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;
}
// ## 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;
// #]
}