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.jrdf.graph.global.molecule.Molecule

        boolean skip = false;
        int i1 = 0, i2;
        while (i1 < length && length > 1) {
            i2 = i1 + 1;
            while (i2 < length) {
                Molecule m1 = moleculeArray.get(i1);
                Molecule m2 = moleculeArray.get(i2);
                Map<BlankNode, BlankNode> map = mapper.createMap(m1, m2);
                Molecule molecule = localMerger.merge(m1, m2, map);
                //map.clear();
                if (molecule != null) {
                    moleculeArray.remove(m1);
                    moleculeArray.remove(m2);
                    moleculeArray.add(molecule);

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Examples of org.jrdf.graph.global.molecule.Molecule

    // TODO if a sub molecule is to be returned, the isTopLevel field isn't correctly set when creating the molecule.
    // TODO Maybe get the top-level molecule and return the subMolecule?
    private Molecule reconstructMolecule(Molecule parentMolecule, Long pid, Long mid) throws GraphException {
        Triple[] roots = iteratorAsTriples(readableIndex.findTriplesForMid(pid, mid));
        Map<BlankNode, Triple> rootTripleMap = getBNodeToRootMap(parentMolecule);
        Molecule molecule = new MoleculeImpl(moleculeComparator, roots);
        molecule = createSubMolecules(mid, molecule);
        if (null == parentMolecule) {
            return molecule;
        } else {
            Triple linkingTriple = findLinkingTriple(parentMolecule, roots, rootTripleMap, molecule);

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Examples of org.jrdf.graph.global.molecule.Molecule

        ClosableIterator<Long> iterator = readableIndex.findMoleculeIDs(tripleAsLongs);
        try {
            while (iterator.hasNext()) {
                final Long mid = iterator.next();
                if (readableIndex.isSubmoleculeOfParentID(1L, mid)) {
                    Molecule m = handler.createMolecule(1L, mid);
                    if (m != null && moleculeComparator.compare(molecule, m) == 0) {
                        AddMoleculeToIndex amti = new AddMoleculeToIndex(writableIndex, localizer);
                        amti.handleTriple(rootTriple);
                        return molecule.add(rootTriple);
                    }

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Examples of org.jrdf.graph.global.molecule.Molecule

        ClosableIterator<Long> iterator = readableIndex.findMoleculeIDs(tripleAsLongs);
        try {
            while (iterator.hasNext()) {
                Long aLong = iterator.next();
                if (readableIndex.isSubmoleculeOfParentID(1L, aLong)) {
                    Molecule m = handler.createMolecule(1L, aLong);
                    if (m != null && moleculeComparator.compare(molecule, m) == 0) {
                        return removeSubMolecules(molecule, rootTriple, tripleAsLongs, aLong);
                    }
                }
            }

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Examples of org.jrdf.graph.global.molecule.Molecule

        try {
            ClosableIterator<Molecule> iterator = iterator();
            try {
                MoleculeHandler tmpHandler = new MoleculeToText(builder, localizer.getLocalizer());
                while (iterator.hasNext()) {
                    Molecule molecule = iterator.next();
                    traverser.traverse(molecule, tmpHandler);
                }
                return builder.toString();
            } finally {
                iterator.close();

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Examples of org.openscience.cdk.Molecule


    if(mol == null && request.getParameter("element") != null && (request.getParameter("element").length() > 0)) {
      String elemSymbol = request.getParameter("element");
      Atom a = new Atom(elemSymbol);
      a.setPoint2d(new Point2d(0.0, 0.0));
      mol = new Molecule();
      mol.addAtom(a);
      makeStructure = false;
    }
    
    if (mol == null){

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Examples of org.openscience.cdk.Molecule

      } else if("text/plain".equals(type) && "Name did not parse!".equals(new BufferedReader(new InputStreamReader(conn.getInputStream())).readLine())) { 
        // Failure from SimpleOPSINServlet
        return null;
      } else if("chemical/x-mdl-molfile".equals(type)) {
        MDLReader mdlr = new MDLReader(conn.getInputStream());
        IMolecule outputMol = (IMolecule)mdlr.read(new Molecule());
        StructureConverter.configureMolecule(outputMol);
        String smiles = generator.createSMILES(outputMol);
        String inchi = ConverterToInChI.getInChI(outputMol);
        Results results = new Results(smiles, inchi, null);
        return results;

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Examples of org.openscience.cdk.Molecule

      Query q = new TermQuery(new Term("InChI", inchi));
      if(indexSearcher.search(q).length() > 0) return;
    }*/
    IMolecule mol;
    try {
      mol = new Molecule();
      mol = ConverterToInChI.getMolFromInChI(inchi);
      StructureConverter.configureMolecule(mol);
      try {
        HueckelAromaticityDetector.detectAromaticity(mol);        
      } catch (Exception e) {

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Examples of org.openscience.cdk.Molecule

    AllRingsFinder ar = new AllRingsFinder();
    IRingSet ringSet = ar.findAllRings(mol);
    List l = RingPartitioner.partitionRings(ringSet);
    for(Object o : l) {
      IAtomContainer ac = RingPartitioner.convertToAtomContainer((IRingSet)o);
      IMolecule nMol = new Molecule(ac);
      System.out.println(new SmilesGenerator().createSMILES(nMol));
    }
  }

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Examples of org.openscience.cdk.Molecule

      } catch (Exception ee) {
        
      }
    }
    try {
      Molecule blank = new Molecule();
      Molecule2Png m2p = new Molecule2Png();
      m2p.fixedWidthAndHeight = true;
      m2p.height = 300;
      m2p.width = 300;
      m2p.renderMolecule(blank, new File(paperDir, "blank.png").toString());

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