Toxtree 2.5.1 is the latest stable release. The latest development version is ToxTree 2.5.8 (Maven repository).

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The list of supported file formats can be found in the user manual. A brief list of the most common formats follows:

• filename.SDF is Structure Data Format
• filename.CSV is comma delimited text file,with mandatory header row. A column,containing SMILES, should have title "SMILES". The number,titles and order of the columns are arbitrary. Example

NAME,CAS,SMILES
Acetic acid,64-19-7,CC(O)=O
Acetoin,513-86-0,CC(O)C(C)=O
    

• filename.TXT is tab delimited text file. A column,containing SMILES, should have title "SMILES". The number,titles and order of the columns are arbitrary.

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Chemical identifiers are resolved via remote server (if enabled). The remote query may fail to retrieve an identifier for the following reasons:

• The identifier is not found at the server.
• Your computer is behind a firewall, blocking port 8080, and preventing the remote query.

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The amount of daily intake (in microgram/day) can be specified as an additional column / SDfile field, with the name "DailyIntake". The following files are example of the proper formatting (the values are for illustration only):

• Input .CSV file example
• Input .SDF file example
• Output .CSV file
• Output .SDF file

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• Java standalone example Toxtree and CDK dependencies are available via Maven repository. Examples how to use Apache Maven for Java project management here. More Toxtree examples coming soon.

import java.io.FileOutputStream;
import java.io.InputStream;
import java.io.OutputStream;

import org.junit.Test;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.io.iterator.IteratingMDLReader;
import org.openscience.cdk.silent.SilentChemObjectBuilder;

import toxTree.core.IDecisionResult;
import toxTree.tree.cramer.CramerRules;



public class ToxTreeAppTest {

        public static void main(String[] args) {
                CramerRules rules = new CramerRules();
                IDecisionResult result = rules.createDecisionResult();
                result.setDecisionMethod(rules);
                InputStream in = new FileInputStream("myfile.sdf");
                IteratingMDLReader reader =
                         new IteratingMDLReader(in,SilentChemObjectBuilder.getInstance());
                OutputStream out = new FileOutputStream("result.sdf");
                MDLWriter writer = new MDLWriter(out);
                while (reader.hasNext()) {
                        IAtomContainer molecule = ((IAtomContainer)reader.next());
                        result.classify(molecule);
                        result.assignResult(molecule);
                        //Just print the result
                        for (String resultProperty : result.getResultPropertyNames())
                                System.out.println(String.format("%s=%s",
                                resultProperty,molecule.getProperty(resultProperty)));
                        //save all properties (both read from the input file and calculated)
                        writer.setSdFields(molecule.getProperties());
                        writer.write(molecule);
                }
                out.close();
                reader.close();
        }
}

• OpenTox API web services.
  
  Toxtree modules are avalable as OpenTox REST API web services. The example assumes your dataset is uploaded to an OpenTox dataset service.

  curl -X POST -d "dataset_uri=http://apps.ideaconsult.net:8080/ambit2/dataset/{yourdataset}" \
                  http://apps.ideaconsult.net:8080/ambit2/model/2 
  

  The dataset service accepts common chemical data formats for upload via HTTP POST calls. More OpenTox API examples.

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