Fix bug that didn't properly check all resonances structures when cre…

…ating training reactions
ReactionMechanismGenerator · Jun 1, 2017 · 23dfe63 · 23dfe63
1 parent 0381ce9
commit 23dfe63
Showing 1 changed file with 13 additions and 12 deletions.
diff --git a/scripts/convertKineticsLibraryToTrainingReactions.ipynb b/scripts/convertKineticsLibraryToTrainingReactions.ipynb
@@ -36,6 +36,7 @@
     "from rmgpy.rmg.model import Species\n",
     "from rmgpy import settings\n",
     "from IPython.display import display, HTML, Image\n",
+    "import itertools\n",
     "from base64 import b64encode\n",
     "if compareKinetics:\n",
     "    import numpy as np\n",
@@ -106,21 +107,21 @@
     "    commentsDict[lib_rxn] = [entry.reference, entry.referenceType, entry.shortDesc, entry.longDesc] #save comments to add to training\n",
     "    # Let's make RMG try to generate this reaction from the families!\n",
     "    fam_rxn_list = []\n",
-    "    rxt_mol_mutation_num = 1\n",
-    "    pdt_mol_mutation_num = 1\n",
-    "    for reactant in lib_rxn.reactants:\n",
-    "        rxt_mol_mutation_num *= len(reactant.molecule)\n",
-    "\n",
-    "    for product in lib_rxn.products:\n",
-    "        pdt_mol_mutation_num *= len(product.molecule)\n",
-    "\n",
-    "    for mutation_i in range(rxt_mol_mutation_num):\n",
-    "        rxts_mol = [spc.molecule[mutation_i%(len(spc.molecule))] for spc in lib_rxn.reactants]\n",
-    "        pdts_mol = [spc.molecule[0] for spc in lib_rxn.products]\n",
+    "    \n",
+    "    #get list of all possible resonance structures of reactant molecules\n",
+    "    if len(lib_rxn.reactants) > 1:\n",
+    "        rxt_resonances = [rxt.molecule for rxt in lib_rxn.reactants]\n",
+    "        rxts_cross = list(itertools.product(*rxt_resonances))\n",
+    "        rxts_cross = [list(cross) for cross in rxts_cross]\n",
+    "    else:\n",
+    "        rxts_cross = [[mol] for mol in lib_rxn.reactants[0].mol] #should have only one reactant\n",
+    "    \n",
+    "    #use families to try find reactions\n",
+    "    for rxts_mol in rxts_cross:\n",
+    "        pdts_mol = [spc.molecule[0] for spc in lib_rxn.products] #do we also need to cross through products.mol\n",
     "        fam_rxn_list.extend(database.kinetics.generateReactionsFromFamilies(\n",
     "                        reactants=rxts_mol, products=pdts_mol))\n",
     "\n",
-    "\n",
     "    if len(fam_rxn_list) == 1:\n",
     "        fam_rxn = fam_rxn_list[0]\n",
     "\n",