Structure Checker Developer's Guide - Implementing fixers tutorial

Contents

• Use a ChemAxon Fixer
• Create a new Fixer
• Implement the new fixer
• Integrate the new fixer

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 "ExternalRemoveAtomMapFixer.java".

    @FixesExternal(DuplicateAtomMapChecker.DUPLICATE_ATOM_MAP_CHECKER_ERROR)
    @FixerInfo(
        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 "RemapReactionFixer.java".

    @FixesExternal(DuplicateAtomMapChecker.DUPLICATE_ATOM_MAP_CHECKER_ERROR)
    @FixerInfo(name = "Remap reaction",
            description = "Remaps the reaction with AutoMapper",
            actionStringToken = "remapreaction")
    public class RemapReactionFixer extends AbstractStructureFixer {

        @Override
        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
                AutoMapper.clearMaps(RxnMolecule.getReaction(result.getMolecule()));
                try {
                    // try to get complete mapping
                    AutoMapper.map(
                            RxnMolecule.getReaction(result.getMolecule()),
                            AutoMapper.COMPLETE);
                    success = true;
                } catch (AutoMapperException e) {
                    // AutoMapper failed
                }
            }
            return success;
        }
    }

Integration

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.

Links

Structure Checker Developer's Guide
List of available checkers
Structure Checker GUI
structurecheck Command Line Application
Structure Checker in MarvinSketch