def get_unit_string(unit):
if isinstance(unit, Unit):
return unit.sid
elif isinstance(unit, int):
# libsbml unit
return libsbml.UnitKind_toString(unit)
if isinstance(unit, str):
if unit == '-':
return libsbml.UnitKind_toString(libsbml.UNIT_KIND_DIMENSIONLESS)
else:
return unit
else:
return None
def unitDefinitionToString(udef):
"""Formating of units.
Units have the general format
(multiplier * 10^scale *ukind)^exponent
(m * 10^s *k)^e
"""
if udef is None:
return "None"
libsbml.UnitDefinition_reorder(udef)
# collect formated nominators and denominators
nom = []
denom = []
for u in udef.getListOfUnits():
m = u.getMultiplier()
s = u.getScale()
e = u.getExponent()
k = libsbml.UnitKind_toString(u.getKind())
# get better name for unit
k_str = UNIT_ABBREVIATIONS.get(k, k)
# (m * 10^s *k)^e
# handle m
if _isclose(m, 1.0):
m_str = ""
else:
m_str = str(m) + "*"
if _isclose(abs(e), 1.0):
e_str = ""
else:
e_str = "^" + str(abs(e))
if _isclose(s, 0.0):
string = "{}{}{}".format(m_str, k_str, e_str)
else:
if e_str == "":
string = "({}10^{})*{}".format(m_str, s, k_str)
else:
string = "(({}10^{})*{}){}".format(m_str, s, k_str, e_str)
# collect the terms
if e >= 0.0:
nom.append(string)
else:
denom.append(string)
nom_str = " * ".join(nom)
denom_str = " * ".join(denom)
if (len(nom_str) > 0) and (len(denom_str) > 0):
return "({})/({})".format(nom_str, denom_str)
if (len(nom_str) > 0) and (len(denom_str) == 0):
return nom_str
if (len(nom_str) == 0) and (len(denom_str) > 0):
return "1/({})".format(denom_str)
return ""
def _create_parameter(pid: str, model: libsbml.Model) -> libsbml.Parameter:
p: libsbml.Parameter = model.createParameter()
p.setId(pid)
p.setValue(1.0)
p.setConstant(False)
unit = libsbml.UnitKind_toString(libsbml.UNIT_KIND_MOLE)
p.setUnits(unit)
return p
def getUnitDefinition(aSBMLmodel):
" [[ Id , Name , [[ Kind , Exponent , Scale , Multiplier , Offset ]] ]] "
LIST = []
if aSBMLmodel.getUnitDefinition(0):
NumUnitDefinition = aSBMLmodel.getNumUnitDefinitions()
for Num1 in range(NumUnitDefinition):
ListOfUnitDefinition = []
anUnitDefinition = aSBMLmodel.getUnitDefinition(Num1)
anId = anUnitDefinition.getId()
aName = anUnitDefinition.getName()
ListOfUnits = []
if anUnitDefinition.getUnit(0):
NumUnit = anUnitDefinition.getNumUnits()
for Num2 in range(NumUnit):
ListOfUnit = []
anUnit = anUnitDefinition.getUnit(Num2)
anUnitKind = anUnit.getKind()
aKind = libsbml.UnitKind_toString(anUnitKind)
anExponent = anUnit.getExponent()
aScale = anUnit.getScale()
aMultiplier = anUnit.getMultiplier()
anOffset = anUnit.getOffset()
ListOfUnit.append(aKind)
ListOfUnit.append(anExponent)
ListOfUnit.append(aScale)
ListOfUnit.append(aMultiplier)
ListOfUnit.append(anOffset)
ListOfUnits.append(ListOfUnit)
ListOfUnitDefinition.append(anId)
ListOfUnitDefinition.append(aName)
ListOfUnitDefinition.append(ListOfUnits)
LIST.append(ListOfUnitDefinition)
return LIST
def uncertainty() -> libsbml.SBMLDocument:
"""Create uncertainty with UncertParameter."""
