rs package
This commit is contained in:
Artur Meski
10
rs/__init__.py
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10
rs/__init__.py
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@@ -0,0 +1,10 @@
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from rs.reaction_system import ReactionSystem
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from rs.context_automaton import ContextAutomaton
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from rs.reaction_system_with_concentrations import ReactionSystemWithConcentrations
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from rs.context_automaton_with_concentrations import ContextAutomatonWithConcentrations
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from rs.reaction_system_with_automaton import ReactionSystemWithAutomaton
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from rs.extended_context_automaton import ExtendedContextAutomaton
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132
rs/context_automaton.py
Normal file
132
rs/context_automaton.py
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@@ -0,0 +1,132 @@
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from sys import exit
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from colour import *
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class ContextAutomaton(object):
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def __init__(self, reaction_system):
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self._states = []
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self._transitions = []
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self._init_state = None
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self._reaction_system = reaction_system
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@property
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def states(self):
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return self._states
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@property
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def transitions(self):
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return self._transitions
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def add_state(self, name):
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if name not in self._states:
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self._states.append(name)
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else:
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print("\'%s\' already added. skipping..." % (name,))
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def add_states(self, states_set):
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for st in states_set:
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self.add_state(st)
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def add_init_state(self, name):
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self.add_state(name)
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self._init_state = self._states.index(name)
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def get_init_state_name(self):
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if self._init_state == None:
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return None
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return self._states[self._init_state]
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def is_state(self, name):
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if name in self._states:
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return True
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else:
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return False
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def get_state_id(self, name):
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try:
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return self._states.index(name)
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except ValueError:
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print_error("Undefined context automaton state: " + repr(name))
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exit(1)
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def get_state_name(self, state_id):
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return self._states[state_id]
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def get_init_state_id(self):
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return self._init_state
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def print_states(self):
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for state in self._states:
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print(state)
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def is_valid_rs_set(self, elements):
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if set(elements).issubset(self._reaction_system.background_set):
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return True
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else:
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return False
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def is_valid_context(self, context):
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return self.is_valid_rs_set(context)
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def get_set_of_ids(self, elements):
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"""Converts a set/list/tuple of entities into a set of their ids"""
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new_set = set()
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for e in set(elements):
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new_set.add(self._reaction_system.get_entity_id(e))
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return new_set
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def add_transition(self, src, context_set, dst):
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if not type(context_set) is set and not type(context_set) is list:
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print("Contexts set must be of type set or list")
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if not self.is_valid_context(context_set):
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raise RuntimeError("one of the entities in the context set is unknown (undefined)!")
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if not self.is_state(src):
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raise RuntimeError("\"" + src + "\" is an unknown (undefined) state")
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if not self.is_state(dst):
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raise RuntimeError("\"" + dst + "\" is an unknown (undefined) state")
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new_context_set = set()
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for e in set(context_set):
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new_context_set.add(self._reaction_system.get_entity_id(e))
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self._transitions.append((self.get_state_id(src),new_context_set,self.get_state_id(dst)))
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def rsset2str(self, elements):
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"""Converts the set of entities ids into the string with their names"""
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if len(elements) == 0:
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return "0"
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s = "{"
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for c in elements:
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s += " " + self._reaction_system.get_entity_name(c)
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s += " }"
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return s
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def context2str(self, ctx):
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return self.rsset2str(ctx)
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def show_transitions(self):
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print(C_MARK_INFO + " Context automaton transitions:")
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for transition in self._transitions:
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str_transition = str(transition[0]) + " --( "
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str_transition += self.context2str(transition[1])
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str_transition += " )--> " + str(transition[2])
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print(" - " + str_transition)
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def show_states(self):
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init_state_name = self.get_init_state_name()
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print(C_MARK_INFO + " Context automaton states:")
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for state in self._states:
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print(" - " + state, end="")
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if state == init_state_name:
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print(" [init]")
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else:
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print()
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def show(self):
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self.show_states()
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self.show_transitions()
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66
rs/context_automaton_with_concentrations.py
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66
rs/context_automaton_with_concentrations.py
Normal file
@@ -0,0 +1,66 @@
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from sys import exit
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from colour import *
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from rs.context_automaton import ContextAutomaton
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class ContextAutomatonWithConcentrations(ContextAutomaton):
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def __init__(self, reaction_system):
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self._states = []
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self._transitions = []
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self._init_state = None
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self._reaction_system = reaction_system
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def is_valid_context(self, context):
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if set([e for e,lvl in context]).issubset(self._reaction_system.background_set):
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return True
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else:
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return False
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def context2str(self, ctx):
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if len(ctx) == 0:
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return "0"
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s = "{"
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for ent,lvl in ctx:
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s += " " + str((self._reaction_system.get_entity_name(ent),lvl))
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s += " }"
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return s
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def add_transition(self, src, context_set, dst):
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if not type(context_set) is set and not type(context_set) is list:
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print("Contexts set must be of type set or list")
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if not self.is_valid_context(context_set):
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raise RuntimeError("one of the entities in the context set is unknown (undefined)!")
