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Updated Ragtimer Format #5

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Updated Ragtimer Format #5

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a6acf15
First edit for new ragtimer format
ifndefJOSH Jan 12, 2024
f933781
Merge pull request #4 from fluentverification/main
ifndefJOSH Jan 25, 2024
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16 changes: 14 additions & 2 deletions src/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,15 +39,27 @@ def create_transition(transition_line, species_idxes):
always_enabled = False
is_consumer = False
for reactant in reactants:
rcount = 1
if reactant == "0":
always_enabled = True
break
transition_vector[species_idxes[reactant]] -= 1
elif '*' in reactant:
reactant, rcount_str = reactant.split("*")
reactant = reactant.strip()
# TODO: better error handling for malformed line
rcount = int(rcount_str)
transition_vector[species_idxes[reactant]] -= rcount
for product in products:
pcount = 1
if product == "0":
is_consumer = True
break
transition_vector[species_idxes[product]] += 1
elif '*' in product:
product, pcount_str = product.split("*")
product = product.strip()
# TODO: better error handling for malformed line
pcount = int(pcount_str)
transition_vector[species_idxes[product]] += pcount
# Is 1.0 iff is reactant
rate_mul_vector = np.array([float(elem < 0) for elem in transition_vector])
# The rate, from rate constant k and reactants A, B, is k * A^count(A) * B^count(B)
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