doc: libsbml.SBMLDocument = _distrib_doc()
model: libsbml.Model = doc.createModel()
# parameter
p: libsbml.Parameter = _create_parameter("p1", model=model)
p_distrib: libsbml.DistribSBasePlugin = p.getPlugin("distrib")
# --------------------------------------------
# Build generic uncertainty for parameter
# --------------------------------------------
# 5.0 (mean) +- 0.3 (std) [2.0 - 8.0]
uncertainty: libsbml.Uncertainty = p_distrib.createUncertainty()
uncertainty.setName("Basic example: 5.0 +- 0.3 [2.0 - 8.0]")
unit = libsbml.UnitKind_toString(libsbml.UNIT_KIND_MOLE)
up_mean: libsbml.UncertParameter = uncertainty.createUncertParameter()
up_mean.setType(libsbml.DISTRIB_UNCERTTYPE_MEAN)
up_mean.setValue(5.0)
up_mean.setUnits(unit)
up_sd: libsbml.UncertParameter = uncertainty.createUncertParameter()
up_sd.setType(libsbml.DISTRIB_UNCERTTYPE_STANDARDDEVIATION)
up_sd.setValue(0.3)
up_sd.setUnits(unit)
up_range = libsbml.UncertSpan()
up_range.setType(libsbml.DISTRIB_UNCERTTYPE_RANGE)
up_range.setValueLower(2.0)
up_range.setValueUpper(8.0)
up_range.setUnits(unit)
check(uncertainty.addUncertParameter(up_range), "add the span")
check(
uncertainty.setAnnotation(
"""
<body xmlns='http://www.w3.org/1999/xhtml'>
<p>Experimental data from study</p>
</body>
"""
),
"set annotations",
)
# add an annotation with SBO terms
uncertainty.setMetaId("meta_uncertainty1")
cv1 = libsbml.CVTerm()
cv1.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
cv1.setBiologicalQualifierType(6) # "BQB_IS_DESCRIBED_BY"
cv1.addResource("https://identifiers.org/pubmed/123456")
check(uncertainty.addCVTerm(cv1), "add cv term")
cv2 = libsbml.CVTerm()
cv2.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
cv2.setBiologicalQualifierType(10) # "BQB_HAS_PROPERTY"
cv2.addResource("http://purl.obolibrary.org/obo/ECO_0006016")
check(uncertainty.addCVTerm(cv2), "add cv term")
# --------------------------------------------
# Set of all UncertParameters
# --------------------------------------------
# create second uncertainty which contains all the individual uncertainties
uncertainty = p_distrib.createUncertainty()
uncertainty.setName("UncertParameter example")
for k, parameter_type in enumerate(
[
libsbml.DISTRIB_UNCERTTYPE_COEFFIENTOFVARIATION,
libsbml.DISTRIB_UNCERTTYPE_KURTOSIS,
libsbml.DISTRIB_UNCERTTYPE_MEAN,
libsbml.DISTRIB_UNCERTTYPE_MEDIAN,
libsbml.DISTRIB_UNCERTTYPE_MODE,
libsbml.DISTRIB_UNCERTTYPE_SAMPLESIZE,
libsbml.DISTRIB_UNCERTTYPE_SKEWNESS,
libsbml.DISTRIB_UNCERTTYPE_STANDARDDEVIATION,
libsbml.DISTRIB_UNCERTTYPE_STANDARDERROR,
libsbml.DISTRIB_UNCERTTYPE_VARIANCE,
]
):
up: libsbml.UncertParameter = uncertainty.createUncertParameter()
up.setType(parameter_type)
up.setValue(k)
up.setUnits(unit)
# --------------------------------------------
# Set of all UncertSpans
# --------------------------------------------
uncertainty = p_distrib.createUncertainty()
uncertainty.setName("UncertSpan example")
for k, parameter_type in enumerate(
[
libsbml.DISTRIB_UNCERTTYPE_CONFIDENCEINTERVAL,
libsbml.DISTRIB_UNCERTTYPE_CREDIBLEINTERVAL,
libsbml.DISTRIB_UNCERTTYPE_INTERQUARTILERANGE,
libsbml.DISTRIB_UNCERTTYPE_RANGE,
]
):
up_range = libsbml.UncertSpan()
up_range.setType(parameter_type)
up_range.setValueLower(k - 1.0)
up_range.setValueUpper(k + 1.0)
up_range.setUnits(unit)
check(uncertainty.addUncertParameter(up_range), "add the span")