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if not self.is_state(src):
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raise RuntimeError("\"" + src + "\" is an unknown (undefined) state")
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if not self.is_state(dst):
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raise RuntimeError("\"" + dst + "\" is an unknown (undefined) state")
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new_context_set = set()
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for ent,lvl in set(context_set):
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new_context_set.add((self._reaction_system.get_entity_id(ent),lvl))
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self._transitions.append((self.get_state_id(src),new_context_set,self.get_state_id(dst)))
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def get_automaton_with_flat_contexts(self, ordinary_reaction_system):
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ca = ContextAutomaton(ordinary_reaction_system)
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ca._states = self._states
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ca._init_state = self._init_state
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for src,ctx,dst in self._transitions:
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new_ctx = set()
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for ent,conc in ctx:
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for i in range(1,conc+1):
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n = self._reaction_system.get_entity_name(ent) + "#" + str(i)
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ca._reaction_system.ensure_bg_set_entity(n)
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new_ctx.add(n)
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ca.add_transition(ca.get_state_name(src),new_ctx,ca.get_state_name(dst))
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return ca
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76
rs/extended_context_automaton.py
Normal file
76
rs/extended_context_automaton.py
Normal file
@@ -0,0 +1,76 @@
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from sys import exit
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from colour import *
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from rs.context_automaton import ContextAutomaton
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class ExtendedContextAutomaton(ContextAutomaton):
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"""Extended Context Automaton"""
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def __init__(self, reaction_system):
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self._actions = []
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super(ExtendedContextAutomaton, self).__init__(reaction_system)
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def add_transition(self, src, action, ctx_reaction, dst):
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ctx_reactants, ctx_inhibitors, ctx_products = ctx_reaction
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if not type(ctx_products) is set and not type(ctx_products) is list:
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print("Contexts set (context products) must be of type set or list")
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if not self.is_valid_rs_set(ctx_reactants):
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raise RuntimeError("one of the entities in the reactants set is unknown (undefined)!")
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if not self.is_valid_rs_set(ctx_inhibitors):
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raise RuntimeError("one of the entities in the inhibitors set is unknown (undefined)!")
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if not self.is_valid_rs_set(ctx_products):
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raise RuntimeError("one of the entities in the context set is unknown (undefined)!")
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if not self.is_state(src):
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raise RuntimeError("\"" + src + "\" is an unknown (undefined) state")
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if not self.is_state(dst):
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raise RuntimeError("\"" + dst + "\" is an unknown (undefined) state")
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src_id = self.get_state_id(src)
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dst_id = self.get_state_id(dst)
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act_id = self.get_action_id(action)
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r_ids = self.get_set_of_ids(ctx_reactants)
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i_ids = self.get_set_of_ids(ctx_inhibitors)
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p_ids = self.get_set_of_ids(ctx_products)
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self._transitions.append((src_id, act_id, (r_ids, i_ids, p_ids), dst_id))
