Second Generation Search Engine Deprecated Features

    Search options

    Ignore tetrahedral stereo / charge / isotope in search - until version 23.17.0

    By default, the specified tetrahedral stereo configuration, charge and isotope value is required to match in the hit structures.

    Here we describe how the ignoretetrahedralstereo option is handled in search. The other two options ignorecharge and ignoreisotope are handled the same way, and are also recommended to apply in SUBSTRUCTURE and FULLFRAGMENT search, but not in DUPLICATE search.

    In order to ignore the tetrahedral stereo configuration specified in the query structures during the search, the ignoretetrahedralstereo option can be used.

    The ignoretetrahedralstereo search option is a query transformation parameter. If ignoretetrahedralstereo is set, the tetrahedral stereo bonds of the query molecule are transformed to single bonds in the background of the search, but the tetrahedral stereo bonds of the target molecules stay intact.

    The usage of ignoretetrahedralstereo search option is recommended in SUBSTRUCTURE and FULLFRAGMENT search, but is not recommended in DUPLICATE search.

    Duplicate search with fully ignored tetrahedral stereo properties - like in JChem Base or JChem Oracle Cartridge - cannot be executed by the products using this second generation search engine. When searching for enantiomers, diastereomers FULLFRAGMENT search with ignoretetrahedralstereo option is recommended with taking into account the other less strict features of FULLFRAGMENT search compared to DUPLICATE search (the hit structures can contain more fragments, isotopes, charged atoms, ...)

    Query Target without ignoretetrahedralstereo
    [Default]    		 with ignoretetrahedralstereo
    images/download/attachments/1806734/no.png
    images/download/attachments/1806734/no.png in substructure and fullfragment search
    in duplicate search

    Repeating units with large repetition number

    Valid only for JPC 25.1.1, Choral 25.1.1, JMS 25.1.3, 25.1.4.

    Repeating units with large repetition number can freeze the indexing processes. Such repeating units usually represent polymer structures, and their transformation to polymers will enable indexing and searching. As a result of the transformation repeating unit type expansion is avoided and structures are interpreted according to polymer search semantics. The custom standardizer action convertrepeatingunittosrupolymer can be applied as part of the standardizer actions of the relevant molecule type. convertrepeatingunittosrupolymer is available from JPC 25.1.1, Choral 25.1.1, JMS 25.1.3. When custom standardizer action convertrepeatingunittosrupolymer is set, the repeating units - having equal or higher repetition number than the configured value (default 10000) - are converted to SRU polymers.
    The action convertrepeatingunittosrupolymer is not part of the product Standardizer.

    Configuration

    • as standardizer action string

      convertrepeatingunittosrupolymer:10000

    • in standardizer xml configuration file

      <ConvertRepeatingUnitToSRUPolymer ID="Convert Repetition Unit" Limit="10000"/>