Universal database

documentation/source/users/rmg/database/modification.rst

@@ -11,15 +11,15 @@ Modifying the Thermo Database
 =============================
 
 Creating Thermo Libraries
-----------------------------------
+-------------------------
 
 
 Adding Thermo Groups
-----------------------------------
+--------------------
 
 
 Adding Thermo to the Depository
-----------------------------------
+-------------------------------
 
 .. _kinetic-database-modification:
 
@@ -42,7 +42,7 @@ Put kinetic parameters into the training set when:
 * You wish for the reaction to be generalized to similar reactions in your mechanism
 
 Creating Kinetics Libraries
-----------------------------------
+---------------------------
 
 Adding New Kinetic Groups and Rate Rules
 ----------------------------------------
@@ -117,9 +117,6 @@ In the family's groups.py, you will need to add an entry of the format::
 		referenceType = "",
 		shortDesc = u"""""",
 		longDesc = u"""""",
-	history = [
-		("Wed Dec  5 10:25:25 2012","Josh Allen <jwallen@mit.edu>","action","""Josh Allen <jwallen@mit.edu> imported this entry from the old RMG database."""),
-	],
 	)
 
 * The index can be any number not already present in the set
@@ -142,7 +139,7 @@ example given in the previous section, the new group would be added under the C_
 .. _kinetic-rules:
 
 Adding Kinetic Rules
----------------------------------------------------
+--------------------
 Rules give generalized kinetic parameters for a specific node template. In most
 cases, your kinetic parameters describe a specific reaction in which case you
 will want to add your reaction to the training set.
@@ -186,9 +183,6 @@ The rule must be added into rules.py in the form::
 
 	Verified by Karma James
 	""",
-		history = [
-			("Wed Jan  9 11:01:40 2013","Josh Allen <jwallen@mit.edu>","action","""Josh Allen <jwallen@mit.edu> imported this entry from the old RMG database."""),
-		],
 	) 
 
 * The index can be any number not already used in rules.py.
@@ -203,8 +197,8 @@ The rule must be added into rules.py in the form::
 
 .. _kinetic-training-set:
 
-Adding Training Reactions 
-----------------------------------------
+Adding Training Reactions
+-------------------------
 
 If you know the kinetics of a specific reaction, rather than a rate rule for a template, you can
 add the kinetics to the database training set.  By default, RMG creates new rate rules from this 

rmgpy/data/base.py

@@ -77,7 +77,6 @@ class Entry:
     `shortDesc`         A brief (one-line) description of the data
     `longDesc`          A long, verbose description of the data
     `rank`              An integer indicating the degree of confidence in the entry data, or ``None`` if not used
-    `history`           A list of tuples containing the date/time of change, author, type of change, and a brief description of the change
     =================== ========================================================
 
     """
@@ -94,7 +93,6 @@ def __init__(self,
                  shortDesc='',
                  longDesc='',
                  rank=None,
-                 history=None
                  ):
         self.index = index
         self.label = label
@@ -107,7 +105,6 @@ def __init__(self,
         self.shortDesc = shortDesc
         self.longDesc = longDesc
         self.rank = rank
-        self.history = history or []
 
     def __str__(self):
         return self.label
@@ -1258,7 +1255,7 @@ def saveOld(self, path):
         """
         self.saveOldDictionary(path)
 
-    def loadEntry(self, label, molecule=None, group=None, shortDesc='', longDesc='', history=None):
+    def loadEntry(self, label, molecule=None, group=None, shortDesc='', longDesc=''):
         """
         Load an entry from the forbidden structures database. This method is
         automatically called during loading of the forbidden structures 
@@ -1282,7 +1279,6 @@ def loadEntry(self, label, molecule=None, group=None, shortDesc='', longDesc='',
             item = item,
             shortDesc = shortDesc,
             longDesc = longDesc.strip(),
-            history = history or [],
         )
 
     def saveEntry(self, f, entry, name='entry'):
@@ -1314,9 +1310,4 @@ def saveEntry(self, f, entry, name='entry'):
         f.write(entry.longDesc.strip() + "\n")
         f.write('""",\n')
 
-        f.write('    history = [\n')
-        for time, user, action, description in entry.history:
-            f.write('        ("{0}","{1}","{2}","""{3}"""),\n'.format(time, user, action, description))
-        f.write('    ],\n')
-
         f.write(')\n\n')

rmgpy/data/kinetics/common.py

@@ -203,10 +203,9 @@ def sortEfficiencies(efficiencies0):
         for line in lines[1:-1]:
             f.write('    {0}\n'.format(line))
         f.write('    ),\n'.format(lines[0]))
-    else:
-        f.write('    reference = None,\n')
 