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def show_transitions(self):
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print(C_MARK_INFO + " Context automaton transitions:")
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for src_id, act_id, reaction, dst_id in self._transitions:
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str_transition = self.get_state_name(src_id) + " --( "
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str_transition += self.get_action_name(act_id) + " | "
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str_transition += "( " + self.rsset2str(reaction[0]) + "," + self.rsset2str(reaction[1]) + "," + self.rsset2str(reaction[2]) + " )"
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str_transition += " )--> " + self.get_state_name(dst_id)
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print(" - " + str_transition)
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def add_action(self, action_name):
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if action_name not in self._actions:
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self._actions.append(action_name)
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else:
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print("\'%s\' already added. skipping..." % (action_name,))
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def get_action_id(self, action_name):
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try:
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return self._actions.index(action_name)
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except ValueError:
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print_error("Undefined context automaton action: " + repr(action_name))
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exit(1)
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def get_action_name(self, action_id):
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return self._actions[action_id]
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def show_actions(self):
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print(C_MARK_INFO + " Context automaton actions:")
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for act in self._actions:
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print(" - " + act)
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def show(self):
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self.show_states()
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self.show_actions()
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self.show_transitions()
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182
rs/reaction_system.py
Normal file
182
rs/reaction_system.py
Normal file
@@ -0,0 +1,182 @@
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from sys import exit
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from colour import *
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class ReactionSystem(object):
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def __init__(self):
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self.reactions = []
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self.background_set = []
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#self.reactions_by_agents = [] # each element is 'reactions_by_prod'
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self.reactions_by_prod = None
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## legacy:
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self.init_contexts = []
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self.context_entities = []
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def assume_not_in_bgset(self, name):
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if self.is_in_background_set(name):
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raise RuntimeError("The entity " + name + " is already on the list")
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def add_bg_set_entity(self, name):
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self.assume_not_in_bgset(name)
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self.background_set.append(name)
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def ensure_bg_set_entity(self, name):
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if not self.is_in_background_set(name):
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self.background_set.append(name)
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def add_bg_set_entities(self, elements):
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for e in elements:
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self.add_bg_set_entity(e)
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def is_in_background_set(self, entity):
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"""Checks if the given name is valid wrt the background set="""
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if entity in self.background_set:
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return True
