def addSBMLToCell(self,_modelFile,_modelName='',_cell=None,_stepSize=1.0,_initialConditions={},_coreModelName='',_modelPathNormalized='',_options=None):
'''
_options is a dictionary with the following keys:
absolute - determines absolute tolerance default 1e-10
relative - determines relative tolerance default 1e-5
stiff - determines if using stiff solver or not default False
'''
import os
import sys
import CompuCell
coreModelName=_modelName
if coreModelName=='':
coreModelName,ext=os.path.splitext(os.path.basename(_modelFile))
modelPathNormalized=self.normalizePath(_modelFile)
dict_attrib = CompuCell.getPyAttrib(_cell)
sbmlDict={}
if dict_attrib.has_key('SBMLSolver'):
sbmlDict=dict_attrib['SBMLSolver']
else:
dict_attrib['SBMLSolver']=sbmlDict
from RoadRunnerPy import RoadRunnerPy
rr=RoadRunnerPy(_path=_modelFile)
#setting stepSize
rr.stepSize=_stepSize
#loading SBML and LLVM-ing it
rr.loadSBML(_externalPath=modelPathNormalized)
#storing rr instance in the cell dictionary
sbmlDict[coreModelName]=rr
#setting initial conditions - this has to be done after loadingSBML
for name,value in _initialConditions.iteritems():
try: # have to catch exceptions in case initial conditions contain "unsettable" entries such as reaction rate etc...
rr.model[name]=value
except :
pass
# we are turning off dynamic python properties because rr is not used in the interactive mode.
# try:
# rr.options.disablePythonDynamicProperties = True
# except:
# pass
# setting output results array size
rr.selections=[] # by default we do not request any output array at each intergration step
if _options:
for name , value in _options.iteritems():
# setattr(rr.simulateOptions,name,value)
# print ' 1 name , value=',(name , value)
# if name=='steps':
# print ' 1 name , value=',(name , value)
# continue
try:
setattr(rr.getIntegrator(),name,value)
except AttributeError:
setattr(rr.getIntegrator(),self.option_name_dict[name],value)
else: # check for global options
globalOptions=self.getSBMLGlobalOptions()
if globalOptions:
for name , value in globalOptions.iteritems():
# print ' 2 name , value=',(name , value)
# print 'name=',name,' value=',value
# if name=='steps':
# continue
try:
setattr(rr.getIntegrator(),name,value)
except (AttributeError,ValueError) as e:
setattr(rr.getIntegrator(),self.option_name_dict[name],value)
# pass
# setting output results array size
rr.selections=[] # by default we do not request any output array at each intergration step
# in case user passes simulate options we set the here
if _options:
for name , value in _options.iteritems():
# setattr(rr.simulateOptions,name,value)
# print ' 1 name , value=',(name , value)
# if name=='steps':
# print ' 1 name , value=',(name , value)
# continue
try:
setattr(rr.getIntegrator(),name,value)
except (AttributeError,ValueError) as e:
setattr(rr.getIntegrator(),self.option_name_dict[name],value)
else: # check for global options
globalOptions=self.getSBMLGlobalOptions()
if globalOptions:
for name , value in globalOptions.iteritems():
# print ' 2 name , value=',(name , value)
# print 'name=',name,' value=',value
# if name=='steps':
# continue
try:
setattr(rr.getIntegrator(),name,value)
except (AttributeError,ValueError) as e:
setattr(rr.getIntegrator(),self.option_name_dict[name],value)
# setattr(rr.simulateOptions,name,value)
for name,value in _initialConditions.iteritems():
rr.model[name]=value
try:
rr.options.disablePythonDynamicProperties = True
except:
pass
# setting output results array size
rr.selections=[] # by default we do not request any output array at each intergration step
# in case user passes simulate options we set the here
if _options:
for name , value in _options.iteritems():
if name == "relative":
rr.getIntegrator().setValue('relative_tolerance',value)
elif name == "absolute":
rr.getIntegrator().setValue('absolute_tolerance',value)
elif name == "stiff":
rr.getIntegrator().setValue('stiff',value)
else:
setattr(rr.simulateOptions,name,value)
else: # check for global options
globalOptions=self.getSBMLGlobalOptions()
if globalOptions:
for name , value in globalOptions.iteritems():
if name == "relative":
rr.getIntegrator().setValue('relative_tolerance',value)
elif name == "absolute":
rr.getIntegrator().setValue('absolute_tolerance',value)
def addSBMLToCell(self, _modelFile='', _modelName='', _cell=None, _stepSize=1.0, _initialConditions={},
_coreModelName='', _modelPathNormalized='', _options=None, _currentStateSBML=None):
"""
Attaches RoadRunner SBML solver to a particular cell. The sbml solver is stored as an element
of the cell's dictionary - cell.dict['SBMLSolver'][_modelName]. The function has a dual operation mode.
