def __init__(self, time_units='second', extent_units='mole', \
sub_units='mole', level=3, version=1):
if level == 1:
raise SystemExit('Error: SimpleSBML does not support SBML level 1')
try:
self.document = libsbml.SBMLDocument(level, version)
except ValueError:
raise SystemExit('Could not create SBMLDocument object')
self.model = self.document.createModel()
self.check(self.model, 'create model')
if self.document.getLevel() == 3:
self.check(self.model.setTimeUnits(time_units),
'set model-wide time units')
self.check(self.model.setExtentUnits(extent_units),
'set model units of extent')
self.check(self.model.setSubstanceUnits(sub_units),
'set model substance units')
per_second = self.model.createUnitDefinition()
self.check(per_second, 'create unit definition')
self.check(per_second.setId('per_second'), 'set unit definition id')
unit = per_second.createUnit()
self.check(unit, 'create unit on per_second')
self.check(unit.setKind(libsbml.UNIT_KIND_SECOND), 'set unit kind')
self.check(unit.setExponent(-1), 'set unit exponent')
self.check(unit.setScale(0), 'set unit scale')
self.check(unit.setMultiplier(1), 'set unit multiplier')
self.addCompartment()
def __init__(
self,
time_units="second",
extent_units="mole",
sub_units="mole",
level=3,
version=1,
):
if level == 1:
raise SystemExit("Error: SimpleSBML does not support SBML level 1")
try:
self.document = libsbml.SBMLDocument(level, version)
except ValueError:
raise SystemExit("Could not create SBMLDocument object")
self.model = self.document.createModel()
self.check(self.model, "create model")
if self.document.getLevel() == 3:
self.check(self.model.setTimeUnits(time_units),
"set model-wide time units")
self.check(self.model.setExtentUnits(extent_units),
"set model units of extent")
self.check(self.model.setSubstanceUnits(sub_units),
"set model substance units")
per_second = self.model.createUnitDefinition()
self.check(per_second, "create unit definition")
self.check(per_second.setId("per_second"), "set unit definition id")
unit = per_second.createUnit()
self.check(unit, "create unit on per_second")
self.check(unit.setKind(libsbml.UNIT_KIND_SECOND), "set unit kind")
self.check(unit.setExponent(-1), "set unit exponent")
self.check(unit.setScale(0), "set unit scale")
self.check(unit.setMultiplier(1), "set unit multiplier")
per_min = self.model.createUnitDefinition()
self.check(per_min, "create unit definition")
self.check(per_min.setId("per_min"), "set unit definition id")
unit = per_min.createUnit()
self.check(unit, "create unit on per_min")
self.check(unit.setKind(libsbml.UNIT_KIND_SECOND), "set unit kind")
self.check(unit.setExponent(-1), "set unit exponent")
self.check(unit.setScale(0), "set unit scale")
self.check(unit.setMultiplier(60), "set unit multiplier")
molperLmin = self.model.createUnitDefinition()
self.check(molperLmin, "create unit definition")
self.check(molperLmin.setId("molperLmin"), "set unit definition id")
unit = molperLmin.createUnit()
self.check(unit, "create unit on per_second")
self.check(unit.setKind(libsbml.UNIT_KIND_MOLE), "set unit kind")
self.check(unit.setExponent(1), "set unit exponent")
self.check(unit.setScale(0), "set unit scale")
self.check(unit.setMultiplier(1), "set unit multiplier")
unit = molperLmin.createUnit()
self.check(unit, "create unit on per_second")
self.check(unit.setKind(libsbml.UNIT_KIND_LITRE), "set unit kind")
self.check(unit.setExponent(-1), "set unit exponent")
self.check(unit.setScale(0), "set unit scale")
self.check(unit.setMultiplier(1), "set unit multiplier")
unit = molperLmin.createUnit()
self.check(unit, "create unit on per_second")
self.check(unit.setKind(libsbml.UNIT_KIND_SECOND), "set unit kind")
self.check(unit.setExponent(-1), "set unit exponent")
self.check(unit.setScale(0), "set unit scale")
self.check(unit.setMultiplier(60), "set unit multiplier")
molperL = self.model.createUnitDefinition()
self.check(molperL, "create unit definition")
self.check(molperL.setId("molperL"), "set unit definition id")
unit = molperL.createUnit()
self.check(unit, "create unit")
self.check(unit.setKind(libsbml.UNIT_KIND_MOLE), "set unit kind")
self.check(unit.setExponent(1), "set unit exponent")
self.check(unit.setScale(0), "set unit scale")
self.check(unit.setMultiplier(1), "set unit multiplier")
unit = molperL.createUnit()
self.check(unit, "create unit")
self.check(unit.setKind(libsbml.UNIT_KIND_LITRE), "set unit kind")
self.check(unit.setExponent(-1), "set unit exponent")
self.check(unit.setScale(0), "set unit scale")
self.check(unit.setMultiplier(1), "set unit multiplier")
Dimension_less = self.model.createUnitDefinition()
self.check(Dimension_less, "create unit definition")
self.check(Dimension_less.setId("Dimension_less"),
"set unit definition id")
unit = Dimension_less.createUnit()
self.check(unit, "create unit")
self.check(unit.setKind(libsbml.UNIT_KIND_DIMENSIONLESS),
"set unit kind")
self.check(unit.setExponent(0), "set unit exponent")
self.check(unit.setScale(0), "set unit scale")
self.check(unit.setMultiplier(0), "set unit multiplier")
self.addCompartment()