-    f.write('    referenceType = "{0}",\n'.format(entry.referenceType))
+    if entry.referenceType != "":
+        f.write('    referenceType = "{0}",\n'.format(entry.referenceType))
     if entry.rank is not None:
         f.write('    rank = {0},\n'.format(entry.rank))
     f.write('    shortDesc = u"""')
@@ -223,9 +222,4 @@ def sortEfficiencies(efficiencies0):
         f.write(entry.longDesc.strip().encode('ascii', 'ignore')+ "\n")
     f.write('""",\n')
 
-    f.write('    history = [\n')
-    for time, user, action, description in entry.history:
-        f.write('        ("{0}","{1}","{2}","""{3}"""),\n'.format(time, user, action, description))
-    f.write('    ],\n')
-
     f.write(')\n\n')

rmgpy/data/kinetics/depository.py

@@ -135,7 +135,6 @@ def loadEntry(self,
                   shortDesc='',
                   longDesc='',
                   rank=None,
-                  history=None
                   ):
 
         reactants = [Molecule().fromAdjacencyList(reactant1)]
@@ -158,7 +157,6 @@ def loadEntry(self,
             shortDesc = shortDesc,
             longDesc = longDesc.strip(),
             rank = rank,
-            history = history or [],
         )
         self.entries['{0:d}:{1}'.format(index,label)] = entry
         return entry

rmgpy/data/kinetics/family.py

@@ -619,13 +619,13 @@ def loadRecipe(self, actions):
             assert action[0] in ['CHANGE_BOND','FORM_BOND','BREAK_BOND','GAIN_RADICAL','LOSE_RADICAL','GAIN_PAIR','LOSE_PAIR']
             self.forwardRecipe.addAction(action)
 
-    def loadForbidden(self, label, group, shortDesc='', longDesc='', history=None):
+    def loadForbidden(self, label, group, shortDesc='', longDesc=''):
         """
         Load information about a forbidden structure.
         """
         if not self.forbidden:
             self.forbidden = ForbiddenStructures()
-        self.forbidden.loadEntry(label=label, group=group, shortDesc=shortDesc, longDesc=longDesc, history=history)
+        self.forbidden.loadEntry(label=label, group=group, shortDesc=shortDesc, longDesc=longDesc)
 
     def saveEntry(self, f, entry):
         """
@@ -863,7 +863,6 @@ def addKineticsRulesFromTrainingSet(self, thermoDatabase=None):
                 reference=entry.reference,
                 shortDesc="Rate rule generated from training reaction {0}. ".format(entry.index) + entry.shortDesc,
                 longDesc="Rate rule generated from training reaction {0}. ".format(entry.index) + entry.longDesc,
-                history=entry.history,
             )
             new_entry.data.A.value_si /= entry.item.degeneracy
             try:
@@ -915,7 +914,6 @@ def addKineticsRulesFromTrainingSet(self, thermoDatabase=None):
                 reference=entry.reference,
                 shortDesc="Rate rule generated from training reaction {0}. ".format(entry.index) + entry.shortDesc,
                 longDesc="Rate rule generated from training reaction {0}. ".format(entry.index) + entry.longDesc,
-                history=entry.history,
             )
             new_entry.data.A.value_si /= item.degeneracy
             try:

rmgpy/data/kinetics/groups.py

@@ -81,7 +81,7 @@ def __init__(self,
     def __repr__(self):
         return '<KineticsGroups "{0}">'.format(self.label)
 
-    def loadEntry(self, index, label, group, kinetics, reference=None, referenceType='', shortDesc='', longDesc='', history=None):
+    def loadEntry(self, index, label, group, kinetics, reference=None, referenceType='', shortDesc='', longDesc=''):
         if group[0:3].upper() == 'OR{' or group[0:4].upper() == 'AND{' or group[0:7].upper() == 'NOT OR{' or group[0:8].upper() == 'NOT AND{':
             item = makeLogicNode(group)
         else:
@@ -95,7 +95,6 @@ def loadEntry(self, index, label, group, kinetics, reference=None, referenceType
             referenceType = referenceType,
             shortDesc = shortDesc,
             longDesc = longDesc.strip(),
-            history = history or [],
         )
 
     def getReactionTemplate(self, reaction):

rmgpy/data/kinetics/library.py

@@ -272,7 +272,6 @@ def loadEntry(self,
                   referenceType='',
                   shortDesc='',
                   longDesc='',
-                  history=None
                   ):
 
         reactants = [Species(label=reactant1.strip().splitlines()[0].strip(), molecule=[Molecule().fromAdjacencyList(reactant1)])]
@@ -305,7 +304,6 @@ def loadEntry(self,
             referenceType = referenceType,
             shortDesc = shortDesc,
             longDesc = longDesc.strip(),
-            history = history or [],
         )
 