When user provides _currentStateSBML, _cell _modelName, _stepSize the addSBMLToCell function creates a clone
of a solver whose state is described by the _currentStateSBML . If _currentStateSBML is None then the new SBML solver
is being created, SBML file (_modelFile) loaded and initial conditions are applied. It is important to always set
_stepSize to make sure that after calling timestep() fcn the solver advances appropriate delta time
:param _modelFile {str}: name of the SBML file - can be relative path (e.g. Simulation/file.sbml) or absolute path
:param _modelName {str}: name of the model - this is a label used to store mode in the cell.dict['SBMLSolver'] dictionary
:param _cell {CellG object}: cc3d cell object
:param _stepSize {float}: time step- determines how much in "real" time units timestep() fcn advances SBML solver
:param _initialConditions {dict}: initial conditions dictionary
:param _coreModelName {str}: deprecated, kept for backward compatibility reasons
:param _modelPathNormalized {str}: deprecated, kept for backward compatibility reasons:
:param _options {dict}: dictionary that currently only defines what type of ODE solver to choose. In the newer versions of RR this might be not necessary. The keys that are supported are the following:
absolute - determines absolute tolerance default 1e-10
relative - determines relative tolerance default 1e-5
stiff - determines if using stiff solver or not default False
:param _currentStateSBML {str}: string representation of the SBML representing current state of the solver.
:return: None
"""
import CompuCell
coreModelName = _modelName
if coreModelName == '':
coreModelName, ext = os.path.splitext(os.path.basename(_modelFile))
if not _modelFile:
warnings.warn('\n\n\n _modelFile argument not provided to addSBMLToCell. This will prevent proper restart of the simulation'
'You may ignore this warning if you are not serializing simulation for future restarts', RuntimeWarning)
modelPathNormalized = self.normalizePath(_modelFile)
dict_attrib = CompuCell.getPyAttrib(_cell)
sbmlDict = {}
if dict_attrib.has_key('SBMLSolver'):
sbmlDict = dict_attrib['SBMLSolver']
else:
dict_attrib['SBMLSolver'] = sbmlDict
from RoadRunnerPy import RoadRunnerPy
if _currentStateSBML is None:
rr = RoadRunnerPy(_path=_modelFile)
# setting stepSize
rr.stepSize = _stepSize
# loading SBML and LLVM-ing it
rr.loadSBML(_externalPath=modelPathNormalized)
else:
rr = RoadRunnerPy(sbml=_currentStateSBML)
# setting stepSize
rr.stepSize = _stepSize
# setting up paths - IMPORTANT FOR RESTARTING
rr.path = _modelFile
if os.path.exists(modelPathNormalized):
rr.absPath = modelPathNormalized
# storing rr instance in the cell dictionary
sbmlDict[coreModelName] = rr
# setting initial conditions - this has to be done after loadingSBML
for name, value in _initialConditions.iteritems():
try: # have to catch exceptions in case initial conditions contain "unsettable" entries such as reaction rate etc...
