Hi
Is there a way to detect implausibility of molecules in general but in
particular about valence errors:
E.g. the SMILES string "[CH4]=O" can of course be parsed to a formally correct
molecule, but it obviously has a valence error on the C atom.
First, I thought the org.openscience.cdk.validate.ValidatorEngine is the
instrument of choice, but either I'm using it wrongly or it is not in the least
concerned about such a molecule.
But after all, for "[O-3]" it works as expected, I'm getting a Warning "Atom O
has charge -3" from the BasicValidator.
I'm running this kind of code:
import org.openscience.cdk.exception.InvalidSmilesException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.validate.BasicValidator;
import org.openscience.cdk.validate.ValidationReport;
import org.openscience.cdk.validate.ValidationTest;
import org.openscience.cdk.validate.ValidatorEngine;
public class Snippet {
private static boolean validate(IAtomContainer molecule) {
ValidatorEngine validatorEngine = new ValidatorEngine();
validatorEngine.addValidator(new BasicValidator());
ValidationReport report = validatorEngine.validateMolecule(molecule);
for (ValidationTest error : report.getErrors()){
System.err.println(error.getDetails());
}
for (ValidationTest cdkerror : report.getCDKErrors()){
System.err.println(cdkerror.getDetails());
}
for (ValidationTest warning : report.getWarnings()){
System.err.println(warning.getDetails());
}
return report.getCount() == report.getOKCount();
}
public static void main(String[] args) throws InvalidSmilesException {
SmilesParser sp = new
SmilesParser(SilentChemObjectBuilder.getInstance());
System.out.println("[O-3] is valid:
"+validate(sp.parseSmiles("[O-3]")));
System.out.println("[CH4]=O is valid:
"+validate(sp.parseSmiles("[CH4]=O")));
}
}
and I'm getting this kind of output:
Atom O has charge -3
[O-3] is valid: false
[CH4]=O is valid: true
Can you give me guidance?
Many thanks and greetings,
Emanuel
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