Example #1
0
  public static TemplateReaction makeTemplateReaction(
      Structure p_structureSp,
      Kinetics[] p_kinetics,
      ReactionTemplate p_template,
      Structure p_structure) {
    double PT = System.currentTimeMillis();
    // Look for pre-existing reaction in Template's reactionDictionaryByStructure.
    TemplateReaction reaction = p_template.getReactionFromStructure(p_structureSp);
    Global.getReacFromStruc =
        Global.getReacFromStruc + (System.currentTimeMillis() - PT) / 1000 / 60;

    if (reaction == null) {
      // Create a new reaction.
      reaction = new TemplateReaction(p_structureSp, p_kinetics, p_template);
      if (reaction.isBackward()) {
        Logger.info(
            "Created new reverse " + p_template.getName() + " reaction: " + reaction.toString());
        TemplateReaction reverse =
            reaction.generateReverseForBackwardReaction(p_structure, p_structureSp);
        if (reverse == null) return null;
        reaction.setReverseReaction(reverse);
      } else {
        Logger.info(
            "Created new forwards " + p_template.getName() + " reaction: " + reaction.toString());
        ReactionTemplate fRT = reaction.getReactionTemplate();
        ReactionTemplate rRT = null;
        if (fRT.isNeutral()) rRT = fRT;
        else rRT = fRT.getReverseReactionTemplate();
        if (rRT != null) {
          TemplateReaction reverse =
              new TemplateReaction(p_structureSp.generateReverseStructure(), p_kinetics, rRT);
          reaction.setReverseReaction(reverse);
          reverse.setReverseReaction(reaction);
          rRT.addReaction(reverse);
        }
      }
      if (!reaction.repOk()) {
        throw new InvalidTemplateReactionException();
      }

      p_template.addReaction(reaction);
    }
    Global.makeTR += (System.currentTimeMillis() - PT) / 1000 / 60;

    if (!reaction.repOk()) {
      throw new InvalidTemplateReactionException();
    }
    return reaction;
  }
Example #2
0
  // ## operation generateReverseForBackwardReaction()
  private TemplateReaction generateReverseForBackwardReaction(Structure fs, Structure fsSp) {
    // #[ operation generateReverseForBackwardReaction()
    // we need to only generate reverse reaction for backward reaction, so that we wont be stuck
    // into a self loop.
    if (!this.isBackward()) {
      return null;
    }
    ReactionTemplate fRT = getReactionTemplate();
    ReactionTemplate rRT = null;

    if (fRT.isForward()) {
      return null;
    } else if (fRT.isNeutral()) {
      rRT = fRT;
    } else if (fRT.isBackward()) {
      rRT = fRT.getReverseReactionTemplate();
    } else {
      throw new InvalidReactionTemplateDirectionException(); // Structure fs = getStructure();
    }
    LinkedList freactant = fs.getReactantList();
    LinkedList fproduct = fs.getProductList();
    Structure rs = new Structure(fproduct, freactant, -1 * this.getDirection());
    Structure rsSp = new Structure(fsSp.products, fsSp.reactants, -1 * this.getDirection());
    // If it's in the reverse ReactionTemplate.reactionDictionaryByStructure then just return that
    // one.
    TemplateReaction rr = rRT.getReactionFromStructure(rsSp);
    if (rr != null) {
      rr.setReverseReaction(this);
      return rr;
    }
    int rNum = fproduct.size();

    Kinetics[] k = rRT.findReverseRateConstant(rs);

    // If that didnt work, what to do....

