rs package

rs/context_automaton_with_concentrations.py

@@ -0,0 +1,66 @@
+from sys import exit
+from colour import *
+
+from rs.context_automaton import ContextAutomaton
+                    
+class ContextAutomatonWithConcentrations(ContextAutomaton):
+
+    def __init__(self, reaction_system):
+        self._states = []
+        self._transitions = []
+        self._init_state = None
+        self._reaction_system = reaction_system
+    
+    def is_valid_context(self, context):
+        if set([e for e,lvl in context]).issubset(self._reaction_system.background_set):
+            return True
+        else:
+            return False
+            
+    def context2str(self, ctx):
+        if len(ctx) == 0:
+            return "0"
+        s = "{"
+        for ent,lvl in ctx:
+            s += " " + str((self._reaction_system.get_entity_name(ent),lvl)) 
+        s += " }"
+        return s
+        
+    def add_transition(self, src, context_set, dst):
+        if not type(context_set) is set and not type(context_set) is list:
+            print("Contexts set must be of type set or list")
+            
+        if not self.is_valid_context(context_set):
+            raise RuntimeError("one of the entities in the context set is unknown (undefined)!")
+            
+        if not self.is_state(src):
+            raise RuntimeError("\"" + src + "\" is an unknown (undefined) state")
+
+        if not self.is_state(dst):
+            raise RuntimeError("\"" + dst + "\" is an unknown (undefined) state")
+
+        new_context_set = set()
+        for ent,lvl in set(context_set):
+            new_context_set.add((self._reaction_system.get_entity_id(ent),lvl))
+        
+        self._transitions.append((self.get_state_id(src),new_context_set,self.get_state_id(dst)))
+
+    def get_automaton_with_flat_contexts(self, ordinary_reaction_system):
+        
+        ca = ContextAutomaton(ordinary_reaction_system)
+        ca._states = self._states
+        ca._init_state = self._init_state
+        
+        for src,ctx,dst in self._transitions:
+            
+            new_ctx = set()
+            
+            for ent,conc in ctx:
+                for i in range(1,conc+1):
+                    n = self._reaction_system.get_entity_name(ent) + "#" + str(i)
+                    ca._reaction_system.ensure_bg_set_entity(n)
+                    new_ctx.add(n)
+            
+            ca.add_transition(ca.get_state_name(src),new_ctx,ca.get_state_name(dst))
+            
+        return ca