module JchemSearcher
  def self.search(query)
    search_options = JChemSearchOptions.new(SearchConstants.SUPERSTRUCTURE)
    search_options.set_absolute_stereo(SearchConstants.ABS_STEREO_ALWAYS_ON)
    search_options.set_homology_broad_translation(HomologyTranslationOption.valueOf('ALL'))
    search_options.set_mix_sgroup_matching(true)
    jcs = JChemSearch.new
    jcs.set_connection_handler(JchemConnection.instance.handler)
    jcs.set_query_structure(query)
    jcs.set_structure_table('C_PATTERNS')
    jcs.set_search_options(search_options)
    jcs.run

    results = self.patterns(jcs.get_results.to_a)
    Struct.new(:pattern_names, :search_errors).new(results, [])
  end

  private

  def self.patterns(ids=[])
    return [] if ids.blank?
    sql = "SELECT C_NAME FROM C_PATTERNS WHERE cd_id IN (#{ids.join(',')})"
    ps = JchemConnection.instance.handler.get_connection.prepare_statement(sql)
    rs = ps.execute_query
    names = []
    while rs.next do
      names << rs.get_string(1)
    end
    names.uniq
  end
end