parsing out photolysis information

etc/translate_mcm.py

@@ -31,67 +31,86 @@
 """
 
 statements = {
-    "number_of_reactions": "SELECT COUNT(DISTINCT ReactionID) FROM Reactions WHERE Mechanism = 'MCM';",
-    "number_of_rate_constants": "SELECT COUNT(DISTINCT RATE) FROM Reactions INNER JOIN Rates USING(Rate) WHERE Mechanism = 'MCM';",
-    "rate_types": "SELECT RateType, COUNT(*) FROM Rates GROUP BY RateType;",
-    "mcm_reactions_with_rate_type": "SELECT rates.RateType, COUNT(*) FROM Reactions r INNER JOIN Rates rates ON r.Rate = rates.Rate WHERE MEchanism = 'MCM' GROUP BY rates.RateType;",
-    "counted": counted
+  "number_of_reactions": "SELECT COUNT(DISTINCT ReactionID) FROM Reactions WHERE Mechanism = 'MCM';",
+  "number_of_rate_constants": "SELECT COUNT(DISTINCT RATE) FROM Reactions INNER JOIN Rates USING(Rate) WHERE Mechanism = 'MCM';",
+  "rate_types": "SELECT RateType, COUNT(*) FROM Rates GROUP BY RateType;",
+  "mcm_reactions_with_rate_type": "SELECT rates.RateType, COUNT(*) FROM Reactions r INNER JOIN Rates rates ON r.Rate = rates.Rate WHERE MEchanism = 'MCM' GROUP BY rates.RateType;",
+  "photolysis_rate_paramters": "SELECT J, l, m, n FROM PhotolysisParameters;",
+  "counted": counted
 }
 
+def convert_to_float(s):
+  if type(s) == str:
+    return float(s.replace('D', 'E'))
+  return s
+
 def get_count(cursor, stmt):
-    cursor.execute(stmt)
-    stmt = cursor.fetchone()[0]
-    return stmt
+  cursor.execute(stmt)
+  stmt = cursor.fetchone()[0]
+  return stmt
 
 def get_all(cursor, stmt):
-    cursor.execute(stmt)
-    stmt = cursor.fetchall()
-    return stmt
+  cursor.execute(stmt)
+  stmt = cursor.fetchall()
+  return stmt
 
 def group_reactions_by_rate_type(reactions):
-    null = []
-    tokenized = []
-    photolysis = []
-    for reaction in reactions:
-        if reaction[2] is None:
-            null.append(reaction)
-        elif reaction[2] == 'Tokenized':
-            tokenized.append(reaction)
-        elif reaction[2] == 'Photolysis':
-            photolysis.append(reaction)
-    return (null, tokenized, photolysis)
+  null = []
+  tokenized = []
+  photolysis = []
+  for reaction in reactions:
+    if reaction[2] is None:
+      null.append(reaction)
+    elif reaction[2] == 'Tokenized':
+      tokenized.append(reaction)
+    elif reaction[2] == 'Photolysis':
+      photolysis.append(reaction)
+  return (null, tokenized, photolysis)
 
 
 def convert_tokenized_rates(rates):
-    pass
+  pass
 
-def convert_photolysis_rates(rates):
-    pass
+def convert_photolysis_rates(rates, photolysis_parameters):
+  print(photolysis_parameters)
+  multiples = [i for i in rates if '*' in i[1]]
+  non_multiples = [i for i in rates if '*' not in i[1]]
+  # for rate in non_multiples[:15]:
+  #   print(rate)
+  # print()
+  # for rate in multiples[:15]:
+  #   print(rate)
 
 def convert_null_rates(rates):
-    pass
+  pass
 
 def translate_mcm():
-    conn = sqlite3.connect('data/mcm.db')
-    cursor = conn.cursor()
-    total_number_of_mcm_reactions = get_count(cursor, statements["number_of_reactions"])
-
-    number_of_rate_types = get_all(cursor, statements["mcm_reactions_with_rate_type"])
-    number_of_rate_types = [(('Null' if rate_type is None else rate_type), count) for rate_type, count in number_of_rate_types]
-    total_number_of_rate_types = sum([x[1] for x in number_of_rate_types])
-
-    assert(total_number_of_mcm_reactions == total_number_of_rate_types)
-    print(tabulate(number_of_rate_types, headers=['Rate Type', 'Count'], tablefmt='github'))
-
-    reactions = get_all(cursor, statements["counted"])
-    assert(len(reactions) == total_number_of_mcm_reactions)
-
-    for reaction in reactions[:15]:
-        print(reaction)
-
-    (null, tokenized, photolysis) = group_reactions_by_rate_type(reactions)
-    tokenized = convert_tokenized_rates(tokenized)
-    photolysis = convert_photolysis_rates(photolysis)
-    null = convert_null_rates(null)
+  conn = sqlite3.connect('data/mcm.db')
+  cursor = conn.cursor()
+  total_number_of_mcm_reactions = get_count(cursor, statements["number_of_reactions"])
+
+  number_of_rate_types = get_all(cursor, statements["mcm_reactions_with_rate_type"])
+  number_of_rate_types = [(('Null' if rate_type is None else rate_type), count) for rate_type, count in number_of_rate_types]
+  total_number_of_rate_types = sum([x[1] for x in number_of_rate_types])
+
+  assert(total_number_of_mcm_reactions == total_number_of_rate_types)
+  print(tabulate(number_of_rate_types, headers=['Rate Type', 'Count'], tablefmt='github'))
+
+  reactions = get_all(cursor, statements["counted"])
+  assert(len(reactions) == total_number_of_mcm_reactions)
+
+  photolysis_parameters = get_all(cursor, statements["photolysis_rate_paramters"])
+  photolysis_parameters = {
+    i[0]: {
+      'l': convert_to_float(i[1]),
+      'm': convert_to_float(i[2]),
+      'n': convert_to_float(i[3])
+    } for i in photolysis_parameters
+  }
+
+  (null, tokenized, photolysis) = group_reactions_by_rate_type(reactions)
+  tokenized = convert_tokenized_rates(tokenized)
+  photolysis = convert_photolysis_rates(photolysis, photolysis_parameters)
+  null = convert_null_rates(null)
 
 translate_mcm()