Implementing Fixers

Creating Fixers for the new Checker

The new Checker has a custom error code, so the stock fixers cannot recognize it. You can use the @FixesExternal annotation to bind a fixer to a result.

Use a ChemAxon Fixer

If you want to use a ChemAxon fixer to fix the problem, the easiest way is to create a subclass of it, and use the @FixesExternal annotation.

Download the example and find "".

name = "Remove duplicated atom maps",
description = "Removes duplicated atom maps.",
actionStringToken = "removeduplicatedmaps")
public class ExternalRemoveAtomMapFixer extends RemoveAtomMapFixer {

Create a new Fixer

To implement a new Fixer, you have to subclass the AbstractStructureFixer class, add the annotations as above, and implement the fix method.

Download the example and find "".

@FixerInfo(name = "Remap reaction",
description = "Remaps the reaction with AutoMapper",
actionStringToken = "remapreaction")
public class RemapReactionFixer extends AbstractStructureFixer {
public boolean fix(StructureCheckerResult result) {
boolean success = false;
// check if we are trying to fix a reaction
if (result.getMolecule().isReaction()) {
// clear the current mapping
try {
// try to get complete mapping
success = true;
} catch (AutoMapperException e) {
// AutoMapper failed
return success;


Export all the classes to a JAR file, and use MarvinSketch Preferences to add the Checker and Fixers from it. Imported Checkers and Fixers will be available in all applications using Structure Checker.