Custom Structure Checker and Fixer in JPC

Create custom structure checker

Based on the documentation available here, you can create a custom structure checker action in Java programming language. As a result of your development, you need to get a jar file which contains the necessary action. The created jar file must be referenced in externalcheckersfixers.xml configuration file which is stored where it is defined in the jchem-psql configuration file.

Artifacts

• jar file containing your custom standardizer action

• externalcheckersfixers.xml containing custom structure checker action factory configuration
  

Where to place the artifacts

• Edit /etc/default/jchem-psql file

  Add the next line (example only) - defining the place of the externalcheckersfixers.xml - to the list of the JCHEM_PSQL_OPTS - in the jchem-psql file:

  -Dchemaxon.structurechecker.factory.ExternalCheckerFixerConfiguration=/<dir>/externalcheckersfixers.xml`
  

  
  Take care, use the absolute path of the xml file in the field.

• Move the externalcheckersfixers.xml file in the above defined place and make it readable.

  The absolute path of the above generated jar file is defined in the externalcheckersfixers.xml.

  Example:

  <?xml version="1.0" encoding="UTF-8"?>
  <configuration>
   <checker-list>
     <checker class="com.checkers.MyChecker" editor-class="" id="MyChecker" jar="file:///home/somebody/custom-checkers.jar"/>
   </checker-list>
   <fixer-list>
     <fixer class="com.checkers.MyFixer" id="MyFixer" jar="file:///home/somebody/custom-checkers.jar"/>
   </fixer-list>
  </configuration>
  

Move the jar file in the above defined place and make it readable.

Use the custom structure checker from cartridge

• Stop Cartridge service.

  sudo service jchem-psql stop

• Start Cartridge service

  sudo service jchem-psql start

The cartridge is ready for use the custom structure checker and fixer:

SELECT chemterm('check(''action_string’')','molecule');

The action string of the custom checker/fixer is defined at Java code level.

In place of the action string, the checker configuration xml (not the externalcheckersfixers.xml) can also be used. See examples in Chemical Terms/Structure checkers documentation page.

SELECT chemterm('check(''mycheckerAction'')','[Na+].CC([O-])=O');

SELECT chemterm('fix(''mycheckerAction->myfixerAction'')','[Na+].CC([O-])=O');