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Fixed model generator incompatible to Python 3.7 (#39)
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@JR-1991
JR-1991 committed Mar 21, 2022
1 parent bb299da commit 48073f6
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11 changes: 11 additions & 0 deletions pyenzyme/enzymeml/core/enzymemldocument.py
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Expand Up @@ -1199,6 +1199,10 @@ def _check_kinetic_model_ids(self, model) -> None:
# Numeric constants are ignored now
continue

elif isinstance(node, ast.Str):
# Python 3.7 compatibility since ast.Constant is ast.Str here
name = node.s

elif isinstance(node, ast.Name):
# If the equation has been done manually
name = node.id
Expand All @@ -1216,13 +1220,20 @@ def _check_kinetic_model_ids(self, model) -> None:
name.replace("'", ""),
).id

if not bool(re.match(r"'[a-zA-Z\d]*'", name)):
name = f"'{name}'"

model.equation = model.equation.replace(name, species_id)
except StopIteration:
# If neither name or ID is found, raise Error
raise SpeciesNotFoundError(
enzymeml_part="Kinetic Model", species_id=name
)

elif not bool(re.match(r"'[a-zA-Z\d]*'", name)):
quoted = f"'{name}'"
model.equation = model.equation.replace(quoted, name)

def _reference_global_parameters(self, model):
"""Removes single parameters and references global parameters if names match"""

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9 changes: 9 additions & 0 deletions tests/enzymeml/core/test_enzymemldocument.py
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Expand Up @@ -275,3 +275,12 @@ def check_consistency(unit, unit_id, kind):
param.unit = "mole / l"

check_consistency("mole / l", param._unit_id, "kinetic parameter")

def test_writing_sbml(self, enzmldoc):
"""Test whether the XML content is as expected"""

expected = open(
"./tests/fixtures/write_xml_string.xml", "r", encoding="utf-8"
).read()

assert enzmldoc.toXMLString() == expected
Empty file added tests/enzymeml/models/__init__.py
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86 changes: 86 additions & 0 deletions tests/enzymeml/models/test_kineticlaw.py
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@@ -0,0 +1,86 @@
from pyenzyme.enzymeml.models.kineticmodel import KineticModel
from pyenzyme.enzymeml.models.kineticmodel import KineticParameter
from pyenzyme.enzymeml.core.ontology import SBOTerm


class TestKineticModel:
def test_content(self):
"""Tests consistency of content"""

# Set up kinetic parameter
param = KineticParameter(
name="kcat",
value=10.0,
unit="1 / s",
initial_value=20.0,
upper=30.0,
lower=0,
is_global=False,
stdev=1.0,
)

assert param.name == "kcat"
assert param.value == 10.0
assert param.unit == "1 / s"
assert param.initial_value == 20.0
assert param.upper == 30.0
assert param.lower == 0.0
assert param.stdev == 1.0
assert not param.is_global

# Set up kinetic model
km = KineticModel(
name="Michaelis Menten Model",
equation="p0*kcat*s0 / (km * s0)",
parameters=[param],
ontology=SBOTerm.MICHAELIS_MENTEN,
)

assert km.name == "Michaelis Menten Model"
assert km.equation == "p0*kcat*s0 / (km * s0)"
assert km.ontology == SBOTerm.MICHAELIS_MENTEN

# Add another paramete
km.addParameter(
name="km",
value=10.0,
unit="mmole / l",
initial_value=20.0,
upper=30.0,
lower=0,
is_global=False,
stdev=1.0,
)

# Check addition has worked
assert km.getParameter("km").name == "km"
assert km.getParameter("km").value == 10.0
assert km.getParameter("km").unit == "mmole / l"
assert km.getParameter("km").initial_value == 20.0
assert km.getParameter("km").upper == 30.0
assert km.getParameter("km").lower == 0.0
assert km.getParameter("km").stdev == 1.0
assert not km.getParameter("km").is_global

def test_model_generator(self, enzmldoc):
"""Tests consistency of the model generator"""

# Set up a generator
generator = KineticModel.createGenerator(
name="Michaelis Menten Model",
equation="protein*kcat*substrate / (km * substrate)",
kcat={"unit": "1 / s", "value": 10.0},
km={"unit": "mmole / l", "value": 10.0},
)

