Source Code for Module SloppyCell.ReactionNetworks.Reactions

  1  import sets 
  2  import SloppyCell.ExprManip as ExprManip 
  3   
  4 -class Reaction: 
  5 -    def __init__(self, id, stoichiometry, kineticLaw = '', name = '', 
  6                   reactant_stoichiometry = None, product_stoichiometry = None): 
  7          self.id = id 
  8          self.stoichiometry = stoichiometry 
  9          # self.reactant_stoichiometry and self.product_stoichiometry 
 10          # are defined to help repserve the stoichiometry defined in an 
 11          # SBML model 
 12          self.reactant_stoichiometry = reactant_stoichiometry 
 13          self.product_stoichiometry = product_stoichiometry 
 14          self.kineticLaw = kineticLaw 
 15          self.name = name 
 16   
 17          variables = ExprManip.extract_vars(kineticLaw) 
 18          self.parameters = variables.difference(sets.Set(stoichiometry.keys())) 
 19   
 20 -    def __eq__(self, other): 
 21          return self.__class__ == other.__class__ and \ 
 22                  self.kineticLaw == other.kineticLaw and \ 
 23                  self.stoichiometry == other.stoichiometry 
 24   
 25 -    def __ne__(self, other): 
 26          return not (self == other) 
 27   
 28 -    def doKwargsSubstitution(self, kwargs): 
 29          oldStoichiometry = self.stoichiometry 
 30          self.stoichiometry = {} 
 31          for base in oldStoichiometry: 
 32              self.stoichiometry[kwargs[base]] = oldStoichiometry[base] 
 33   
 34          self.kineticLaw = ExprManip.sub_for_vars(self.kineticLaw, kwargs) 
 35   
 36 -    def change_stoichiometry(self, species, stoich): 
 37          """ 
 38          Change stoichiometry will update self.stoichiometry. 
 39          It also updates self.reactant_stoichiometry and self.product_stoichiometry, 
 40          if they are defined, to keep the two stoichiometry tracking systems in sync. 
 41          """ 
 42          self.stoichiometry[species] = stoich 
 43          if self.reactant_stoichiometry != None and self.product_stoichiometry != None: 
 44              if species in self.reactant_stoichiometry.keys(): 
 45                  del self.reactant_stoichiometry[species] 
 46              self.product_stoichiometry[species] = [stoich] 
 47   
 48   
 49 -class HomodimerizationReaction(Reaction): 
 50 -    def __init__(self, id, **kwargs): 
 51          self.kineticLaw = 'rate * reactant**2' 
 52          self.stoichiometry = {'reactant': -2, 
 53                                'dimer': +1} 
 54          self.doKwargsSubstitution(kwargs) 
 55          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
 56   
 57 -class HeterodimerizationReaction(Reaction): 
 58 -    def __init__(self, id, **kwargs): 
 59          self.kineticLaw = 'rate * A * B' 
 60          self.stoichiometry = {'A': -1, 
 61                                'B': -1, 
 62                                'dimer': +1} 
 63          self.doKwargsSubstitution(kwargs) 
 64          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
 65   
 66 -class HomodimerDissociationReaction(Reaction): 
 67 -    def __init__(self, id, **kwargs): 
 68          self.kineticLaw = 'rate * dimer' 
 69          self.stoichiometry = {'reactant': +2, 
 70                                'dimer': -1} 
 71          self.doKwargsSubstitution(kwargs) 
 72          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
 73   
 74 -class HeterodimerDissociationReaction(Reaction): 
 75 -    def __init__(self, id, **kwargs): 
 76          self.kineticLaw = 'rate * dimer' 
 77          self.stoichiometry = {'A': +1, 
 78                                'B': +1, 
 79                                'dimer': -1} 
 80          self.doKwargsSubstitution(kwargs) 
 81          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
 82   
 83 -class ExponentialDecayReaction(Reaction): 
 84 -    def __init__(self, id, **kwargs): 
 85          self.kineticLaw = 'rate * species' 
 86          self.stoichiometry = {'species': -1} 
 87          self.doKwargsSubstitution(kwargs) 
 88          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
 89   
 90 -class MichaelisMentenReaction(Reaction): 
 91 -    def __init__(self, id, **kwargs): 
 92          self.kineticLaw = 'k * E * S / (S + Km)' 
 93          self.stoichiometry = {'E': 0, 
 94                                'S': -1, 
 95                                'P': 1}  
 96          self.doKwargsSubstitution(kwargs) 
 97          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
 98   
 99 -class ConstructionReaction(Reaction): 
