"""
Utility classes for computing bifurcations.
"""
from __future__ import print_function, division, absolute_import
import os.path
from rrplugins import Plugin
from roadrunner import RoadRunner
[docs]def bifurcation(model, parameter, lowerBound, upperBound, maxPoints=5000, scanPositive=True):
"""Plot a bifurcation diagram.
:param model: A path to an SBML or Antimony file, or raw SBML or Antimony string.
:param parameter: The principal continuation parameter.
:param lowerBound: The lower bound of the continuation.
:param upperBound: The upper bound of the continuation.
:param maxPoints: The maximum number of points.
:param scanPositive: Scan from lower to upper bound (direction is reversed if false).
"""
if isinstance(model, RoadRunner):
sbml = model.getSBML()
elif os.path.exists(model) and os.path.isfile(model):
# it's a file path
if os.path.splitext(model)[1] == '.sb':
# it's an Antimony file
with open(model) as f:
sbml = antimonyConverter.antimonyToSBML(f.read())
elif os.path.splitext(model)[1] == '.txt':
raise RuntimeError('File ending in ".txt" is ambiguous - pass an SBML file (.xml) or an Antimony file (.sb).')
else:
with open(model) as f:
sbml = f.read()
else:
# check if it's Antimony source
try:
sbml = antimonyConverter.antimonyToSBML(model)
except:
# it better be SBML
import tesbml as libsbml
# this will throw if it's not SBML
libsbml.readSBML(model)
auto = Plugin('tel_auto2000')
# Set SBML source
auto.setProperty('SBML', sbml)
# Set parameters
auto.setProperty('ScanDirection', 'Positive' if scanPositive else 'Negative')
auto.setProperty('PrincipalContinuationParameter', parameter)
auto.setProperty('PCPLowerBound', lowerBound)
auto.setProperty('PCPUpperBound', upperBound)
# Set maximum numberof points
auto.setProperty('NMX', maxPoints)
# execute the plugin
auto.execute()
# plot Bifurcation diagram
pts = auto.BifurcationPoints
lbls = auto.BifurcationLabels
biData = auto.BifurcationData
return pts, lbls, biData
[docs]def plotBifurcation(model, parameter, lowerBound, upperBound, maxPoints=5000, scanPositive=True):
"""Plot a bifurcation diagram.
:param model: A path to an SBML or Antimony file, or raw SBML or Antimony string.
:param parameter: The principal continuation parameter.
:param lowerBound: The lower bound of the continuation.
:param upperBound: The upper bound of the continuation.
:param maxPoints: The maximum number of points.
:param scanPositive: Scan from lower to upper bound (direction is reversed if false).
"""
pts, lbls, biData = bifurcation(model, parameter, lowerBound, upperBound, maxPoints, scanPositive)
biData.plotBifurcationDiagram(pts, lbls)