rr.model[name] = value
except:
pass
# we are turning off dynamic python properties because rr is not used in the interactive mode.
# rr.options.disablePythonDynamicProperties = True
# setting output results array size
rr.selections = [] # by default we do not request any output array at each intergration step
if _options:
for name, value in _options.iteritems():
try:
setattr(rr.getIntegrator(), name, value)
except AttributeError:
setattr(rr.getIntegrator(), self.option_name_dict[name], value)
else:
# check for global options
globalOptions = self.getSBMLGlobalOptions()
if globalOptions:
for name, value in globalOptions.iteritems():
try:
setattr(rr.getIntegrator(), name, value)
except (AttributeError, ValueError) as e:
setattr(rr.getIntegrator(), self.option_name_dict[name], value)
CompuCellSetup.freeFloatingSBMLSimulator[_modelName] = rr
# setting initial conditions - this has to be done after loadingSBML
for name, value in _initialConditions.iteritems():
rr.model[name] = value
# rr.options.disablePythonDynamicProperties = True
# setting output results array size
rr.selections = [] # by default we do not request any output array at each intergration step
# in case user passes simulate options we set the here
if _options:
for name, value in _options.iteritems():
try:
setattr(rr.getIntegrator(), name, value)
except (AttributeError, ValueError) as e:
setattr(rr.getIntegrator(), self.option_name_dict[name], value)
else:
# check for global options
globalOptions = self.getSBMLGlobalOptions()
if globalOptions:
for name, value in globalOptions.iteritems():
# print ' 2 name , value=',(name , value)
# print 'name=',name,' value=',value
# if name=='steps':
# continue
try:
setattr(rr.getIntegrator(), name, value)
except (AttributeError, ValueError) as e:
def addSBMLToCell(self,
_modelFile,
_modelName='',
_cell=None,
_stepSize=1.0,
_initialConditions={},
_coreModelName='',
_modelPathNormalized='',
_options=None):
'''
_options is a dictionary with the following keys:
absolute - determines absolute tolerance default 1e-10
relative - determines relative tolerance default 1e-5
stiff - determines if using stiff solver or not default False
'''
import os
import sys
import CompuCell
coreModelName = _modelName
if coreModelName == '':
coreModelName, ext = os.path.splitext(os.path.basename(_modelFile))
modelPathNormalized = self.normalizePath(_modelFile)
dict_attrib = CompuCell.getPyAttrib(_cell)
sbmlDict = {}
if dict_attrib.has_key('SBMLSolver'):
sbmlDict = dict_attrib['SBMLSolver']
else:
dict_attrib['SBMLSolver'] = sbmlDict
from RoadRunnerPy import RoadRunnerPy
rr = RoadRunnerPy(_path=_modelFile)
#setting stepSize
rr.stepSize = _stepSize
#loading SBML and LLVM-ing it
rr.loadSBML(_externalPath=modelPathNormalized)
#storing rr instance in the cell dictionary
sbmlDict[coreModelName] = rr
#setting initial conditions - this has to be done after loadingSBML
for name, value in _initialConditions.iteritems():
try: # have to catch exceptions in case initial conditions contain "unsettable" entries such as reaction rate etc...
rr.model[name] = value
except:
pass
# we are turning off dynamic python properties because rr is not used in the interactive mode.
# try:
# rr.options.disablePythonDynamicProperties = True
# except:
# pass
# setting output results array size
rr.selections = [
] # by default we do not request any output array at each intergration step
if _options:
for name, value in _options.iteritems():
# setattr(rr.simulateOptions,name,value)
# print ' 1 name , value=',(name , value)
# if name=='steps':
# print ' 1 name , value=',(name , value)
# continue
try:
setattr(rr.getIntegrator(), name, value)
except AttributeError:
setattr(rr.getIntegrator(), self.option_name_dict[name],
value)
else: # check for global options
globalOptions = self.getSBMLGlobalOptions()
if globalOptions:
for name, value in globalOptions.iteritems():
# print ' 2 name , value=',(name , value)
# print 'name=',name,' value=',value
# if name=='steps':
# continue
try:
setattr(rr.getIntegrator(), name, value)
except (AttributeError, ValueError) as e:
setattr(rr.getIntegrator(),
self.option_name_dict[name], value)
