Advanced Structure Checker Button

/*
* Advanced Structure Checker Button
* 
* Runs the structure checker against the currently selected row
* Runs in either <check> or <fix> mode
* Uses XML definition file which can be created with Structure Checker application
* see https://docs.chemaxon.com/display/structurechecker/Creating+a+Configuration+StrCh
* for more checkers see:
* https://docs.chemaxon.com/display/structurechecker/Checker+List
*
* Usage:
* 1. Edit the name of the Structure field
* 2. Set either <check> or <fix> mode
* 3. Provide the xmlConfigFilePath parameter
* 2. Run button script
*
* @author David Pech <dpech@chemaxon.com>
* @author Zsolt Mohacsi <zmohacsi@chemaxon.com>
*/
import com.im.df.api.*
import com.im.df.api.support.SelectionDescription
import com.im.ijc.core.api.util.IJCCoreUtils
import chemaxon.checkers.*
import chemaxon.struc.Molecule
import com.im.df.api.chem.MarvinStructure
import chemaxon.formats.MolImporter
import chemaxon.checkers.FixMode;
import chemaxon.checkers.logger.PropertyCheckerLogger;
import chemaxon.checkers.runner.AdvancedCheckerRunner;
import chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader;
import chemaxon.checkers.runner.configuration.reader.ConfigurationReader;
import chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader;
init = { widget ->
}
destroy = { widget ->
}
evaluate = { widget ->
    def ety = dataTree.rootVertex.entity // assumes you have reference to the data tree
    def edp = ety.schema.dataProvider.getEntityDataProvider(ety)
    def molFld = ety.fields.items.find { it.name == 'Structure' } // find the structure field
    def rs = ety.schema.dataProvider.getDefaultResultSet(dataTree, false, DFEnvironmentRO.DEV_NULL) // find the ResultSet
    def rootVS = rs.getVertexState(dataTree.rootVertex) // obtain the VertexState

    List ids = rootVS.getSelectedRowsIds() // get the selected IDs
    if (ids.size == 1) {
        Map rows = rootVS.getData(ids, DFEnvironmentRO.DEV_NULL) // get the data
        Map row = rows[ids[0]] // get the first and only row
        MarvinStructure mol = row[molFld.id] // Get the Structure. Its a com.im.df.api.chem.MarvinStructure instance
        Molecule cxnMol = mol.getNative() // obtain the chemaxon.struc.Molecule instance

        // parameters for structure checker
        String mode = "fix" // [check|fix] - in fix mode, the structure is rewritten in the database
        String configSource = "xml" // [xml|actionstring]
        String xmlConfigFilePath = "/path/to/checkers.xml" // [<xml config file path>|<action string>]
        // actionString can be used instead of XML configuration
        //String actionString = "" // for example something like "valence->fixvalence"
        // read configuration
        ConfigurationReader checkerConfigurationReader;
        if (configSource.equalsIgnoreCase("xml") && xmlConfigFilePath != null) { // XML configuration
            File configFile = new File(xmlConfigFilePath);
            checkerConfigurationReader = new XMLBasedConfigurationReader(new FileInputStream(configFile));
        } else if (configSource.equalsIgnoreCase("actionstring") && actionString != null) { // action string configuration
            checkerConfigurationReader = new ActionStringBasedConfigurationReader(actionString);
        } else {
            println "Cannot read configuration"
            return;
        }
        // create CheckerRunner
        AdvancedCheckerRunner checkerRunner = new AdvancedCheckerRunner(checkerConfigurationReader);
        // in a non-interactive environment ASK mode has no meaning, so we change it to fix mode
        for (chemaxon.checkers.StructureChecker checker : checkerRunner.getCheckerConfiguration()) {
            if (FixMode.ASK.equals(checker.getDescriptor().getFixMode())) {
                checker.getDescriptor().setFixMode(FixMode.FIX);
            }
        }
        // set error logger
        PropertyCheckerLogger logger = new PropertyCheckerLogger();
        checkerRunner.setLogger(logger);
        // set molecule
        checkerRunner.setMolecule(cxnMol);
        // run the checker+fixer
        if (mode.equalsIgnoreCase("fix")) {
            checkerRunner.fix()
            // rewrite structure in the database with the fixed one
            // in case that fix mode is set
            def dataToUpdate = [(molFld.id):cxnMol.toFormat("sdf")]
            def lock = edp.lockable.withLock('Updating') { envRW ->
                def ud = DFUpdateDescription.create(ety, ids[0], dataToUpdate)
                def submitList = Collections.singletonList(ud)
                edp.update(submitList, DFUndoConfig.OFF, envRW)
            }
        } else {
            checkerRunner.checkAndWait()
        }
        // see report in molecule properties
        println cxnMol.toFormat("sdf")

    } else {
        println "bad selection"
    }
}
on_change = { widget, button ->

}
 
 

For example Structure Checker configuration see checkers.xml

Attached, you can also find a version of this script, where the fix|check mode is selected with a checkbox in a popup. StructureCheckerImproved.groovy