Converting an imported molecule to smiles

Hello

I am working on trying to import an SD file and iterate through the molecules/contents contained.  As I iterate I would like to convert each molecule to smiles so I can check against a database for duplicates.  I have the following code so far:

 

      while (recordCount > -1){

            File file = new File(sdfFilePath);

            FileInputStream inputStream = new FileInputStream(file)

            MolImporter moleculeImporter = new MolImporter(inputStream, "sdf:MULTISET,Usg")

            moleculeImporter.seekRecord(recordCount, null)

            Molecule molecule = moleculeImporter.read()

   String mySMILES

            try {

               mySMILES = MolExporter.exportToFormat(molecule, "smiles");

                } catch (IOException e){

                println(e)

                }

            println(mySMILES)

            recordCount--

        }

 

However I am getting a ClassNotFoundException (Message: chemaxon.util.concurrent.ConcurrentProcessor) at the following line

   mySMILES = MolExporter.exportToFormat(molecule, "smiles");

Which I do not understand as I have imported the MolExporter class, does the code above look ok otherwise?  Are there multiple MolExporter classes in the Chemaxon libs?  I was going off of this API doc 

Thank you for any help

Dennis

Ok I figured out what was going on, I did not have the MarvinBeans-formats-smiles.jar or MarvinBeans-smarts.jar in my lib folder. 

At this point I changed the code a bit and I am a bit stuck on how I can then get access to the smiles string?

 

  MolImporter importer = new MolImporter(inputStream);

        Molecule mol;

        while ((mol = importer.read()) != null) {

            MolHandler molHandler = new MolHandler(mol)

            molHandler.clean(true, null)

            molHandler.toFormat("smiles")

            Molecule smiles = molHandler.getMolecule()

            ....

}

Thank you for any help you can provide,

Dennis

Got everything working with the following (probably no need to have the molHandler function).

  MolImporter importer = new MolImporter(inputStream);

        Molecule mol;

        while ((mol = importer.read()) != null) {

            // do something with the molecule

            println(mol)

            MolHandler molHandler = new MolHandler(mol)

            molHandler.clean(true, null)

            molHandler.toFormat("smiles")

            Molecule smiles = molHandler.getMolecule()

            println(MolExporter.exportToFormat(mol, "smiles"));

        }

 

Here is my question....what libraries do I need for this?  It seems a bit overkill to add ALL Marvin libraries to a project (which is what I did to resolve the issue).

Thanks

 

dennis

Hello Dennis,

You are right,  the MolHandler is not needed in this case.

Necessary libraries: 
com.chemaxon-io.jar
com.chemaxon-core.jar
com.chemaxon-license.jar
com.chemaxon-common.jar
com.chemaxon-concurrent.jar
com.chemaxon-io-mdl.jar
com.chemaxon-io-smiles.jar

Regards,
Mate 

Thank you for the reply. Concurrent.jar!  That is what was throwing me, I thought that was a regular java issue! 

Dennis