# --------------------------------------------
# Use math for distribution definition
# --------------------------------------------
# 5.0 dimensionless * normal(1.0 mole, 3.0 mole)
uncertainty = p_distrib.createUncertainty()
uncertainty.setName("math example: 5.0 dimensionless * normal(1.0 mole, 3.0 mole)")
up = uncertainty.createUncertParameter()
up.setType(libsbml.DISTRIB_UNCERTTYPE_DISTRIBUTION)
up.setDefinitionURL("http://www.sbml.org/sbml/symbols/distrib/normal")
ast = libsbml.parseL3FormulaWithModel(
"5.0 dimensionless * normal(1.0 mole, 3.0 mole)", model
)
if not ast:
raise ValueError
up.setMath(ast)
# --------------------------------------------
# Use externalParameter
# --------------------------------------------
# https://sites.google.com/site/probonto/
uncertainty = p_distrib.createUncertainty()
uncertainty.setName("ExternalParameter example")
up = uncertainty.createUncertParameter()
up.setType(libsbml.DISTRIB_UNCERTTYPE_EXTERNALPARAMETER)
up.setName("skewness")
up.setValue(0.25)
up.setUnits(unit)
up.setDefinitionURL("http://purl.obolibrary.org/obo/STATO_0000068")
# --------------------------------------------
# Use external distribution definition
# --------------------------------------------
uncertainty = p_distrib.createUncertainty()
uncertainty.setName("External distribution example")
up = uncertainty.createUncertParameter()
up.setType(libsbml.DISTRIB_UNCERTTYPE_DISTRIBUTION)
up.setName("Geometric 1")
up.setDefinitionURL("http://www.probonto.org/ontology#PROB_k0000782")
up.setUnits(unit)
# success probability of Geometric-1
up_mean_geo1 = up.createUncertParameter()
up_mean_geo1.setType(libsbml.DISTRIB_UNCERTTYPE_EXTERNALPARAMETER)
up_mean_geo1.setName("success probability of Geometric 1")
up_mean_geo1.setValue(0.4)
up_mean_geo1.setDefinitionURL("http://www.probonto.org/ontology#PROB_k0000789")
return doc
def unitDefinitionToString(udef: libsbml.UnitDefinition) -> str:
"""Render formatted string for units.
Units have the general format
(multiplier * 10^scale *ukind)^exponent
(m * 10^s *k)^e
:param udef: unit definition which is to be converted to string
"""
if udef is None:
return "None"
libsbml.UnitDefinition_reorder(udef)
# collect formated nominators and denominators
nom = []
denom = []
for u in udef.getListOfUnits():
m = u.getMultiplier()
s = u.getScale()
e = u.getExponent()
k = libsbml.UnitKind_toString(u.getKind())
# get better name for unit
k_str = UNIT_ABBREVIATIONS.get(k, k)
# (m * 10^s *k)^e
# handle m
if _isclose(m, 1.0):
m_str = ""
else:
m_str = str(m) + "*"
if _isclose(abs(e), 1.0):
e_str = ""
else:
e_str = "^" + str(abs(e))
if _isclose(s, 0.0):
string = f"{m_str}{k_str}{e_str}"
else:
if e_str == "":
string = f"({m_str}10^{s})*{k_str}"
else:
string = f"(({m_str}10^{s})*{k_str}){e_str}"
# collect the terms
if e >= 0.0:
nom.append(string)
else:
denom.append(string)
nom_str = " * ".join(nom)
denom_str = " * ".join(denom)
if (len(nom_str) > 0) and (len(denom_str) > 0):
return f"({nom_str})/({denom_str})"
if (len(nom_str) > 0) and (len(denom_str) == 0):
return nom_str
if (len(nom_str) == 0) and (len(denom_str) > 0):
return f"1/({denom_str})"
return ""
def parseStream(self, outS):
"""parseStream(outStream)
parses SBML model and writes SBML-shorthand to outStream"""
outS.write('@model:')
outS.write(str(self.d.getLevel()) + '.')
outS.write(str(self.d.getVersion()) + '.')
self.mangle = 10 * self.d.getLevel() + self.d.getVersion()
outS.write('0=' + self.m.getId())
if (self.m.getName() != ""):
outS.write(' "' + self.m.getName() + '"')
outS.write('\n')