    if (k == null && rRT.name.equals("R_Recombination")) {
      ChemGraph cg = ((ChemGraph) fproduct.get(0));
      Graph g = cg.getGraph();
      Node n = (Node) g.getCentralNodeAt(2);
      if (n == null) {
        cg = ((ChemGraph) fproduct.get(1));
        g = cg.getGraph();
        n = (Node) g.getCentralNodeAt(2);
      }
      g.clearCentralNode();
      g.setCentralNode(1, n);
      k = rRT.findRateConstant(rs);
    } else if (k == null && rRT.name.equals("H_Abstraction")) {
      ChemGraph cg1 = ((ChemGraph) fproduct.get(0));
      Graph g1 = cg1.getGraph();
      Node n3 = (Node) g1.getCentralNodeAt(3);
      if (n3 == null) {
        cg1 = ((ChemGraph) fproduct.get(1));
        g1 = cg1.getGraph();
        n3 = (Node) g1.getCentralNodeAt(3);
        Node n2 = (Node) g1.getCentralNodeAt(2);
        g1.clearCentralNode();
        g1.setCentralNode(1, n3);
        g1.setCentralNode(2, n2);
        ChemGraph cg2 = ((ChemGraph) fproduct.get(0));
        Graph g2 = cg2.getGraph();
        Node n1 = (Node) g2.getCentralNodeAt(1);
        g2.clearCentralNode();
        g2.setCentralNode(3, n1);
      } else {
        Node n2 = (Node) g1.getCentralNodeAt(2);
        g1.clearCentralNode();
        g1.setCentralNode(1, n3);
        g1.setCentralNode(2, n2);
        ChemGraph cg2 = ((ChemGraph) fproduct.get(1));
        Graph g2 = cg2.getGraph();
        Node n1 = (Node) g2.getCentralNodeAt(1);
        g2.clearCentralNode();
        g2.setCentralNode(3, n1);
      }
      k = rRT.findRateConstant(rs);
    }
    /*
     * Added by MRH on 27-Aug-2009 This hard-coding is necessary for rxn family templates that are labeled
     * "thermo_consistence". After the chemgraphs are mutated, the central nodes for the products are not correct
     * (see example below). These hard-coded portions are necessary for RMG to find Kinetics for the structure.
     * Example: CH4 + H CH4 1 *1 C 0 {2,S} {3,S} {4,S} {5,S} 2 *2 H 0 {1,S} 3 H 0 {1,S} 4 H 0 {1,S} 5 H 0 {1,S} H 1
     * *3 H 1 After RMG has "reactChemGraph" and "mutate" the chemgraphs of the reactants, the products would look
     * as such: prod1 1 *1 C 1 {2,S} {3,S} {4,S} 2 H 0 {1,S} 3 H 0 {1,S} 4 H 0 {1,S} prod2 1 *3 H 0 {2,S} 2 *2 H 0
     * {1,S} Assuming the reaction as written (CH4+H=CH3+H2) is endothermic at 298K, RMG will label this structure
     * as direction=-1 (backward). When attempting to find Kinetics for the backward reaction, RMG will try to match
     * the prod1 graph against the generic graphs X_H and Y_rad_birad. It cannot match Y_rad_birad (because there is
     * no *3 node) and it cannot match X_H (because there is no *2 node). Thus, a "null" Kinetics will be returned
     * from the findReverseRateConstant call. We then relabel the central nodes on prod1 and prod2 and attempt to
     * get Kinetics for this structure. I am adding the following bit of code to work with the new reaction family
     * Aaron Vandeputte is adding to RMG: "".
     */
    else if (k == null && rRT.name.equals("intra_substitutionS_isomerization")) {
      ChemGraph cg1 = ((ChemGraph) fproduct.get(0));
      Graph g1 = cg1.getGraph();
      Node n1 = (Node) g1.getCentralNodeAt(1);
      Node n2 = (Node) g1.getCentralNodeAt(2);
      Node n3 = (Node) g1.getCentralNodeAt(3);
      Node n4 = (Node) g1.getCentralNodeAt(4);
      Node n5 = (Node) g1.getCentralNodeAt(5);
      Node n6 = (Node) g1.getCentralNodeAt(6);
      Node n7 = (Node) g1.getCentralNodeAt(7);
      g1.clearCentralNode();
      g1.setCentralNode(1, n1);
      g1.setCentralNode(2, n3);
      g1.setCentralNode(3, n2);
      if (n7 != null) {
        g1.setCentralNode(7, n4);
        g1.setCentralNode(6, n5);
        g1.setCentralNode(5, n6);
        g1.setCentralNode(4, n7);
      } else if (n6 != null) {
        g1.setCentralNode(6, n4);
        g1.setCentralNode(5, n5);
        g1.setCentralNode(4, n6);
      } else if (n5 != null) {
        g1.setCentralNode(5, n4);
        g1.setCentralNode(4, n5);
      } else if (n4 != null) g1.setCentralNode(4, n4);
      k = rRT.findRateConstant(rs);
    }
    // Adding another elseif statement for Aaron Vandeputte rxn family
    // RMG expects to find *1 and *2 in the same ChemGraph (for this rxn family)
    // but will instead find *1 and *3 in the same ChemGraph (if we've reached this far)
    // Need to switch *2 and *3
    else if (k == null && (rRT.name.equals("substitutionS") || rRT.name.equals("Substitution_O"))) {
      ChemGraph cg1 = ((ChemGraph) fproduct.get(0));
      ChemGraph cg2 = ((ChemGraph) fproduct.get(1));
      Graph g1 = cg1.getGraph();
      Graph g2 = cg2.getGraph();
      Node n3 = (Node) g1.getCentralNodeAt(3);
      if (n3 == null) {
        // Switch the identities of cg1/g1 and cg2/g2
        cg1 = ((ChemGraph) fproduct.get(1));
        g1 = cg1.getGraph();
        cg2 = ((ChemGraph) fproduct.get(0));
        g2 = cg2.getGraph();
        n3 = (Node) g1.getCentralNodeAt(3);
      }
      Node n1 = (Node) g1.getCentralNodeAt(1);
      g1.clearCentralNode();
      g1.setCentralNode(2, n3);
      g1.setCentralNode(1, n1);
      Node n2 = (Node) g2.getCentralNodeAt(2);
      g2.clearCentralNode();
      g2.setCentralNode(3, n2);
      k = rRT.findRateConstant(rs);
    } else if (k == null && rRT.name.equals("intra_H_migration")) {
      ChemGraph cg = ((ChemGraph) fproduct.get(0));
      Graph g = cg.getGraph();

