Structure Checker Web Services

    {info} Structure Checker Web Services provide methods for

    • structure checking
    • structure fixing

    This documentation describes installation, administration and usage of Structure Checker Web Services.

    Structure Checker Web Services make possible to reach the chemical functionality provided by Chemaxon's product Structure Checker.

    Structure Checker Web Services application is available in two modes:

    1. As part of a microservices system

    2. As a standalone web application

    Microservices system mode

    In microservices system mode, the Structure Checker Web Services runs together with the Config, Discovery and Gateway services. These three services are mandatory, and optionally other services can also be part of the system. All configuration must be done in the Config service.

    The default configuration applies to the microservices system mode.

    The web application runs on host <server-host> and listens on port <gateway-server-port>.

    Standalone web application mode

    In standalone web application mode, the Structure Checker Web Services runs alone, without the Config, Discovery and Gateway services (however, the installer installs them as well).

    The default configuration must be changed according to the standalone web application mode; set

    eureka.client.enabled=false in file, and

    up to version 22.2.0 and in file

    from version 22.9.0

    set and comment out line spring.config.import= in file.

    All configuration must be done in the Structure Checker module.

    The web application runs on host <server-host> and listens on port <server-port>.


    See here.

    Software requirements

    See here


    See here.

    Module is installed into folder: jws/jws-structurechecker


    See here.


    See here.


    Default configuration:
    spring.config.import=configserver:${CONFIG_SERVER_URI:http\://localhost\:8888}?fail-fast=true&max-attempts=100&max-interval=60000&multiplier=1.2&initial-interval=3000 Added in version 22.6.0.
    eureka.client.enabled=true set eureka.client.enabled=false to switch to standalone Structure Checker Web Services application mode #Removed in version 22.6.0.${CONFIG_SERVER_URI:http\://localhost\:8888/} #Removed in version 22.6.0. #Removed in version 22.6.0. #Removed in version 22.6.0. #Removed in version 22.6.0. #Removed in version 22.6.0. #Removed in version 22.6.0.

    For more configuration options, see the Spring documentation page.

    Running the server

    Prerequisites in case of microservices system mode:

    1. Config service is running

    2. Discovery service is running

    3. Gateway service is running

    Run the service in command line in folder jws/jws-structurechecker:

    jws-structurechecker-service.exe --install
    jws-structurechecker-service.exe --start (on Windows in administrator's terminal)

    jws-structurechecker-service start (on Linux)


    run-jws-structurechecker.exe (on Windows)

    run-jws-structurechecker (on Linux)

    API documentation

    Find and try out the API on the Swagger UI.

    Mode URL of Swagger UI Default URL of Swagger UI
    microservices system <serverhost>:<gateway-port>/jws-checker-fixer/API/ localhost:8080/jws-checker-fixer/API/
    standalone web application mode <serverhost>:server-port>/API/ localhost:8066/API/

    Demo site

    For detailed description check out the JWS Structure Checker demo site:

    How to write custom structure checker / structure fixer

    Here you find an example.

    The above example shows how to send custom structurechecker/fixer request when using json format structurechecker/fixer configuration.

    Here we document the requirements of sending custom structurechecker/fixer request when using xml format structurechecker/fixer configuration.

    • Place the custom created jar file in <jws-home>/extra-libs/.

    • Create externalcheckersfixers.xml and place it in <jws-home>/extra-libs/ or in any other folder but jws-user must have the right to read it. Example externalcheckersfixers.xml when it is also in <jws-home>/extra-libs/:

      <?xml version="1.0" encoding="UTF-8"?> 
        <checker class="com.checkers.MyChecker" editor-class="" id="MyChecker" jar="custom-checkers.jar"/> 
        <fixer class="com.checkers.MyFixer" id="MyFixer" jar="custom-checkers.jar"/> 
      </fixer-list> </configuration>

      If externalcheckersfixers.xml is placed in another folder you have to reference to the jar file as:

      <checker class="com.checkers.MyChecker" editor-class="" id="MyChecker" jar="file:///home/somebody/custom-checkers.jar"/>
      <fixer class="com.checkers.MyFixer" id="MyFixer" jar="file:///home/somebody/custom-checkers.jar"/>
    • Add the following line to the .vmoptions file of run-jws-structurechecker and/or jws-structurechecker-service:




      where <dir> is the absolute path of the xml file.

    • Start the service jws-structurechecker

    • Use the /rest-v1/checker-fixer/xml-based endpoint


    The guidelines, examples on the Demo siteor on the Swagger UI API documentation of your installed module display the methods and syntax implemented for reaching the functionalities of Structure Checker product.

    Checker descriptor

    Lists the available checkers, fixers, the checkers with their corresponding fixers and the stored checker-fixer configurations.


    Provides endpoints for structure checking and fixing together.

    Here is an endpoint provided for executing previously stored checker-fixer actions: /rest-v1/checker-fixer/stored/{presetName}

    The checker-fixer configurations can be stored in xml or in json format in the file of the jws-srtucturechecker module and also in the file of the jws-config module.


    com.chemaxon.structurechecker.presets.exampleXML=<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<checkers>\n  <AbbreviatedGroupChecker contracted=\"true\" excluded=\"\" expanded=\"true\" fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ContractGroupFixer\"/>\n</checkers>
    com.chemaxon.structurechecker.presets.exampleJSON=[{"checkerSettings": {"checkerClass": "MissingAtomMapChecker","displayName": "MyStructureChecker"},"fixerSettings": {"displayName": "MyStructureFixer","exportFormat": "mrv","fixerClass": "MapMoleculeFixer"}},{"checkerSettings": {"checkerClass": "AtomMapChecker","displayName": "MyStructureChecker"}}]

    General checker

    Provides endpoint for executing multiple structure checkers simultaneously.

    Single checker

    Provides endpoints for detecting errors by structure checkers one-by-one.