# level 3 global units...
if (self.mangle >= 30):
first = True
if self.m.isSetSubstanceUnits():
if first == True:
outS.write(' ')
first = False
else:
outS.write(',')
outS.write('s=' + str(self.m.getSubstanceUnits()))
if self.m.isSetTimeUnits():
if first == True:
outS.write(' ')
first = False
else:
outS.write(',')
outS.write('t=' + str(self.m.getTimeUnits()))
if self.m.isSetVolumeUnits():
if first == True:
outS.write(' ')
first = False
else:
outS.write(',')
outS.write('v=' + str(self.m.getVolumeUnits()))
if self.m.isSetAreaUnits():
if first == True:
outS.write(' ')
first = False
else:
outS.write(',')
outS.write('a=' + str(self.m.getAreaUnits()))
if self.m.isSetLengthUnits():
if first == True:
outS.write(' ')
first = False
else:
outS.write(',')
outS.write('l=' + str(self.m.getLengthUnits()))
if self.m.isSetExtentUnits():
if first == True:
outS.write(' ')
first = False
else:
outS.write(',')
outS.write('e=' + str(self.m.getExtentUnits()))
if self.m.isSetConversionFactor():
if first == True:
outS.write(' ')
first = False
else:
outS.write(',')
outS.write('c=' + str(self.m.getConversionFactor()))
if (first == False):
outS.write('\n')
n = self.m.getNumUnitDefinitions()
if (n > 0):
outS.write('@units\n')
for i in range(n):
ud = self.m.getUnitDefinition(i)
outS.write(' ' + ud.getId())
for j in range(ud.getNumUnits()):
if (j == 0):
outS.write('=')
else:
outS.write('; ')
u = ud.getUnit(j)
kind = u.getKind()
outS.write(libsbml.UnitKind_toString(kind))
e = u.getExponent()
m = u.getMultiplier()
o = u.getOffset()
s = u.getScale()
first = True
if (e != 1):
if first == True:
outS.write(':')
first = False
else:
outS.write(',')
outS.write('e=' + str(e))
if (m != 1):
if first == True:
outS.write(':')
first = False
else:
outS.write(',')
outS.write('m=' + str(m))
if (o != 0):
if first == True:
outS.write(':')
first = False
else:
outS.write(',')
outS.write('o=' + str(o))
if (s != 0):
if first == True:
outS.write(':')
first = False
else:
outS.write(',')
outS.write('s=' + str(s))
if (ud.isSetName()):
outS.write(' "' + ud.getName() + '"')
outS.write('\n')
if self.m.getNumCompartments():
outS.write('@compartments\n')
for c in self.m.getListOfCompartments():
outS.write(' ' + c.getId())
if (c.isSetOutside()):
outS.write('<' + c.getOutside())
if (c.isSetSize()):
outS.write('=' + str(c.getSize()))
if (c.isSetName()):
outS.write(' "' + c.getName() + '"')
outS.write('\n')
if self.m.getNumSpecies():
outS.write('@species\n')
for s in self.m.getListOfSpecies():
outS.write(' ' + s.getCompartment() + ':')
if (s.isSetInitialConcentration()):
outS.write('[' + s.getId() + ']=' +
str(s.getInitialConcentration()))
elif (s.isSetInitialAmount()):
outS.write(s.getId() + '=' + str(s.getInitialAmount()))
else:
outS.write('[' + s.getId() + ']=' +
str(s.getInitialConcentration()))
if (s.getHasOnlySubstanceUnits()):
outS.write('s')
if (s.getBoundaryCondition()):
outS.write('b')
if (s.getConstant()):
outS.write('c')
if (s.isSetName()):
outS.write(' "' + s.getName() + '"')
outS.write('\n')
if self.m.getNumParameters():
outS.write('@parameters\n')
for p in self.m.getListOfParameters():
outS.write(' ' + p.getId() + '=')
outS.write(str(p.getValue()))
c = p.getConstant()
if (c != 1):
outS.write('v')
if (p.isSetName()):
outS.write(' "' + p.getName() + '"')
outS.write('\n')
if self.m.getNumRules():
outS.write('@rules\n')
for r in self.m.getListOfRules():
if (r.isAssignment()):
outS.write(' ' + r.getVariable() + ' = ' + r.getFormula())
outS.write('\n')
elif (r.isRate()):
outS.write(' @rate:' + r.getVariable() + ' = ' +
r.getFormula())
outS.write('\n')
else:
