custom-checker-fixer

How to write custom Structure Checker / Structure Fixer for JChem Microservices

This repository contains an example project, on how to create your own Structure Checkers and Structure Fixers. In the end, you can build the application and use the jar in JChem Microservices.

How to build the project

First of all, you have to obtain your access keys as described in the gradle-panel here. You can write these information to the gradle.properties file.

Execute the build with: ./gradlew build command (it requires that you have the appropriate license).

The built jar can be found in build/libs folder.

How to use the built jar in JChem Microservices

Copy the jar file to the extra-libs folder in your JChem Microservices installation.

Send a request with content:

{
  "checkerSettings": [
    {
      "checkerClass": "com.chemaxon.exampe.jms.ccf.MyCustomChecker",
      "displayName": "ExampleChecker"
    }
  ],
  "filter": {
    "untriggered": false
  },
  "structure": {
    "source": "C1C=CC=CC=1CC(N)CCl"
  }
}

to jws-checker-fixer/rest-v1/checker/ endpoint.

What you should expect

Our dummy checker checks for atoms with higher atom number than Oxygen. In the input we have a Chlorine atom, that should be found by the checker

How to use our fixer with our checker

Send the following example input to the /rest-v1/checker-fixer/ endpoint.

Example input:

{
  "exportFormat": "smiles",
  "filter": {
    "fixed": false,
    "untriggered": false
  },
  "settings": [
    {
      "checkerSettings": {
        "checkerClass": "com.chemaxon.exampe.jms.ccf.MyCustomChecker",
        "displayName": "ExampleChecker"
      },
      "fixerSettings": {
        "displayName": "ExampleFixer",
        "exportFormat": "smiles",
        "fixerClass": "com.chemaxon.exampe.jms.ccf.MyCustomFixer"
      }
    }
  ],
  "structure": {
    "source": "C1C=CC=CC=1CC(N)CCl"
  }
}

What you should expect

Our dummy fixer replaces all atoms found by the checker with Oxygen. In the final result molecule you should not see any Chlorine atoms, but Oxygens in their places.