Modify ipython notebook script to be compatible with createKineticsLi…

…brary Specifically changed the way it reads comments, so that it can copy shortDesc and longDesc from the library entry. This is needed in the case where we make the library as an intermediate to making training reactions.
ReactionMechanismGenerator · Jun 1, 2017 · 0381ce9 · 0381ce9
1 parent 925fdba
commit 0381ce9
Showing 1 changed file with 16 additions and 3 deletions.
diff --git a/scripts/convertKineticsLibraryToTrainingReactions.ipynb b/scripts/convertKineticsLibraryToTrainingReactions.ipynb
@@ -91,6 +91,7 @@
    "outputs": [],
    "source": [
     "reactionDict = {}\n",
+    "commentsDict = {} #key is a :class:Reaction object, value is a list of entry attributes [reference, referenceType, shortDesc, longDesc]\n",
     "kineticLibrary = database.kinetics.libraries[libraryName]\n",
     "\n",
     "# html table settings\n",
@@ -102,6 +103,7 @@
     "    lib_rxn.kinetics = entry.data \n",
     "    lib_rxn.index = entry.index\n",
     "    lib_rxn.kinetics.comment = entry.label # Assign the entry's label to the comment\n",
+    "    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",
@@ -343,7 +345,18 @@
     "    reactions = reactionDict[familyName]\n",
     "    print 'reactions.py previously has {} rxns. Now adding {} new rxn(s).'.format(len(trainingDatabase.entries.values()), len(reactions))\n",
     "    print '================='\n",
-    "    kineticFamily.saveTrainingReactions(reactions, shortDesc='Training reaction from kinetics library: {0}'.format(libraryName))"
+    "    for reaction in reactions:\n",
+    "        shortDesc = ''\n",
+    "        #If the library entry has a shortDesc and longDesc to the training reaction \n",
+    "        if commentsDict[reaction][2]:\n",
+    "            shortDesc = commentsDict[reaction][2]\n",
+    "            reaction.kinetics.comment = str(commentsDict[reaction][3])\n",
+    "        else:\n",
+    "            shortDesc = 'Training reaction from kinetics library: {0}'.format(libraryName)\n",
+    "        kineticFamily.saveTrainingReactions([reaction],\n",
+    "                                            reference = commentsDict[reaction][0],\n",
+    "                                            referenceType = commentsDict[reaction][1],\n",
+    "                                            shortDesc=shortDesc)"
    ]
   },
   {
@@ -530,7 +543,7 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python [default]",
+   "display_name": "Python 2",
    "language": "python",
    "name": "python2"
   },
@@ -544,7 +557,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
-   "version": "2.7.12"
+   "version": "2.7.13"
   }
  },
  "nbformat": 4,