         # Convert SMILES to Molecule objects in collision efficiencies

rmgpy/data/kinetics/rules.py

@@ -82,7 +82,6 @@ def loadEntry(self,
                   shortDesc='',
                   longDesc='',
                   rank=None,
-                  history=None
                   ):
 
         reactants = []
@@ -119,7 +118,6 @@ def loadEntry(self,
             shortDesc = shortDesc,
             longDesc = longDesc.strip(),
             rank = rank,
-            history = history or [],
         )
         try:
             self.entries[label].append(entry)

rmgpy/data/solvation.py

@@ -228,7 +228,6 @@ def loadEntry(self,
                   referenceType='',
                   shortDesc='',
                   longDesc='',
-                  history=None
                   ):
         self.entries[label] = Entry(
             index = index,
@@ -238,7 +237,6 @@ def loadEntry(self,
             referenceType = referenceType,
             shortDesc = shortDesc,
             longDesc = longDesc.strip(),
-            history = history or [],
         )
 
     def load(self, path):
@@ -276,7 +274,6 @@ def loadEntry(self,
                   referenceType='',
                   shortDesc='',
                   longDesc='',
-                  history=None
                   ):
         self.entries[label] = Entry(
             index = index,
@@ -287,7 +284,6 @@ def loadEntry(self,
             referenceType = referenceType,
             shortDesc = shortDesc,
             longDesc = longDesc.strip(),
-            history = history or [],
         )
 
     def load(self, path):
@@ -332,7 +328,6 @@ def loadEntry(self,
                   referenceType='',
                   shortDesc='',
                   longDesc='',
-                  history=None
                   ):
         if group[0:3].upper() == 'OR{' or group[0:4].upper() == 'AND{' or group[0:7].upper() == 'NOT OR{' or group[0:8].upper() == 'NOT AND{':
             item = makeLogicNode(group)
@@ -347,7 +342,6 @@ def loadEntry(self,
             referenceType = referenceType,
             shortDesc = shortDesc,
             longDesc = longDesc.strip(),
-            history = history or [],
         )
 
     def saveEntry(self, f, entry):

rmgpy/data/statmech.py

@@ -83,11 +83,6 @@ def saveEntry(f, entry):
     f.write(entry.longDesc.strip() + "\n")
     f.write('\n""",\n')
 
-    f.write('    history = [\n')
-    for time, user, action, description in entry.history:
-        f.write('        ("{0}","{1}","{2}","""{3}"""),\n'.format(time, user, action, description))
-    f.write('    ],\n')
-
     f.write(')\n\n')
 
 def generateOldLibraryEntry(data):
@@ -135,7 +130,6 @@ def loadEntry(self,
                   referenceType='',
                   shortDesc='',
                   longDesc='',
-                  history=None
                   ):
         self.entries[label] = Entry(
             index = index,
@@ -146,7 +140,6 @@ def loadEntry(self,
             referenceType = referenceType,
             shortDesc = shortDesc,
             longDesc = longDesc.strip(),
-            history = history or [],
         )
 
     def saveEntry(self, f, entry):
@@ -174,7 +167,6 @@ def loadEntry(self,
                   referenceType='',
                   shortDesc='',
                   longDesc='',
-                  history=None
                   ):
         self.entries[label] = Entry(
             index = index,
@@ -185,7 +177,6 @@ def loadEntry(self,
             referenceType = referenceType,
             shortDesc = shortDesc,
             longDesc = longDesc.strip(),
-            history = history or [],
         )
 
     def saveEntry(self, f, entry):
@@ -228,7 +219,6 @@ def loadEntry(self,
                   referenceType='',
                   shortDesc='',
                   longDesc='',
-                  history=None
                   ):
         if ( group[0:3].upper() == 'OR{' or
              group[0:4].upper() == 'AND{' or
@@ -247,7 +237,6 @@ def loadEntry(self,
             referenceType = referenceType,
             shortDesc = shortDesc,
             longDesc = longDesc.strip(),
-            history = history or [],
         )
 
     def saveEntry(self, f, entry):