Second Generation Search Engine

    This document describes the main features, configuration possibilities and functional features of the second generation search engine implemented in the following products.

    New features

    Relevance ordering

    The hits of substructure search are given back ordered by the relevance (similarity) between the hit structure and the query structure.

    Hit as you draw

    The most relevant hit structures are given back almost simultaneously with the modification of the query structure.


    Technical parameters

    The Xmx size, cache sizes, and further parameters need to be set before running the servers. Here is a helping page provided for the calculation of the approximate configuration parameters.

    JChem Engines cache and memory calculator

    Business rules

    The business rules relating the interpretation mode of the chemical structures are defined in molecule types. These rules cover the followings:

    • standardizer actions to be executed on the structures
    • tautomer search mode
    • assumption of stereo interpretation mode

    Molecule type

    The molecule types must be set before initializing the new servers.

    Where to define molecule type(s)
    JChem Choral <choral_home>/data/tapes/<type_name.type> files
    JChem PostgreSQl Cartridge /etc/chemaxon/types/<type_name.type> files
    JChem Microservices DB jws-config/common-config/ file or
    jws-db/config/ file
    Application mode of molecule type(s)
    JChem Choral as index type and as search type
    JChem PostgreSQl Cartridge as column type
    JChem Microservices DB as table property
    Standardizer rules

    The standardizer actions can be defined in two forms as

    • standardizer action string
    • standardizer file
    Tautomer mode

    There are three tautomer search modes provided

    • OFF Tautomers are not taken into account during the search

    • GENERIC The generic tautomer - representing all theoretically possible tautomers - of the target is matched with the query structure itself. This method is applied in substructure search, full fragment search, duplicate, and superstructure search.


      It is a hybrid tautomer search mode. The query structure is compared to the generic tautomer of target at substructure and similarity search , while normal canonical tautomers are compared at duplicate search. In full fragment search from version 20.12 to 20.14 the generic tautomer of the target is used, while from version 20.15 normal canonical tautomers are compared.

    Query Target Tautomer mode
    Tautomer mode
    Tautomer mode
    Stereo assumption

    By default, all stereo molecules - independently of the presence or absence of the chiral flag - are regarded as molecules with absolute stereo configuration.

    If you want exclusively molecules with chiral to be handled as absolute (and molecules without chiral flag to be handled as relative) you must set stereoAssumption = RELATIVE in the molecule type definition.

    Query Target Stereo assumption
    Stereo assumption

    Functional features

    Search options

    Ignore tetrahedral stereo search

    By default, the specified tetrahedral stereo configuration is required to match in the hit structures. In order to ignore the tetrahedral stereo configuration specified in the query structures during the search, the ignoretetrahedralstereo option can be used.

    Query Target without ignoretetrahedralstereo
    with ignoretetrahedralstereo
    images/download/attachments/1806734/no.png in substructure search
    in duplicate search
    option name
    JChem Choral ignoretetrahedralstereo
    JChem PostgreSQl Cartridge ignoretetrahedralstereo
    JChem Microservices DB stereoSearchIgnoreTetrahedralStereo

    Stereo search on marked double bond only

    By default, the double bond stereo configuration of all the double bonds of the hit structures must be the same as that of the query structures. See first examples below.

    The dbsmarkedonly search option makes possible to check the E/Z configuration of only those double bonds that are marked.

    Query Target without dbsmarkedonly
    with dbsmarkedonly
    option name
    JChem Choral dbsmarkedonly
    JChem PostgreSQl Cartridge dbsmarkedonly
    JChem Microservices DB stereoSearchOnMarkedDoubleBondOnly

    Hit highlight

    The highlight function compares a query structure with a target structure and highlights the bonds and atoms of the target structure matching with the query structure. The alignment mode and the color applied for highlighting can be set. Three alignment modes are available:

    • off

      The hit structure's position on the screen is the same as that of the target structure.

    • rotate

      The hit structure is rotated till its part corresponding to the query gets the same position as the query structure has.

    • partial clean

      The hit structure's position on the screen is partially aligned to the query structure.

    Query Target Alignment
    partial clean
    option name
    JChem Choral function highlight
    operator hit_highlight
    JChem PostgreSQl Cartridge function highlight
    JChem Microservices DB /rest-v1/db/highlight