# probably an algebraic rule!
sys.stderr.write("Unsupported rule type\n")
raise (ParseError)
if self.m.getNumReactions():
outS.write('@reactions\n')
for r in self.m.getListOfReactions():
if (r.getReversible()):
outS.write('@rr=')
else:
outS.write('@r=')
outS.write(r.getId())
if (r.isSetName()):
outS.write(' "' + r.getName() + '"')
outS.write('\n ')
for j in range(r.getNumReactants()):
sr = r.getReactant(j)
if (j > 0):
outS.write('+')
sto = sr.getStoichiometry()
if (sto != 1):
outS.write(str(int(sto)))
outS.write(sr.getSpecies())
outS.write(' -> ')
for j in range(r.getNumProducts()):
sr = r.getProduct(j)
if (j > 0):
outS.write('+')
sto = sr.getStoichiometry()
if (sto != 1):
outS.write(str(int(sto)))
outS.write(sr.getSpecies())
for j in range(r.getNumModifiers()):
sr = r.getModifier(j)
if (j == 0):
outS.write(' : ')
outS.write(sr.getSpecies())
else:
outS.write(', ')
outS.write(sr.getSpecies())
outS.write('\n')
if (r.isSetKineticLaw()):
kl = r.getKineticLaw()
outS.write(' ' + kl.getFormula())
for k in range(kl.getNumParameters()):
if (k == 0):
outS.write(' : ')
else:
outS.write(', ')
p = kl.getParameter(k)
outS.write(p.getId() + '=' + str(p.getValue()))
outS.write('\n')
if self.m.getNumEvents():
outS.write('@events\n')
for e in self.m.getListOfEvents():
outS.write(" " + e.getId() + "= ")
trig = e.getTrigger()
trigger = libsbml.formulaToString(trig.getMath())
outS.write(trigger)
if e.isSetDelay():
outS.write(' ; ')
dmath = e.getDelay()
delay = libsbml.formulaToString(dmath.getMath())
outS.write(delay)
outS.write(' : ')
nea = e.getNumEventAssignments()
for eai in range(nea):
if (eai > 0):
if (self.mangle >= 23):
outS.write('; ')
else:
outS.write(', ')
ea = e.getEventAssignment(eai)
outS.write(ea.getVariable() + "=")
m = ea.getMath()
mf = libsbml.formulaToString(m)
outS.write(mf)
if e.isSetName():
outS.write(' "' + e.getName() + '"')
outS.write("\n")
def test_UnitKind_toString(self): s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_AMPERE) self.assert_(( "ampere" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_BECQUEREL) self.assert_(( "becquerel" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_CANDELA) self.assert_(( "candela" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_CELSIUS) self.assert_(( "Celsius" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_COULOMB) self.assert_(( "coulomb" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_DIMENSIONLESS) self.assert_(( "dimensionless" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_FARAD) self.assert_(( "farad" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_GRAM) self.assert_(( "gram" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_GRAY) self.assert_(( "gray" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_HENRY) self.assert_(( "henry" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_HERTZ) self.assert_(( "hertz" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_ITEM) self.assert_(( "item" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_JOULE) self.assert_(( "joule" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_KATAL) self.assert_(( "katal" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_KELVIN) self.assert_(( "kelvin" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_KILOGRAM) self.assert_(( "kilogram" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_LITER) self.assert_(( "liter" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_LITRE) self.assert_(( "litre" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_LUMEN) self.assert_(( "lumen" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_LUX) self.assert_(( "lux" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_METER) self.assert_(( "meter" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_METRE) self.assert_(( "metre" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_MOLE) self.assert_(( "mole" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_NEWTON) self.assert_(( "newton" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_OHM) self.assert_(( "ohm" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_PASCAL) self.assert_(( "pascal" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_RADIAN) self.assert_(( "radian" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_SECOND) self.assert_(( "second" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_SIEMENS) self.assert_(( "siemens" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_SIEVERT) self.assert_(( "sievert" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_STERADIAN) self.assert_(( "steradian" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_TESLA) self.assert_(( "tesla" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_VOLT) self.assert_(( "volt" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_WATT) self.assert_(( "watt" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_WEBER) self.assert_(( "weber" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_INVALID) self.assert_(( "(Invalid UnitKind)" == s )) s = libsbml.UnitKind_toString(-1) self.assert_(( "(Invalid UnitKind)" == s )) s = libsbml.UnitKind_toString(libsbml.UNIT_KIND_INVALID + 1) self.assert_(( "(Invalid UnitKind)" == s )) pass
def udef_to_string(
udef: Optional[Union[libsbml.UnitDefinition, str]],
model: Optional[libsbml.Model] = None,
format: str = "latex",
) -> Optional[str]:
"""Render formatted string for units.
