artur/reactics
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Translation RSC->RS for meta-reactions.

Browse Source
This commit is contained in:
Artur Meski
2016-02-21 14:55:48 +01:00
parent 060f5dc1f5
commit b21a0cee48
3 changed files with 82 additions and 40 deletions
Download Patch File Download Diff File Expand all files Collapse all files

42
rctsys.py
View File

@@ -484,7 +484,11 @@ class ReactionSystemWithConcentrations(ReactionSystem):
print("[*] Meta reactions:")
for incr_ent,reactions in self.meta_reactions.items():
for r_type,reactants,inhibitors in reactions:
print("\t - [ Type=" + repr(r_type) + " Parameter=( " + self.get_entity_name(incr_ent) + " ) ] -- ( R={" + self.state_to_str(reactants) + "}, \tI={" + self.state_to_str(inhibitors) + "} )")
if r_type == "inc":
print("\t - [ Type=" + repr(r_type) + " Parameter=( " + self.get_entity_name(incr_ent) + \
" ) ] -- ( R={" + self.state_to_str(reactants) + "}, \tI={" + self.state_to_str(inhibitors) + "} )")
else:
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
def show(self, soft=False):
self.show_background_set()
@@ -548,6 +552,42 @@ class ReactionSystemWithConcentrations(ReactionSystem):
rs.add_reaction(new_reactants,new_inhibitors,new_products)
for incr_ent,reactions in self.meta_reactions.items():
for r_type,reactants,inhibitors in reactions:
if r_type == "inc":
incr_ent_name = self.get_entity_name(incr_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)
pre_conc = incr_ent_name + "_" + str(1)
rs.ensure_bg_set_entity(pre_conc)
for i in range(1,self.max_concentration):
succ_conc = incr_ent_name + "_" + str(i+1)
rs.ensure_bg_set_entity(succ_conc)
new_products = []
for j in range(1,i+1):
new_p = incr_ent_name + "_" + str(j)
rs.ensure_bg_set_entity(new_p)
new_products.append(new_p)
new_products.append(succ_conc)
rs.add_reaction(new_reactants + [pre_conc], new_inhibitors, new_products)
pre_conc = succ_conc
else:
raise RuntimeError("Unknown meta-reaction type: " + repr(r_type))
return rs