Examples of Molecule

org.jrdf.graph.global.molecule.Molecule
A molecule is a container of a subgraph of RDF triples. It contains a collection of triples that share some common chain of blank nodes. Molecules consist of a set of root triples. These share a blank node - typically the subject but it can be the object as well. For example, _1 p o, s p2 _1 is a simple molecule. The highest in this set of root triples (as defined by some ordering) is the head triple. The typical ordering is most grounded (fewest blank nodes), followed by URIs, Literals and then alphabetical ordering. The chain of blank nodes creates a molecule that contains submolecules. If a triple in the root has a blank node as its object it is a linking triple. This is how the chains to submolecules are created. From one molecule to the next the object and subject nodes are swapped. For example, the linking triple _1 p _2 will link to a triple in a submolecule _2 p o. @author Andrew Newman @version $Id: Molecule.java 2894 2009-01-27 21:25:13Z newmana $
org.openscience.cdk.Molecule
org.wymiwyg.rdf.molecules.Molecule
A set of triples that cannot be decomposed without reducing its meaning. A Molecule is not necessarly a Graph, as the identity may be determined by the id of b-nodes, this is in a model-referencing decomposition @author reto

Examples of org.openscience.cdk.Molecule

      //System.out.println("Use IGF!");
      try {
        lock.lock();
        //getInstance().igf.
        IAtomContainer iac = igf.getInChIToStructure(InChI).getAtomContainer();
        IMolecule mol = new Molecule(iac);
        molCache.put(InChI, mol);


        return mol;
        //return getInstance().igf.getInChIGenerator(mol).getInchi();
      } catch (Exception e) {

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Examples of org.openscience.cdk.Molecule

      //proc.waitFor();
      /* This loop seems to work better under windows than proc.waitFor(), which hangs */
      
      //System.out.println(tmpMolFile.getAbsolutePath());
      
      IMolecule mol = (IMolecule)new MDLReader(new InputStreamReader(new FileInputStream(tmpMolFile), "UTF-8")).read(new Molecule());
      
      //System.out.println(FileTools.readTextFile(tmpMolFile));
      
      tmpMolFile.delete();
      tmpInChIAuxFile.delete();

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Examples of org.openscience.cdk.Molecule

      }
    } 
    if(!done) {
      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) {

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Examples of org.openscience.cdk.Molecule

  }
  
  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);

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Examples of org.openscience.cdk.Molecule

    private static final long serialVersionUID = -4683096180546540588L;
    private IMolecule itsMolecule;
    private TwoDimensionList<Double> itsDistanceMatrix;


    public DistanceMatrix() {
        this.setMolecule(new Molecule());
        this.setDistanceMatrix(new TwoDimensionList<Double>());
    }

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Examples of org.openscience.cdk.Molecule


    private IMolecule itsMolecule;
    private TwoDimensionList<Integer> itsDistanceMatrix;


    public TopologicalDistanceMatrix() {
        this.setMolecule(new Molecule());
        this.setDistanceMatrix(new TwoDimensionList<Integer>());
    }

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Examples of org.openscience.cdk.Molecule


        return theMoleculeSet;
    }


    private IMolecule __getChemicalShiftAndMpeoeAndCdeapBySDFormat(Nmr1dUnit thePeak, int theMoleculeIndex) {
        IMolecule theMolecule = new Molecule();
        int theAnnotatedAtomNumber = thePeak.getAnnotatedAtomNumber();


        theMolecule.setProperty(this.CHEMICAL_SHIFT_COLUMN_NAME_IN_RESULT_FILE, thePeak.getChemicalShift());
        theMolecule.setProperty(this.MPEOE_COLUMN_NAME_IN_RESULT_FILE, this.getMPEOEListByMolecules().get(theMoleculeIndex).get(theAnnotatedAtomNumber));
        theMolecule.setProperty(this.CDEAP_COLUMN_NAME_IN_RESULT_FILE, this.getCDEAPListByMolecules().get(theMoleculeIndex).get(theAnnotatedAtomNumber));


        return theMolecule;
    }

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Examples of org.openscience.cdk.Molecule


        return theMoleculeSet;
    }


    private IMolecule __getHoseCodeDescriptorBySDFormat(Nmr1dUnit thePeak, int theHoseCodeLevel, int theMoleculeIndex) {
        IMolecule theMolecule = new Molecule();
        int theAnnotatedAtomNumber = thePeak.getAnnotatedAtomNumber();


        if (this.getMPEOEListByMolecules().get(theMoleculeIndex).get(theAnnotatedAtomNumber) != this.NOT_CONTAIN_PROPERTY_VALUE
                && !this.getSFEList().get(theMoleculeIndex).equals(this.INCORRECT_VALUE)) {
            HoseCodeDescriptor theHoseCodeDescriptor = new HoseCodeDescriptor(this.getMoleculeSet().getMolecule(theMoleculeIndex), theHoseCodeLevel);


            theMolecule.setProperty(this.CHEMICAL_SHIFT_COLUMN_NAME_IN_RESULT_FILE, thePeak.getChemicalShift());
            theMolecule.setProperty(this.MPEOE_COLUMN_NAME_IN_RESULT_FILE, this.getMPEOEListByMolecules().get(theMoleculeIndex).get(theAnnotatedAtomNumber));
            theMolecule.setProperty(this.CDEAP_COLUMN_NAME_IN_RESULT_FILE, this.getCDEAPListByMolecules().get(theMoleculeIndex).get(theAnnotatedAtomNumber));
            theMolecule.setProperty(this.SFE_COULUMN_NAME_IN_RESULT_FILE, this.getSFEList().get(theMoleculeIndex));
            theMolecule.setProperties(this.__getHoseCodeDescriptorBySDFormat(this.getMoleculeSet().getMolecule(theMoleculeIndex), theAnnotatedAtomNumber, theHoseCodeLevel));
        }


        return theMolecule;
    }

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Examples of org.openscience.cdk.Molecule

        return theMolecule;
    }


    private Map<Object, Object> __getHoseCodeDescriptorBySDFormat(IMolecule theMolecule, int theAnnotatedAtomNumber, int theHoseCodeLevel) {
        HoseCodeDescriptor theHoseCodeDescriptor = new HoseCodeDescriptor(theMolecule, theHoseCodeLevel);
        IMolecule theDataMolecule = new Molecule();


        for (int pi = 0, pEnd = theHoseCodeDescriptor.getHoseCodeNameList().size(); pi < pEnd; pi++) {
            theDataMolecule.setProperty(theHoseCodeDescriptor.getHoseCodeNameList().get(pi), theHoseCodeDescriptor.getHoseCodeValue2dList().get(theAnnotatedAtomNumber).get(pi));
        }


        return theDataMolecule.getProperties();
    }

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Examples of org.openscience.cdk.Molecule

    private final int NITROGEN_SYMBOL_INDEX = 14;
    private final int PHOSPHATE_SYMBOL_INDEX = 15;
    private final int SULFUR_SYMBOL_INDEX = 16;


    public HoseCodeDescriptor() {
        this.setMolecule(new Molecule());
        this.setHoseCodeNameList(new ArrayList<String>());
        this.setHoseCodeValue2dList(new TwoDimensionList<Integer>());
        this.setHoseCodeLevel(-1);
    }

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