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else:
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return False
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def get_entity_id(self, name):
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try:
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return self.background_set.index(name)
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except ValueError:
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print("Undefined background set entity: " + repr(name))
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exit(1)
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def get_state_ids(self, state):
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ids = []
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for entity in state:
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ids.append(self.get_entity_id(entity))
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return ids
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def get_entity_name(self, entity_id):
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"""Returns the string corresponding to the entity"""
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return self.background_set[entity_id]
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def add_reaction(self, R, I, P):
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"""Adds a reaction"""
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if R == [] or P == []:
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raise RuntimeError("No reactants or products defined")
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reactants = []
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for entity in R:
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reactants.append(self.get_entity_id(entity))
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inhibitors = []
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for entity in I:
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inhibitors.append(self.get_entity_id(entity))
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products = []
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for entity in P:
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products.append(self.get_entity_id(entity))
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self.reactions.append((reactants, inhibitors, products))
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def add_initial_context_set(self, context_set):
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if context_set == []:
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print("Empty context set is not allowed")
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raise
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integers = []
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for entity in context_set:
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if not entity in self.background_set:
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print("The entity", entity, "is not in the background set")
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raise
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else:
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integers.append(self.get_entity_id(entity))
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self.init_contexts.append(integers)
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def set_context_entities(self, entities):
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for entity in entities:
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entity_id = self.get_entity_id(entity)
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self.context_entities.append(entity_id)
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def entities_names_set_to_str(self, entities):
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s = ""
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for entity in entities:
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s += entity + ", "
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s = s[:-2]
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return s
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def entities_ids_set_to_str(self, entities):
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s = ""
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for entity in entities:
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s += self.get_entity_name(entity) + ", "
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s = s[:-2]
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return s
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def state_to_str(self, state):
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return self.entities_ids_set_to_str(state)
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def show_reactions(self, soft=False):
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print(C_MARK_INFO + " Reactions:")
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if soft and len(self.reactions) > 50:
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print(" -> there are more than 50 reactions (" + str(len(self.reactions)) + ")")
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else:
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print(" "*4 + "{0: ^35}{1: ^25}{2: ^15}".format("reactants"," inhibitors"," products"))
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for reaction in self.reactions:
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# print("\t( R={" + self.state_to_str(reaction[0]) + "}, I={" + self.state_to_str(reaction[1]) + "}, P={" + self.state_to_str(reaction[2]) + "} )")
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print(" " + "- {0: ^35}{1: ^25}{2: ^15}".format("{ " + self.state_to_str(reaction[0]) + " }",
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" { " + self.state_to_str(reaction[1]) + " }",
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" { " + self.state_to_str(reaction[2]) + " }"))
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def show_background_set(self):
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print(C_MARK_INFO + " Background set: {" + self.entities_names_set_to_str(self.background_set) + "}")
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def show_initial_contexts(self):
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if len(self.init_contexts) > 0:
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print(C_MARK_INFO + " Initial context sets:")
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for ctx in self.init_contexts:
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print(" - {" + self.entities_ids_set_to_str(ctx) + "}")
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def show_context_entities(self):
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if len(self.context_entities) > 0:
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print(C_MARK_INFO + " Context entities: " + self.entities_ids_set_to_str(self.context_entities))
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def show(self, soft=False):
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self.show_background_set()
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self.show_initial_contexts()
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self.show_reactions(soft)
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self.show_context_entities()
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def get_reactions_by_product(self):
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"""Sorts reactions by their products and returns a dictionary of products"""
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if self.reactions_by_prod != None:
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return self.reactions_by_prod
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producible_entities = set()
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for reaction in self.reactions:
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producible_entities = producible_entities.union(set(reaction[2]))
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reactions_by_prod = {}
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for prod_entity in producible_entities:
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reactions_by_prod[prod_entity] = []
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for reaction in self.reactions:
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if prod_entity in reaction[2]:
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reactions_by_prod[prod_entity].append([reaction[0],reaction[1]])
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# save in cache
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self.reactions_by_prod = reactions_by_prod
|
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return reactions_by_prod
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def sanity_check(self):
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"""Performs a sanity check on the defined reaction system"""
|
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|
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if self.reactions == []:
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print("No reactions defined")
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exit(1)
|
||||
|
||||
if self.background_set == []:
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print("Empty background set")
|
||||
exit(1)
|
||||
36
rs/reaction_system_with_automaton.py
Normal file
36
rs/reaction_system_with_automaton.py
Normal file
@@ -0,0 +1,36 @@
|
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from sys import exit
|
||||
from colour import *
|
||||
|
||||
from rs.reaction_system_with_concentrations import ReactionSystemWithConcentrations
|
||||
from rs.context_automaton_with_concentrations import ContextAutomatonWithConcentrations
|
||||
|
||||
class ReactionSystemWithAutomaton(object):
|
||||
|
||||
def __init__(self, reaction_system, context_automaton):
|
||||
self.rs = reaction_system
|
||||
self.ca = context_automaton
|
||||
|
||||
def show(self, soft=False):
|
||||
