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Structure Manipulation

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

  • 1
    extracting textbox content from the structures,

  • 1
    cutting structures into their fragment structures,

  • 1
    two-dimensional and three-dimensional cleaning of chemical structures,

  • 1
    converting to JSON format

  • 1
    standardizing structures

  • 1
    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



up to version 22.2.0

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



from version 22.9.0

set spring.cloud.config.enabled=false and comment out line spring.config.import= in application.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
spring.config.import=configserver:${CONFIG_SERVER_URI:http://localhost:8888}?fail-fast=true&max-attempts=100&max-interval=60000&multiplier=1.2&initial-interval=3000 Added in version 22.6.0.
eureka.client.enabled=true set eureka.client.enabled=false to switch to standalone Structure Manipulation application mode
bootstrap.properties
spring.cloud.config.failFast=true #Removed in version 22.6.0.
spring.cloud.config.uri=${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 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.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.

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.