예제 #1
0
  private synchronized double calRelation(IReaction reaction, IMappingAlgorithm theory) {
    try {
      Map<Integer, IAtomContainer> educts =
          synchronizedSortedMap(new TreeMap<Integer, IAtomContainer>());
      for (int i = 0; i < reaction.getReactantCount(); i++) {
        educts.put(i, reaction.getReactants().getAtomContainer(i));
      }

      Map<Integer, IAtomContainer> products =
          synchronizedSortedMap(new TreeMap<Integer, IAtomContainer>());
      for (int i = 0; i < reaction.getProductCount(); i++) {
        products.put(i, reaction.getProducts().getAtomContainer(i));
      }

      GameTheoryMatrix EDSH = new GameTheoryMatrix(theory, reaction, removeHydrogen);

      IGameTheory gameTheory = make(theory, reaction, removeHydrogen, educts, products, EDSH);

      this.reactionBlastMolMapping = gameTheory.getReactionMolMapping();
      EDSH.Clear();

      return gameTheory.getDelta();
    } catch (Exception e) {
      logger.error(e);
      return -1;
    }
  }
예제 #2
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  @Test
  public void testReaction() throws Exception {
    String cmlString =
        "<reaction>"
            + "<reactantList><reactant><molecule id='react'/></reactant></reactantList>"
            + "<productList><product><molecule id='product'/></product></productList>"
            + "<substanceList><substance><molecule id='water'/></substance></substanceList>"
            + "</reaction>";

    IChemFile chemFile = parseCMLString(cmlString);
    IReaction reaction = checkForSingleReactionFile(chemFile);

    Assert.assertEquals(1, reaction.getReactantCount());
    Assert.assertEquals(1, reaction.getProductCount());
    Assert.assertEquals(1, reaction.getAgents().getMoleculeCount());
    Assert.assertEquals("react", reaction.getReactants().getMolecule(0).getID());
    Assert.assertEquals("product", reaction.getProducts().getMolecule(0).getID());
    Assert.assertEquals("water", reaction.getAgents().getMolecule(0).getID());
  }
예제 #3
0
  /**
   * Depict a reaction.
   *
   * @param rxn reaction instance
   * @return depiction
   * @throws CDKException a depiction could not be generated
   */
  public Depiction depict(IReaction rxn) throws CDKException {

    ensure2dLayout(rxn); // can reorder components!

    final Color fgcol =
        getParameterValue(StandardGenerator.AtomColor.class)
            .getAtomColor(rxn.getBuilder().newInstance(IAtom.class, "C"));

    final List<IAtomContainer> reactants = toList(rxn.getReactants());
    final List<IAtomContainer> products = toList(rxn.getProducts());
    final List<IAtomContainer> agents = toList(rxn.getAgents());

    // set ids for tagging elements
    int molId = 0;
    for (IAtomContainer mol : reactants) {
      setIfMissing(mol, MarkedElement.ID_KEY, "mol" + ++molId);
      setIfMissing(mol, MarkedElement.CLASS_KEY, "reactant");
    }
    for (IAtomContainer mol : products) {
      setIfMissing(mol, MarkedElement.ID_KEY, "mol" + ++molId);
      setIfMissing(mol, MarkedElement.CLASS_KEY, "product");
    }
    for (IAtomContainer mol : agents) {
      setIfMissing(mol, MarkedElement.ID_KEY, "mol" + ++molId);
      setIfMissing(mol, MarkedElement.CLASS_KEY, "agent");
    }

    final Map<IChemObject, Color> myHighlight = new HashMap<>();
    if (highlightAtomMap) {
      myHighlight.putAll(makeHighlightAtomMap(reactants, products));
    }
    // user highlight buffer pushes out the atom-map highlight if provided
    myHighlight.putAll(highlight);
    highlight.clear();

    final List<Double> reactantScales = prepareCoords(reactants);
    final List<Double> productScales = prepareCoords(products);
    final List<Double> agentScales = prepareCoords(agents);

    // highlight parts
    for (Map.Entry<IChemObject, Color> e : myHighlight.entrySet())
      e.getKey().setProperty(StandardGenerator.HIGHLIGHT_COLOR, e.getValue());

    // setup the model scale based on bond length
    final double scale = this.caclModelScale(rxn);
    final DepictionGenerator copy = this.withParam(BasicSceneGenerator.Scale.class, scale);
    final RendererModel model = copy.getModel();

    // reactant/product/agent element generation, we number the reactants, then products then agents
    List<Bounds> reactantBounds = copy.generate(reactants, model, 1);
    List<Bounds> productBounds =
        copy.generate(toList(rxn.getProducts()), model, rxn.getReactantCount());
    List<Bounds> agentBounds =
        copy.generate(
            toList(rxn.getAgents()), model, rxn.getReactantCount() + rxn.getProductCount());

    // remove current highlight buffer
    for (IChemObject obj : myHighlight.keySet())
      obj.removeProperty(StandardGenerator.HIGHLIGHT_COLOR);

    // generate a 'plus' element
    Bounds plus = copy.generatePlusSymbol(scale, fgcol);

    // reset the coordinates to how they were before we invoked depict
    resetCoords(reactants, reactantScales);
    resetCoords(products, productScales);
    resetCoords(agents, agentScales);

    final Bounds emptyBounds = new Bounds();
    final Bounds title =
        copy.getParameterValue(BasicSceneGenerator.ShowReactionTitle.class)
            ? copy.generateTitle(rxn, scale)
            : emptyBounds;
    final List<Bounds> reactantTitles = new ArrayList<>();
    final List<Bounds> productTitles = new ArrayList<>();
    if (copy.getParameterValue(BasicSceneGenerator.ShowMoleculeTitle.class)) {
      for (IAtomContainer reactant : reactants)
        reactantTitles.add(copy.generateTitle(reactant, scale));
      for (IAtomContainer product : products) productTitles.add(copy.generateTitle(product, scale));
    }

    final Bounds conditions =
        generateReactionConditions(rxn, fgcol, model.get(BasicSceneGenerator.Scale.class));

    return new ReactionDepiction(
        model,
        reactantBounds,
        productBounds,
        agentBounds,
        plus,
        rxn.getDirection(),
        dimensions,
        reactantTitles,
        productTitles,
        title,
        conditions,
        fgcol);
  }