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
On 21 September 2015 at 10:20, Schmid Emanuel (ID SIS) <
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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>
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>
>
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