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 <[email protected]>
* @author Zsolt Mohacsi <[email protected]>
*/
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