self.rs.show(soft)
|
||||
self.ca.show()
|
||||
|
||||
def is_with_concentrations(self):
|
||||
if not isinstance(self.rs, ReactionSystemWithConcentrations):
|
||||
return False
|
||||
if not isinstance(self.ca, ContextAutomatonWithConcentrations):
|
||||
return False
|
||||
return True
|
||||
|
||||
def sanity_check(self):
|
||||
pass
|
||||
|
||||
def get_ordinary_reaction_system_with_automaton(self):
|
||||
|
||||
if not self.is_with_concentrations():
|
||||
raise RuntimeError("Not RS/CA with concentrations")
|
||||
|
||||
ors = self.rs.get_reaction_system()
|
||||
oca = self.ca.get_automaton_with_flat_contexts(ors)
|
||||
|
||||
return ReactionSystemWithAutomaton(ors, oca)
|
||||
|
||||
414
rs/reaction_system_with_concentrations.py
Normal file
414
rs/reaction_system_with_concentrations.py
Normal file
@@ -0,0 +1,414 @@
|
||||
from sys import exit
|
||||
from colour import *
|
||||
|
||||
from rs.reaction_system import ReactionSystem
|
||||
|
||||
class ReactionSystemWithConcentrations(ReactionSystem):
|
||||
|
||||
def __init__(self):
|
||||
|
||||
self.reactions = []
|
||||
self.meta_reactions = dict()
|
||||
self.permanent_entities = dict()
|
||||
self.background_set = []
|
||||
self.context_entities = [] # legacy. to be removed
|
||||
self.reactions_by_prod = None
|
||||
self.max_concentration = 0
|
||||
self.max_conc_per_ent = dict()
|
||||
|
||||
def add_bg_set_entity(self, e):
|
||||
name = ""
|
||||
def_max_conc = -1
|
||||
if type(e) is tuple and len(e) == 2:
|
||||
name,def_max_conc = e
|
||||
elif type(e) is str:
|
||||
name = e
|
||||
print("\n\nWARNING: no maximal concentration level specified for:", e, "\n\n")
|
||||
else:
|
||||
raise RuntimeError("Bad entity type when adding background set element")
|
||||
|
||||
self.assume_not_in_bgset(name)
|
||||
self.background_set.append(name)
|
||||
|
||||
if def_max_conc != -1:
|
||||
ent_id = self.get_entity_id(name)
|
||||
self.max_conc_per_ent.setdefault(ent_id, 0)
|
||||
if self.max_conc_per_ent[ent_id] < def_max_conc:
|
||||
self.max_conc_per_ent[ent_id] = def_max_conc
|
||||
if self.max_concentration < def_max_conc:
|
||||
self.max_concentration = def_max_conc
|
||||
|
||||
def get_max_concentration_level(self, e):
|
||||
|
||||
if e in self.max_conc_per_ent:
|
||||
return self.max_conc_per_ent[e]
|
||||
else:
|
||||
return self.max_concentration
|
||||
|
||||
def is_valid_entity_with_concentration(self, e):
|
||||
"""Sanity check for entities with concentration"""
|
||||
|
||||
if type(e) is tuple:
|
||||
if len(e) == 2 and type(e[1]) is int:
|
||||
return True
|
||||
|
||||
if type(e) is list:
|
||||
if len(e) == 2 and type(e[1]) is int:
|
||||
return True
|
||||
|
||||
print("FATAL. Invalid entity+concentration:")
|
||||
print(e)
|
||||
exit(1)
|
||||
|
||||
return False
|
||||
|
||||
def get_state_ids(self, state):
|
||||
"""Returns entities of the given state without levels"""
|
||||
return [e for e,c in state]
|
||||
|
||||
def has_non_zero_concentration(self, elem):
|
||||
if elem[1] < 1:
|
||||
raise RuntimeError("Unexpected concentration level in state: " + str(elem))
|
||||
|
||||
def process_rip(self, R, I, P, ignore_empty_R=False):
|
||||
"""Chcecks concentration levels and converts entities names into their ids"""
|
||||
|
||||
if R == [] and not ignore_empty_R:
|
||||
raise RuntimeError("No reactants defined")
|
||||
|
||||
reactants = []
|
||||
for r in R:
|
||||
self.is_valid_entity_with_concentration(r)
|
||||
self.has_non_zero_concentration(r)
|
||||
entity,level = r
|
||||
reactants.append((self.get_entity_id(entity),level))
|
||||
if self.max_concentration < level:
|
||||
self.max_concentration = level
|
||||
inhibitors = []
|
||||
for i in I:
|
||||
self.is_valid_entity_with_concentration(i)
|
||||
self.has_non_zero_concentration(i)
|
||||
entity,level = i
|
||||
inhibitors.append((self.get_entity_id(entity),level))
|
||||
if self.max_concentration < level:
|
||||
self.max_concentration = level
|
||||
products = []
|
||||
for p in P:
|
||||
self.is_valid_entity_with_concentration(p)
|
||||
self.has_non_zero_concentration(p)
|
||||
entity,level = p
|
||||
products.append((self.get_entity_id(entity),level))
|
||||
|
||||
return reactants,inhibitors,products
|
||||
|
||||
def add_reaction(self, R, I, P):
|
||||
"""Adds a reaction"""
|
||||
|
||||
if P == []:
|
||||
raise RuntimeError("No products defined")
|
||||
reaction = self.process_rip(R,I,P)
|
||||
self.reactions.append(reaction)
|
||||
|
||||
def add_reaction_without_reactants(self, R, I, P):
|
||||
"""Adds a reaction"""
|
||||
|
||||
if P == []:
|
||||
raise RuntimeError("No products defined")
|
||||
reaction = self.process_rip(R,I,P,ignore_empty_R=True)
|
||||
self.reactions.append(reaction)
|
||||
|
||||
def add_reaction_inc(self, incr_entity, incrementer, R, I):
|
||||
"""Adds a macro/meta reaction for increasing the value of incr_entity"""
|
||||
|
||||
reactants,inhibitors,products = self.process_rip(R,I,[],ignore_empty_R=True)
|
||||
incr_entity_id = self.get_entity_id(incr_entity)
|
||||
self.meta_reactions.setdefault(incr_entity_id,[])
|
||||
