Structure Manipulation Web Services

    Structure Manipulation Web Services provides endpoints for the following:

    • standardizing structures with Chemaxon's toolkit Standardizer,
    • extracting textbox content from the structures,
    • cutting structures into their fragment structures,
    • two-dimensional and three-dimensional cleaning of chemical structures,
    • exporting multistep reactions.

    This documentation describes installation, administration and usage of Structure Manipulation Web Services. As all JChem Microservices modules, it 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 Manipulation 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 Manipulation 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 the following in the application.properties file

    • eureka.client.enabled=false
    • spring.cloud.config.enabled=false
    • If you are using a version earlier than 25.3.0 remove the line that starts with spring.config.import=

    All configuration must be done in the Structure-Manipulation module.

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

    Download

    See here.

    System requirements

    See here

    Installation

    See here.

    Module is installed into folder: jws/jws-structure

    Licenses

    See here.

    Logging

    See here.

    Configuration

    Default configuration:

    application.properties
    server.port=8063
    logging.file.name=../logs/jws-structure.log
    spring.config.import=optional:configserver:${CONFIG_SERVER_URI:http\://localhost\:8888} Added in version 22.6.0.
    eureka.client.enabled=true set eureka.client.enabled=false to switch to standalone Structure Manipulation application mode
    bootstrap.properties
    spring.cloud.config.failFast=true #Removed in version 22.6.0.
    spring.cloud.config.uri=${CONFIG_SERVER_URI:http\://localhost\:8888/} #Removed in version 22.6.0.
    spring.cloud.config.retry.initialInterval=3000 #Removed in version 22.6.0.
    spring.cloud.config.retry.multiplier=1.2 #Removed in version 22.6.0.
    spring.cloud.config.retry.maxInterval=60000 #Removed in version 22.6.0.
    spring.cloud.config.retry.maxAttempts=100 #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-structure:

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

    jws-structure-service start (on Linux)

    or

    run-jws-structure.exe (on Windows)

    run-jws structure (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>/structure-manipulation/API/ localhost:8080/structure-manipulation/API/
    Standalone web application mode <serverhost>:<server-port>/API/ localhost:8063/API/

    Demo site

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

    https://jchem-microservices.chemaxon.com/structure-manipulation/api/index.html

    Usage

    Follow the guidelines, examples on the Demo site or on the Swagger UI API documentation of your installed module.

    Extractor

    This controller makes extraction of textbox content from chemical structures - represented in string - possible.

    Fragmenter

    This controller provides endpoints for cutting chemical structures - represented in string - to their fragments. It can cut:

    • any molecules into components,

    • markush molecules into scaffold and rgroups,

    • markush reaction molecules into components,

    • simple molecules into fragments,

    • reaction molecules into components.

    For input structures plain text chemical file formats are supported.

    The output format can be set as a parameter.

    JSON Converter

    Converts different molecular string representations into JSON format and molecular JSON representations to string.

    Molecule Cleaner

    Methods for 2D and 3D cleaning of chemical structures.

    For input structures plain text chemical file formats are supported.

    The format of the output structure is MRV.

    Different cleaning options can be set for the 2D and 3D cleaning procedures.

    Molecule Standardizer

    Available from version 19.26.0

    Standardizes the input list of molecules according to the specified standardizer actions.

    The guidelines, examples on the Demo site or on the Swagger UI API documentation of your installed module display the methods and syntax implemented for reaching the functionalities of Standardizer Actions product.

    Multistep Reaction Exporter

    Available from version 19.24.0

    Creates a multistep reaction from the input single step reactions.