Structure Manipulation

    {info} Structure Manipulation Web Services provide methods for the next manipulations on chemical structures:

    • extracting textbox content from the structures,
    • cutting structures into their fragment structures,
    • two-dimensional and three-dimensional cleaning of chemical structures,
    • converting to JSON format
    • standardizing structures
    • exporting multistep reactions

    Structure Manipulation Web Services make possible to reach the functionality provided by ChemAxon's toolkit Standardizer.

    Structure Manipulation Web Services application is available in two modes:

    1. As part of a microservices system

    2. As standalone web application

    Microservices system mode

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

    The default configuration applies to the microservices system mode.

    The web application runs on host and listens on port .

    Standalone web application mode

    In standalone web application mode the Structure Manipulation Web Service runs alone, without the Config service, Discovery service and Gateway service (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 application.properties file, and

    spring.cloud.config.failFast=false and spring.cloud.config.enabled=false in bootstrap.properties file.

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

    The web application runs on host and listens on port .

    Download

    See here.

    Software 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
    eureka.client.enabled=true set eureka.client.enabled=false to switch to standalone Structure Manipulation application mode
    bootstrap.properties
    spring.cloud.config.failFast=true
    spring.cloud.config.uri=${CONFIG_SERVER_URI:http\://localhost\:8888/}
    spring.cloud.config.retry.initialInterval=3000
    spring.cloud.config.retry.multiplier=1.2
    spring.cloud.config.retry.maxInterval=60000
    spring.cloud.config.retry.maxAttempts=100

    For more settings possibilities see 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 start (on Windows)

    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.

    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.