Examples of HydrogenAdder

Examples of org.openscience.cdk.tools.HydrogenAdder

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      mol = ConverterToInChI.getMolFromInChI(inchi);
      if(mol != null) {
        mol = new Molecule(mol);
        try {
          StructureConverter.configureMolecule(mol);
          new HydrogenAdder(new ValencyHybridChecker()).addExplicitHydrogensToSatisfyValency(mol);
          StructureConverter.addHydrogensForSilicon(mol);
        } catch (Exception e) {
          throw new Error(e);
        }
        HydrogenRemover.removeInsignificantHydrogens(mol);
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Examples of org.openscience.cdk.tools.HydrogenAdder

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  private void prepareMolecule() throws Exception {
    ConverterToInChI.clearInChIFromCache(targetInChI);
    mol = ConverterToInChI.getMolFromInChI(targetInChI);
    mol = new Molecule(mol);
   
    new HydrogenAdder().addExplicitHydrogensToSatisfyValency(mol);
    StructureConverter.addHydrogensForSilicon(mol);

    //System.out.println(mol);
    StructureConverter.configureMoleculeIsotopes(mol);
    HydrogenRemover.removeInsignificantHydrogens(mol, false);
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Examples of org.openscience.cdk.tools.HydrogenAdder

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  public ChEBIGenerics() {
    try {
      cache = new HashMap<String,List<String>>();
      sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
      ha = new HydrogenAdder(new ValencyHybridChecker());
      OBOOntology o = OBOOntology.getInstance();
     
      qacs = new HashMap<String, QueryAtomContainer>();
      qsmiles = new HashMap<String, String>();
      qid = new HashMap<String, String>();
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Examples of org.openscience.cdk.tools.HydrogenAdder

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    return myInstance;
  }
 
  private StructureConverter() throws Exception {
    checker = new ValencyHybridChecker();
    hydrogenAdder = new HydrogenAdder(checker);   
  }
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