Hi John
Thanks a lot for the suggestion. This approach indeed looks very promising to
me!
Instead of the ValidatorEngine, the following method let me reliably detect
faulty molecules in both cases:
private static boolean validate(IAtomContainer molecule) throws
CDKException {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
for (int i=0; i < molecule.getAtomCount(); i++) {
if (null == molecule.getAtom(i).getValency()) {
System.err.println("Valence Error on "+molecule.getAtom(i));
return false;
}
}
return true;
}
public static void main(String[] args) throws CDKException {
SmilesParser sp = new
SmilesParser(SilentChemObjectBuilder.getInstance());
System.out.println("[O-2] is valid:
"+validate(sp.parseSmiles("[O-2]")));
System.out.println("[O-3] is valid:
"+validate(sp.parseSmiles("[O-3]")));
System.out.println("[CH2]=O is valid:
"+validate(sp.parseSmiles("[CH2]=O")));
System.out.println("[CH3]=O is valid:
"+validate(sp.parseSmiles("[CH3]=O")));
}
Just what I wanted!
Many thanks and greetings,
Emanuel
From: John M [mailto:john.wilkinson...@gmail.com]
Sent: Monday, September 21, 2015 8:25 PM
To: cdkuser
Subject: Re: [Cdk-user] Molecule Validation
Hi,
One approach would be to try and assign atom types and check for null.. or it
might even throw an exception.
AtomContainerManipulator.perceiveAndConfigureAtomTypes(mol); // or something
similar
The atom types are finite opposed to empirical rules so might be too strict
depending on your use case.
Regards,
John W May
john.wilkinson...@gmail.com<mailto:john.wilkinson...@gmail.com>
On 21 September 2015 at 10:20, Schmid Emanuel (ID SIS)
<emanuel.sch...@id.ethz.ch<mailto:emanuel.sch...@id.ethz.ch>> wrote:
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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