Format can be either 'str' or 'latex'
Units have the general format
(multiplier * 10^scale *ukind)^exponent
(m * 10^s *k)^e
Returns None if udef is None or no units in UnitDefinition.
:param udef: unit definition which is to be converted to string
"""
if udef is None:
return None
ud: libsbml.UnitDefinition
if isinstance(udef, str):
# check for internal unit
if libsbml.UnitKind_forName(udef) != libsbml.UNIT_KIND_INVALID:
return short_names.get(udef, udef)
else:
ud = model.getUnitDefinition(udef) # type: ignore
else:
ud = udef
# collect nominators and denominators
nom: str = ""
denom: str = ""
if ud:
for u in ud.getListOfUnits():
m = u.getMultiplier()
s: int = u.getScale()
e = u.getExponent()
k = libsbml.UnitKind_toString(u.getKind())
# (m * 10^s *k)^e
# parse with pint
term = Q_(float(m) * 10**s, k)**float(abs(e))
try:
term = term.to_compact()
except KeyError:
pass
if np.isclose(term.magnitude, 1.0):
term = Q_(1, term.units)
us = f"{term:~}" # short formating
# handle min and hr
us = us.replace("60.0 s", "1 min")
us = us.replace("3600.0 s", "1 hr")
us = us.replace("3.6 ks", "1 hr")
us = us.replace("86.4 ks", "1 day")
us = us.replace("10.0 mm", "1 cm")
# remove 1.0 prefixes
us = us.replace("1 ", "")
# exponent
us = us.replace(" ** ", "^")
if e >= 0.0:
nom = us if nom == "" else f"{nom}*{us}"
else:
denom = us if denom == "" else f"{denom}*{us}"
else:
nom = "-"
if format == "str":
denom = denom.replace("*", "/")
if nom and denom:
ustr = f"{nom}/{denom}"
elif nom and not denom:
ustr = nom
elif not nom and denom:
ustr = f"1/{denom}"
elif not nom and not denom:
ustr = "-"
elif format == "latex":
nom = nom.replace("*", " \\cdot ")
denom = denom.replace("*", " \\cdot ")
if nom and denom:
ustr = f"\\frac{{{nom}}}{{{denom}}}"
elif nom and not denom:
ustr = nom
elif not nom and denom:
ustr = f"\\frac{{1}}{{{denom}}}"
elif not nom and not denom:
ustr = "-"
else:
raise ValueError
if ustr == "1":
ustr = "-"
# json escape
return ustr
def parseStream(self, outS):
"""parseStream(outStream)
parses SBML model and writes LaTeX to outStream"""
outS.write('@model:')
outS.write(str(self.d.getLevel()) + '.')
outS.write(str(self.d.getVersion()) + '.')
self.mangle = 10 * self.d.getLevel() + self.d.getVersion()
outS.write('0=' + self.m.getId())
if (self.m.getName() != ""):
outS.write(' "' + self.m.getName() + '"')
outS.write('\n')
n = self.m.getNumUnitDefinitions()
if (n > 0):
outS.write('@units\n')
for i in range(n):
ud = self.m.getUnitDefinition(i)
outS.write(' ' + ud.getId())
for j in range(ud.getNumUnits()):
if (j == 0):
outS.write('=')
else:
outS.write('; ')
u = ud.getUnit(j)
kind = u.getKind()
outS.write(libsbml.UnitKind_toString(kind))
e = u.getExponent()
m = u.getMultiplier()
o = u.getOffset()
s = u.getScale()
first = True
if (e != 1):
if first == True:
outS.write(':')
first = False
else:
outS.write(',')
outS.write('e=' + str(e))
if (m != 1):
if first == True:
outS.write(':')
first = False
else:
outS.write(',')
outS.write('m=' + str(m))
if (o != 0):
if first == True:
outS.write(':')
first = False
else:
outS.write(',')
outS.write('o=' + str(o))
if (s != 0):
if first == True:
outS.write(':')
first = False
else:
outS.write(',')
outS.write('s=' + str(s))
if (ud.isSetName()):
outS.write(' "' + ud.getName() + '"')
outS.write('\n')
if self.m.getNumCompartments():
outS.write('@compartments\n')
for c in self.m.getListOfCompartments():
outS.write(' ' + c.getId())
if (c.isSetOutside()):
