def test_compare_equations_fail(self):
#Typo in Reaction 10 where it generates PX instead of X
antimony_str_fail = '''
// Reactions:
Reaction1: X => ; kd_mRNA*X;
Reaction2: Y => ; kd_mRNA*Y;
Reaction3: Z => ; kd_mRNA*Z;
Reaction4: => PX; k_tl*X;
Reaction5: => PY; k_tl*Y;
Reaction6: => PZ; k_tl*Z;
Reaction7: PX => ; kd_prot*PX;
Reaction8: PY => ; kd_prot*PY;
Reaction9: PZ => ; kd_prot*PZ;
Reaction10: => PX; a0_tr + a_tr*KM^n/(KM^n + PZ^n);
Reaction11: => Y; a0_tr + a_tr*KM^n/(KM^n + PX^n);
Reaction12: => Z; a0_tr + a_tr*KM^n/(KM^n + PY^n);
'''
reaction_test = onlinegen.gen_reactions(antimony_str_fail)
eqn_clean = ['']
before = len(reaction_test)
after = 0
while before != after:
before = len(reaction_test)
reaction_test = onlinegen.clean_reactions(reaction_test)
after = len(reaction_test)
for eqn in reaction_test:
eqn = onlinegen.eqnreplace(eqn)
eqn_clean.append(eqn)
assert eqn_clean == eqn_sample, 'Reactions not sorted properly'
return reaction_test, eqn_clean
def test_compare_equations(self):
#Tests whether reactions pertaining to the same species are combined
global eqn_sample
antimony_str_test = '''
// Reactions:
Reaction1: X => ; kd_mRNA*X;
Reaction2: Y => ; kd_mRNA*Y;
Reaction3: Z => ; kd_mRNA*Z;
Reaction4: => PX; k_tl*X;
Reaction5: => PY; k_tl*Y;
Reaction6: => PZ; k_tl*Z;
Reaction7: PX => ; kd_prot*PX;
Reaction8: PY => ; kd_prot*PY;
Reaction9: PZ => ; kd_prot*PZ;
Reaction10: => X; a0_tr + a_tr*KM^n/(KM^n + PZ^n);
Reaction11: => Y; a0_tr + a_tr*KM^n/(KM^n + PX^n);
Reaction12: => Z; a0_tr + a_tr*KM^n/(KM^n + PY^n);
'''
reaction_test = onlinegen.gen_reactions(antimony_str_test)
print(reaction_test)
eqn_clean = ['']
before = len(reaction_test)
after = 0
while before != after:
before = len(reaction_test)
reaction_test = onlinegen.clean_reactions(reaction_test)
after = len(reaction_test)
for eqn in reaction_test:
eqn = onlinegen.eqnreplace(eqn)
eqn_clean.append(eqn)
assert eqn_clean == eqn_sample, 'Reactions not sorted properly'