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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.

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 <server-host> and listens on port <gateway-server-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 file and in file.

All configuration must be done in the Structure-Manipulation 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-structure


See here.


See here.


Default configuration:



set eureka.client.enabled=false to switch to standalone Structure Manipulation application mode${CONFIG_SERVER_URI:http\://localhost\:8888/}

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)


run-jws-structure.exe (on Windows)

run-jws-structure (on Linux)

API documentation

Find and try out the API on the Swagger UI.

ModeURL of Swagger UIDefault 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:


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


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


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

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.