      // Current max is 8 identified nodes
      Node n1 = (Node) g.getCentralNodeAt(1);
      Node n2 = (Node) g.getCentralNodeAt(2);
      Node n3 = (Node) g.getCentralNodeAt(3);
      Node n4 = (Node) g.getCentralNodeAt(4);
      Node n5 = (Node) g.getCentralNodeAt(5);
      Node n6 = (Node) g.getCentralNodeAt(6);
      Node n7 = (Node) g.getCentralNodeAt(7);
      Node n8 = (Node) g.getCentralNodeAt(8);

      g.clearCentralNode();
      // Swap the locations of the central nodes 1 and 2
      g.setCentralNode(1, n2);
      g.setCentralNode(2, n1);
      // Retain the location of the central node at 3
      g.setCentralNode(3, n3);

      if (n8 != null) {
        g.setCentralNode(4, n5);
        g.setCentralNode(5, n4);
        g.setCentralNode(6, n8);
        g.setCentralNode(7, n7);
        g.setCentralNode(8, n6);
      } else if (n7 != null) {
        g.setCentralNode(4, n5);
        g.setCentralNode(5, n4);
        g.setCentralNode(6, n7);
        g.setCentralNode(7, n6);
      } else if (n6 != null) {
        g.setCentralNode(4, n5);
        g.setCentralNode(5, n4);
        g.setCentralNode(6, n6);
      } else if (n5 != null) { // Swap the locations of the central nodes 4 and 5, if node 5 exists
        g.setCentralNode(4, n5);
        g.setCentralNode(5, n4);
      } else if (n4 != null) { // if only central node 4 exists, retain that location
        g.setCentralNode(4, n4);
      }

      k = rRT.findRateConstant(rs);
      //            rr = rRT.calculateForwardRateConstant(cg, rs);
      //            if (!rr.isForward()) {
      //                String err = "Backward:"
      //                        + structure.toString()
      //                        + String.valueOf(structure
      //                                .calculateKeq(new Temperature(298, "K")))
      //                        + '\n';
      //                err = err
      //                        + "Forward:"
      //                        + rr.structure.toString()
      //                        + String.valueOf(rr.structure
      //                                .calculateKeq(new Temperature(298, "K")));
      //                throw new InvalidReactionDirectionException(err);
      //            }
      //           rr.setReverseReaction(this);
      //           rRT.addReaction(rr);
      //           return rr;

    } else if (k == null && rRT.name.equals("H_shift_cyclopentadiene")) {
      ChemGraph cg = ((ChemGraph) fproduct.get(0));
      Graph g = cg.getGraph();

      // Current max is 6 identified nodes
      Node n1 = (Node) g.getCentralNodeAt(1);
      Node n2 = (Node) g.getCentralNodeAt(2);
      Node n3 = (Node) g.getCentralNodeAt(3);
      Node n4 = (Node) g.getCentralNodeAt(4);
      Node n5 = (Node) g.getCentralNodeAt(5);
      Node n6 = (Node) g.getCentralNodeAt(6);

      g.clearCentralNode();

      // Swap the locations of the central nodes 1 to 6
      g.setCentralNode(1, n2);
      g.setCentralNode(2, n1);
      g.setCentralNode(3, n5);
      g.setCentralNode(4, n4);
      g.setCentralNode(5, n3);
      g.setCentralNode(6, n6);
      k = rRT.findRateConstant(rs);
    }
    if (k == null) {
      Logger.error(
          "Couldn't find the rate constant for reaction: "
              + rs.toChemkinString(true)
              + " with "
              + rRT.name);
      // System.exit(0);
      return null;
    }
    rr = new TemplateReaction(rsSp, k, rRT);
    if (!rr.isForward()) {
      String err =
          "Backward:"
              + structure.toString()
              + String.valueOf(structure.calculateKeq(new Temperature(298, "K")))
              + '\n';
      err =
          err
              + "Forward:"
              + rr.structure.toString()
              + String.valueOf(rr.structure.calculateKeq(new Temperature(298, "K")));
      throw new InvalidReactionDirectionException(err);
    }
    rr.setReverseReaction(this);
    rRT.addReaction(rr);
    return rr;
    // #]
  }