self.meta_reactions[incr_entity_id].append(("inc", self.get_entity_id(incrementer), reactants, inhibitors))
|
||||
|
||||
def add_reaction_dec(self, decr_entity, decrementer, R, I):
|
||||
"""Adds a macro/meta reaction for decreasing the value of incr_entity"""
|
||||
|
||||
reactants,inhibitors,products = self.process_rip(R,I,[],ignore_empty_R=True)
|
||||
decr_entity_id = self.get_entity_id(decr_entity)
|
||||
self.meta_reactions.setdefault(decr_entity_id,[])
|
||||
self.meta_reactions[decr_entity_id].append(("dec", self.get_entity_id(decrementer), reactants, inhibitors))
|
||||
|
||||
def add_permanency(self, ent, I):
|
||||
"""Sets entity to be permanent unless it is inhibited"""
|
||||
|
||||
ent_id = self.get_entity_id(ent)
|
||||
|
||||
if ent_id in self.permanent_entities:
|
||||
raise RuntimeError("Permanency for {0} already defined.".format(ent))
|
||||
|
||||
inhibitors = self.process_rip([],I,[],ignore_empty_R=True)[1]
|
||||
self.permanent_entities[ent_id] = inhibitors
|
||||
|
||||
def set_context_entities(self, entities):
|
||||
raise NotImplementedError
|
||||
|
||||
def entities_names_set_to_str(self, entities):
|
||||
s = ""
|
||||
for entity in entities:
|
||||
s += entity + ", "
|
||||
s = s[:-2]
|
||||
return s
|
||||
|
||||
def entities_ids_set_to_str(self, entities):
|
||||
s = ""
|
||||
for entity in entities:
|
||||
s += self.get_entity_name(entity) + ", "
|
||||
s = s[:-2]
|
||||
return s
|
||||
|
||||
def state_to_str(self, state):
|
||||
s = ""
|
||||
for ent,level in state:
|
||||
s += self.get_entity_name(ent) + "=" + str(level) + ", "
|
||||
s = s[:-2]
|
||||
return s
|
||||
|
||||
def show_background_set(self):
|
||||
print(C_MARK_INFO + " Background set: {" + self.entities_names_set_to_str(self.background_set) + "}")
|
||||
|
||||
def show_meta_reactions(self):
|
||||
print(C_MARK_INFO + " Meta reactions:")
|
||||
for param_ent,reactions in self.meta_reactions.items():
|
||||
for r_type,command,reactants,inhibitors in reactions:
|
||||
if r_type == "inc" or r_type == "dec":
|
||||
print(" - [ Type=" + repr(r_type) + " Operand=( " + self.get_entity_name(param_ent) + \
|
||||
" ) Command=( " + self.get_entity_name(command) + " ) ] -- ( R={" + self.state_to_str(reactants) + "}, I={" + self.state_to_str(inhibitors) + "} )")
|
||||
else:
|
||||
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
|
||||
|
||||
def show_max_concentrations(self):
|
||||
print(C_MARK_INFO + " Maximal allowed concentration levels (for optimized translation to RS):")
|
||||
for e,max_conc in self.max_conc_per_ent.items():
|
||||
print(" - {0:^20} = {1:<6}".format(self.get_entity_name(e),max_conc))
|
||||
|
||||
def show_permanent_entities(self):
|
||||
print(C_MARK_INFO + " Permanent entities:")
|
||||
for e,inhibitors in self.permanent_entities.items():
|
||||
print(" - {0:^20}{1:<6}".format(self.get_entity_name(e) + ": ","I={" + self.state_to_str(inhibitors) + "}"))
|
||||
|
||||
def show(self, soft=False):
|
||||
self.show_background_set()
|
||||
self.show_reactions(soft)
|
||||
self.show_permanent_entities()
|
||||
self.show_meta_reactions()
|
||||
self.show_max_concentrations()
|
||||
|
||||
def get_reactions_by_product(self):
|
||||
"""Sorts reactions by their products and returns a dictionary of products"""
|
||||
|
||||
if self.reactions_by_prod != None:
|
||||
return self.reactions_by_prod
|
||||
|
||||
producible_entities = set()
|
||||
|
||||
for reaction in self.reactions:
|
||||
product_entities = [e for e,c in reaction[2]]
|
||||
producible_entities = producible_entities.union(set(product_entities))
|
||||
|
||||
reactions_by_prod = {}
|
||||
|
||||
for p_e in producible_entities:
|
||||
reactions_by_prod[p_e] = []
|
||||
rcts_for_p_e = reactions_by_prod[p_e]
|
||||
|
||||
for r in self.reactions:
|
||||
product_entities = [e for e,c in r[2]]
|
||||
|
||||
if p_e in product_entities:
|
||||
reactants = r[0]
|
||||
inhibitors = r[1]
|
||||
products = [(e,c) for e,c in r[2] if e == p_e]
|
||||
|
||||
prod_conc = products[0][1]
|
||||
insert_place = None
|
||||
|
||||
# we need to order the reactions w.r.t. the concentration levels produced (increasing order)
|
||||
for i in range(0,len(rcts_for_p_e)):
|
||||
|
||||
checked_conc = rcts_for_p_e[i][2][0][1]
|
||||
if prod_conc <= checked_conc:
|
||||
insert_place = i
|
||||
break
|
||||
|
||||
if insert_place == None: # empty or the is only one element which is smaller than the element being added
|
||||
rcts_for_p_e.append((reactants, inhibitors, products)) # we append (to the end)
|
||||
else:
|
||||
rcts_for_p_e.insert(insert_place,(reactants, inhibitors, products))
|
||||
|
||||
|
||||
# save in cache
|
||||
self.reactions_by_prod = reactions_by_prod
|
||||
|
||||
return reactions_by_prod
|
||||
|
||||
def get_reaction_system(self):
|
||||
|
||||
rs = ReactionSystem()
|
||||
|
||||
for reactants,inhibitors,products in self.reactions:
|
||||
|
||||
new_reactants = []
|
||||
new_inhibitors = []
|
||||
new_products = []
|
||||
|
||||
for ent,conc in reactants:
|
||||
n = self.get_entity_name(ent) + "#" + str(conc)
|
||||
rs.ensure_bg_set_entity(n)
|
||||
new_reactants.append(n)
|
||||
|
||||