100 -    def __init__(self, id, **kwargs): 
101          self.kineticLaw = 'rate * template' 
102          self.stoichiometry = {'product': 1, 
103                                'template': 0}  
104          self.doKwargsSubstitution(kwargs) 
105          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
106   
107 -class TransformationReaction(Reaction): 
108 -    def __init__(self, id, **kwargs): 
109          self.kineticLaw = 'rate * old' 
110          self.stoichiometry = {'old': -1, 
111                             'new': +1} 
112          self.doKwargsSubstitution(kwargs) 
113          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
114   
115 -class ProductionReaction(Reaction): 
116 -    def __init__(self, id, **kwargs): 
117          self.kineticLaw = 'rate' 
118          self.stoichiometry = {'product': 1} 
119          self.doKwargsSubstitution(kwargs) 
120          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
121   
122 -class PromoterReaction(Reaction): 
123 -    def __init__(self, id, **kwargs): 
124          self.kineticLaw = 'vmax * kP * P / (kP * P + ((kR1 * R1)**h) + ((kR2 * R2)**h) + 1.0)' 
125          self.stoichiometry = {'P': 0, 
126                                'R1': 0, 
127                                'R2': 0, 
128                                'mRNA': +1}  
129          self.doKwargsSubstitution(kwargs) 
130          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
131   
132 -class CoPromoterReaction(Reaction): 
133 -    def __init__(self, id, **kwargs): 
134          self.kineticLaw = 'vmax * (kP1 + kP2_1 * P) / (kP1 + kP2_2 * P + ((kR1 * R1 / (1 + kR2 * R2))**h) + 1.0)' 
135          self.stoichiometry = {'P': 0, 
136                                'R1': 0, 
137                                'R2': 0, 
138                                'mRNA': +1}  
139          self.doKwargsSubstitution(kwargs) 
140          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
141   
142 -class MichaelisMentenDegradationReaction(Reaction): 
143 -    def __init__(self, id, **kwargs): 
144          self.kineticLaw = 'k * S / (S + Km)' 
145          self.stoichiometry = {'S': -1}  
146          self.doKwargsSubstitution(kwargs) 
147          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
148   
149 -class SelfCatalyticMichaelisMentenReaction(Reaction): 
150 -    def __init__(self, id, **kwargs): 
151          self.kineticLaw = 'k * S / (S + Km)' 
152          self.stoichiometry = {'S': -1, 
153                                'P': +1} 
154          self.doKwargsSubstitution(kwargs) 
155          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
156   
157 -class FirstOrderReaction(Reaction): 
158 -    def __init__(self, id, **kwargs): 
159          self.kineticLaw = 'rate * reactant' 
160          self.stoichiometry = {'product': 1, 
161                                'reactant': -1}  
162          self.doKwargsSubstitution(kwargs) 
163          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
164   
165 -class TwoProductFirstOrderReaction(Reaction): 
166 -    def __init__(self, id, **kwargs): 
167          self.kineticLaw = 'rate * reactant' 
168          self.stoichiometry = {'product_1': 1, 
169                                'product_2': 1, 
170                                'reactant': -1}  
171          self.doKwargsSubstitution(kwargs) 
172          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
173   
174 -class SecondOrderReaction(Reaction): 
175 -    def __init__(self, id, **kwargs): 
176          self.kineticLaw = 'rate * reactant_1 * reactant_2' 
177          self.stoichiometry = {'product': 1, 
178                                'reactant_1': -1, 
179                                'reactant_2': -1} 
180          self.doKwargsSubstitution(kwargs) 
181          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
182   
183 -class HillDegradationReaction(Reaction): 
184 -    def __init__(self, id, **kwargs): 
185          self.kineticLaw = 'vmax * (S**h) / ((Km**h) + (S**h))' 
186          self.stoichiometry = {'S': -1} 
187          self.doKwargsSubstitution(kwargs) 
188          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
189   
190 -class HillTransportReaction(Reaction): 
191 -    def __init__(self, id, **kwargs): 
192          self.kineticLaw = 'vmax * (S**h) / ((Km**h) + (S**h))' 
193          self.stoichiometry = {'S': -1, 
194                                'P': +1} 
195          self.doKwargsSubstitution(kwargs) 
196          Reaction.__init__(self, id, self.stoichiometry, self.kineticLaw) 
197