def rxn(self, string, k = 1, rtype = 'condensed'):
""" Dummy function for generating reactions between formal species """
reactants, products = string.split('->')
reactants = reactants.split('+')
products = products.split('+')
reactants = [self.cplx(x) for x in reactants]
products = [self.cplx(x) for x in products]
rxn = PepperReaction(reactants, products, rtype.strip())
rxn.rate_constant = k
self.reactions.add(rxn)
def test_condense_simple(self):
complexes, reactions = read_pil("""
# File generated by peppercorn-v0.5.0
# Domain Specifications
length d1 = 15
length t0 = 5
# Resting-set Complexes
c1 = t0 d1
c2 = d1( + ) t0*
c4 = t0( d1( + ) )
c5 = d1
# Transient Complexes
c3 = t0( d1 + d1( + ) )
# Detailed Reactions
reaction [bind21 = 100 /M/s ] c1 + c2 -> c3
reaction [open = 50 /s ] c3 -> c1 + c2
reaction [branch-3way = 50 /s ] c3 -> c4 + c5
""")
# (rs1) c1 c4 (rs3)
# \ /
# <---> c3 ---->
# / \
# (rs2) c2 c5 (rs4)
enum = Enumerator(complexes.values(), reactions)
enum.enumerate()
enum.condense()
for con in enum.condensed_reactions:
assert con.rate_constant[0] == 50
del enum
# old interface ...
c1 = PepperMacrostate([complexes['c1']])
c2 = PepperMacrostate([complexes['c2']])
c4 = PepperMacrostate([complexes['c4']])
c5 = PepperMacrostate([complexes['c5']])
cond_react = PepperReaction([c1, c2], [c4, c5], 'condensed')
cond_react.rate_constant = 20, None
enum = Enumerator(complexes.values(), reactions)
enum.dry_run()
enumRG = PepperCondensation(enum)
enumRG.condense()
for con in enumRG.condensed_reactions:
assert con.rate_constant[0] == 20