for ent,conc in inhibitors:
|
||||
n = self.get_entity_name(ent) + "#" + str(conc)
|
||||
rs.ensure_bg_set_entity(n)
|
||||
new_inhibitors.append(n)
|
||||
|
||||
for ent,conc in products:
|
||||
for i in range(1,conc+1):
|
||||
n = self.get_entity_name(ent) + "#" + str(i)
|
||||
rs.ensure_bg_set_entity(n)
|
||||
new_products.append(n)
|
||||
|
||||
rs.add_reaction(new_reactants,new_inhibitors,new_products)
|
||||
|
||||
for param_ent,reactions in self.meta_reactions.items():
|
||||
for r_type,command,reactants,inhibitors in reactions:
|
||||
|
||||
param_ent_name = self.get_entity_name(param_ent)
|
||||
|
||||
new_reactants = []
|
||||
new_inhibitors = []
|
||||
|
||||
for ent,conc in reactants:
|
||||
n = self.get_entity_name(ent) + "#" + str(conc)
|
||||
rs.ensure_bg_set_entity(n)
|
||||
new_reactants.append(n)
|
||||
|
||||
for ent,conc in inhibitors:
|
||||
n = self.get_entity_name(ent) + "#" + str(conc)
|
||||
rs.ensure_bg_set_entity(n)
|
||||
new_inhibitors.append(n)
|
||||
|
||||
max_cmd_c = self.max_concentration
|
||||
if command in self.max_conc_per_ent:
|
||||
max_cmd_c = self.max_conc_per_ent[command]
|
||||
else:
|
||||
print("WARNING:\n\tThere is no maximal concentration level defined for " + self.get_entity_name(command))
|
||||
print("\tThis is a very bad idea -- expect degraded performance\n")
|
||||
|
||||
for l in range(1,max_cmd_c+1):
|
||||
|
||||
cmd_ent = self.get_entity_name(command) + "#" + str(l)
|
||||
rs.ensure_bg_set_entity(cmd_ent)
|
||||
|
||||
if r_type == "inc":
|
||||
|
||||
# pre_conc -- predecessor concentration
|
||||
# succ_conc -- successor concentration concentration
|
||||
|
||||
for i in range(1,self.max_concentration):
|
||||
pre_conc = param_ent_name + "#" + str(i)
|
||||
rs.ensure_bg_set_entity(pre_conc)
|
||||
new_products = []
|
||||
succ_value = i+l
|
||||
for j in range(1,succ_value+1):
|
||||
if j > self.max_concentration: break
|
||||
new_p = param_ent_name + "#" + str(j)
|
||||
rs.ensure_bg_set_entity(new_p)
|
||||
new_products.append(new_p)
|
||||
if new_products != []:
|
||||
rs.add_reaction(set(new_reactants + [pre_conc,cmd_ent]), set(new_inhibitors), set(new_products))
|
||||
|
||||
elif r_type == "dec":
|
||||
for i in range(1,self.max_concentration+1):
|
||||
pre_conc = param_ent_name + "#" + str(i)
|
||||
rs.ensure_bg_set_entity(pre_conc)
|
||||
new_products = []
|
||||
succ_value = i-l
|
||||
for j in range(1,succ_value+1):
|
||||
if j > self.max_concentration: break
|
||||
new_p = param_ent_name + "#" + str(j)
|
||||
rs.ensure_bg_set_entity(new_p)
|
||||
new_products.append(new_p)
|
||||
if new_products != []:
|
||||
rs.add_reaction(set(new_reactants + [pre_conc,cmd_ent]), set(new_inhibitors), set(new_products))
|
||||
|
||||
else:
|
||||
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
|
||||
|
||||
for ent,inhibitors in self.permanent_entities.items():
|
||||
|
||||
max_c = self.max_concentration
|
||||
if ent in self.max_conc_per_ent:
|
||||
max_c = self.max_conc_per_ent[ent]
|
||||
else:
|
||||
print("WARNING:\n\tThere is no maximal concentration level defined for " + self.get_entity_name(ent))
|
||||
print("\tThis is a very bad idea -- expect degraded performance\n")
|
||||
|
||||
def e_value(i):
|
||||
return self.get_entity_name(ent) + "#" + str(i)
|
||||
|
||||
for value in range(1,max_c+1):
|
||||
|
||||
new_reactants = []
|
||||
new_inhibitors = []
|
||||
new_products = []
|
||||
|
||||
new_reactants = [e_value(value)]
|
||||
|
||||
for e_inh,conc in inhibitors:
|
||||
n = self.get_entity_name(e_inh) + "#" + str(conc)
|
||||
rs.ensure_bg_set_entity(n)
|
||||
new_inhibitors.append(n)
|
||||
|
||||
for i in range(1,value+1):
|
||||
new_products.append(e_value(i))
|
||||
|
||||
rs.add_reaction(new_reactants,new_inhibitors,new_products)
|
||||
|
||||
return rs
|
||||
|
||||
|
||||
class ReactionSystemWithAutomaton(object):
|
||||
|
||||
def __init__(self, reaction_system, context_automaton):
|
||||
self.rs = reaction_system
|
||||
self.ca = context_automaton
|
||||
|
||||
def show(self, soft=False):
|
||||
self.rs.show(soft)
|
||||
self.ca.show()
|
||||
|
||||
def is_with_concentrations(self):
|
||||
if not isinstance(self.rs, ReactionSystemWithConcentrations):
|
||||
return False
|
||||
if not isinstance(self.ca, ContextAutomatonWithConcentrations):
|
||||
return False
|
||||
return True
|
||||
|
||||
def sanity_check(self):
|
||||
pass
|
||||
|
||||
def get_ordinary_reaction_system_with_automaton(self):
|
||||
|
||||
if not self.is_with_concentrations():
|
||||
raise RuntimeError("Not RS/CA with concentrations")
|
||||
|
||||
ors = self.rs.get_reaction_system()
|
||||
oca = self.ca.get_automaton_with_flat_contexts(ors)
|
||||
|
||||
return ReactionSystemWithAutomaton(ors, oca)
|
||||
|
||||
|
||||
# class ReactionSystemWithConcentrationWithAutomaton(ReactionSystemWithAutomaton):
|
||||
#
|
||||
# def __init__(self, reaction_system, context_automaton):
|
||||
# self.rs = reaction_system
|
||||
# self.ca = context_automaton
|
||||
#
|
||||
# def show(self, soft=False):
|
||||
# self.rs.show(soft)
|
||||
# self.ca.show()
|
||||
Reference in New Issue
Block a user