/usr/share/cain/state/convert.py is in cain 1.9-8.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | """Convert the state classes to simulation classes."""
# If we are running the unit tests.
if __name__ == '__main__':
import sys
sys.path.insert(1, '..')
from simulation.Model import Model
from simulation.Species import Species
from simulation.SpeciesReference import SpeciesReference
from simulation.Reaction import Reaction
from simulation.TimeEvent import TimeEvent
from simulation.TriggerEvent import TriggerEvent
from simulation.Parameter import Parameter
from simulation.TimeSeriesUniform import TimeSeriesUniform
# CONTINUE: Check for errors.
def makeModel(model, method):
"""Make a simulation.Model from a state.Model and a state.Method."""
m = Model(method.startTime)
for key in model.species:
m.species[key] = Species(model.species[key].initialAmountValue)
for r in model.reactions:
reactants = [SpeciesReference(x.species, x.stoichiometry) for x in
r.reactants]
products = [SpeciesReference(x.species, x.stoichiometry) for x in
r.products]
if r.massAction:
propensity = '(' + r.propensity + ')'
denominator = 1.0
for x in reactants:
propensity += '*%s' % x.species
for i in range(1, x.stoichiometry):
propensity += '*(%s-%d)' % (x.species, i)
for i in range(1, x.stoichiometry + 1):
denominator *= i
if denominator != 1:
propensity += '*' + repr(1./denominator)
else:
propensity = r.propensity
m.reactions[r.id] = Reaction(m, reactants, products, propensity)
for x in model.timeEvents:
m.timeEvents[x.id] = TimeEvent(m, x.assignments, eval(x.times))
for x in model.triggerEvents:
m.triggerEvents[x.id] = TriggerEvent(m, x.assignments, x.trigger,
x.delay,
x.useValuesFromTriggerTime)
# Parameters and compartments are grouped together.
for key in model.compartments:
initialValue = model.compartments[key].value
if not initialValue:
initialValue = 1.
m.parameters[key] = Parameter(initialValue)
for key in model.parameters:
m.parameters[key] = Parameter(model.parameters[key].value)
return m
def makeTimeSeriesUniform(solver, model, output):
"""Make a simulation.TimeSeriesUniform from a solver, a state.Model, and a
state.TimeSeriesFrames."""
recordedSpecies = [model.speciesIdentifiers[index] for index in
output.recordedSpecies]
recordedReactions = [model.reactions[index].id for index in
output.recordedReactions]
return TimeSeriesUniform(solver, recordedSpecies, recordedReactions,
output.frameTimes)
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