outS.write('<' + c.getOutside())
if (c.isSetSize()):
outS.write('=' + str(c.getSize()))
if (c.isSetName()):
outS.write(' "' + c.getName() + '"')
outS.write('\n')
if self.m.getNumSpecies():
outS.write('@species\n')
for s in self.m.getListOfSpecies():
outS.write(' ' + s.getCompartment() + ':')
if (s.isSetInitialConcentration()):
outS.write('[' + s.getId() + ']=' +
str(s.getInitialConcentration()))
elif (s.isSetInitialAmount()):
outS.write(s.getId() + '=' + str(s.getInitialAmount()))
else:
outS.write('[' + s.getId() + ']=' +
str(s.getInitialConcentration()))
if (s.getHasOnlySubstanceUnits()):
outS.write('s')
if (s.getBoundaryCondition()):
outS.write('b')
if (s.getConstant()):
outS.write('c')
if (s.isSetName()):
outS.write(' "' + s.getName() + '"')
outS.write('\n')
if self.m.getNumParameters():
outS.write('@parameters\n')
for p in self.m.getListOfParameters():
outS.write(' ' + p.getId() + '=')
outS.write(str(p.getValue()))
if (p.isSetName()):
outS.write(' "' + p.getName() + '"')
outS.write('\n')
if self.m.getNumRules():
outS.write('@rules\n')
for r in self.m.getListOfRules():
outS.write(' ' + r.getVariable() + ' = ' + r.getFormula())
outS.write('\n')
if self.m.getNumReactions():
outS.write('%%% START Reactions\n')
outS.write('\\begin{align*}\n')
for r in self.m.getListOfReactions():
# if (r.getReversible()):
# outS.write('@rr=')
# else:
# outS.write('@r=')
# outS.write(r.getId())
# if (r.isSetName()):
# outS.write(' "'+r.getName()+'"')
# outS.write('\n ')
for j in range(r.getNumReactants()):
sr = r.getReactant(j)
if (j > 0):
outS.write('+')
sto = sr.getStoichiometry()
if (sto != 1):
outS.write(str(int(sto)))
outS.write('\\mathsf{' +
sr.getSpecies().replace('_', '\\_') + '}')
if (r.getReversible()):
outS.write(' &\\longleftrightarrow ')
else:
outS.write(' &\\longrightarrow ')
for j in range(r.getNumProducts()):
sr = r.getProduct(j)
if (j > 0):
outS.write('+')
sto = sr.getStoichiometry()
if (sto != 1):
outS.write(str(int(sto)))
outS.write('\\mathsf{' +
sr.getSpecies().replace('_', '\\_') + '}')
for j in range(r.getNumModifiers()):
sr = r.getModifier(j)
if (j == 0):
outS.write(' : ')
outS.write('\\mathsf{' +
sr.getSpecies().replace('_', '\\_') + '}')
else:
outS.write(', ')
outS.write('\\mathsf{' +
sr.getSpecies().replace('_', '\\_') + '}')
outS.write(' & \n')
if (r.isSetKineticLaw()):
kl = r.getKineticLaw()
outS.write(' \\mathit{rate}&= \\mathit{' +
kl.getFormula().replace(
'*', ' \\times ').replace('_', '\\_') + '}')
for k in range(kl.getNumParameters()):
if (k == 0):
outS.write(' : ')
else:
outS.write(', ')
p = kl.getParameter(k)
outS.write(p.getId().replace('_', '\\_') + '=' +
str(p.getValue()))
outS.write(' \\\\ \n')
outS.write('\\end{align*}\n')
outS.write('%%% END Reactions\n')
if self.m.getNumEvents():
outS.write('@events\n')
for e in self.m.getListOfEvents():
outS.write(" " + e.getId() + "= ")
trig = e.getTrigger()
trigger = libsbml.formulaToString(trig.getMath())
outS.write(trigger)
if e.isSetDelay():
outS.write(' ; ')
dmath = e.getDelay()
delay = libsbml.formulaToString(dmath.getMath())
outS.write(delay)
outS.write(' : ')
nea = e.getNumEventAssignments()
for eai in range(nea):
if (eai > 0):
if (self.mangle >= 23):
outS.write('; ')
else:
outS.write(', ')
ea = e.getEventAssignment(eai)
outS.write(ea.getVariable() + "=")
m = ea.getMath()
mf = libsbml.formulaToString(m)
outS.write(mf)
if e.isSetName():
outS.write(' "' + e.getName() + '"')
outS.write("\n")