# Generate kinetic model
km = generator(protein="p0", substrate="s0")

assert km.name == "Michaelis Menten Model"
assert km.equation == "'p0'*kcat*'s0' / (km * 's0')"

# Add model to reaction
enzmldoc.reaction_dict["r0"].setModel(km, enzmldoc)

assert km.name == "Michaelis Menten Model"
assert km.equation == "p0*kcat*s0 / (km * s0)"
142 changes: 142 additions & 0 deletions tests/fixtures/write_xml_string.xml
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@@ -0,0 +1,142 @@
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model id="Test" name="Test">
<annotation>
<enzymeml:references xmlns:enzymeml="http://sbml.org/enzymeml/version2">
<enzymeml:doi>DOI</enzymeml:doi>
<enzymeml:pubmedID>https://identifiers.org/pubmed:PubMedID</enzymeml:pubmedID>
<enzymeml:url>URL</enzymeml:url>
</enzymeml:references>
</annotation>
<listOfUnitDefinitions>
<unitDefinition metaid="METAID_U0" id="u0" name="ml">
<listOfUnits>
<unit kind="litre" exponent="1" scale="-3" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="METAID_U1" id="u1" name="mmole / l">
<listOfUnits>
<unit kind="litre" exponent="-1" scale="1" multiplier="1"/>
<unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="METAID_U2" id="u2" name="K">
<listOfUnits>
<unit kind="kelvin" exponent="1" scale="1" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="METAID_U3" id="u3" name="1 / s">
<listOfUnits>
<unit kind="second" exponent="-1" scale="1" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="METAID_U4" id="u4" name="s">
<listOfUnits>
<unit kind="second" exponent="1" scale="1" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="v0" name="Vessel" spatialDimensions="3" size="10" units="u0" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species metaid="METAID_P0" sboTerm="SBO:0000252" id="p0" name="Protein" compartment="v0" initialConcentration="10" substanceUnits="u1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="true">
<annotation>
<enzymeml:protein xmlns:enzymeml="http://sbml.org/enzymeml/version2">
<enzymeml:sequence>HLPMV</enzymeml:sequence>
<enzymeml:ECnumber>1.1.1.1</enzymeml:ECnumber>
<enzymeml:uniprotID>P02357</enzymeml:uniprotID>
<enzymeml:organism>E.coli</enzymeml:organism>
<enzymeml:organismTaxID>27367</enzymeml:organismTaxID>
</enzymeml:protein>
</annotation>
</species>
<species metaid="METAID_C0" sboTerm="SBO:0000296" id="c0" name="Complex" compartment="v0" initialConcentration="10" substanceUnits="u1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<enzymeml:complex xmlns:enzymeml="http://sbml.org/enzymeml/version2">
<enzymeml:participant>s0</enzymeml:participant>
<enzymeml:participant>p0</enzymeml:participant>
</enzymeml:complex>
</annotation>
</species>
<species metaid="METAID_S0" sboTerm="SBO:0000247" id="s0" name="Reactant" compartment="v0" initialConcentration="10" substanceUnits="u1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<enzymeml:reactant xmlns:enzymeml="http://sbml.org/enzymeml/version2">
<enzymeml:inchi>InChI:HJJH</enzymeml:inchi>
<enzymeml:smiles>[H]O[H]</enzymeml:smiles>
<enzymeml:chebiID>CHEBI:09823</enzymeml:chebiID>
</enzymeml:reactant>
</annotation>
</species>
<species metaid="METAID_S1" sboTerm="SBO:0000247" id="s1" name="Reactant2" compartment="v0" initialConcentration="10" substanceUnits="u1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<enzymeml:reactant xmlns:enzymeml="http://sbml.org/enzymeml/version2">
<enzymeml:inchi>InChI:HJJH</enzymeml:inchi>
<enzymeml:smiles>[H]O[H]</enzymeml:smiles>
<enzymeml:chebiID>CHEBI:09823</enzymeml:chebiID>
</enzymeml:reactant>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
<annotation>
<enzymeml:data xmlns:enzymeml="http://sbml.org/enzymeml/version2">
<enzymeml:formats>
<enzymeml:format id="format0">
<enzymeml:column type="time" unit="u4" index="0"/>
<enzymeml:column replica="repl_p0_0" species="p0" type="conc" unit="u1" index="1" isCalculated="False"/>
<enzymeml:column replica="repl_s0_0" species="s0" type="conc" unit="u1" index="2" isCalculated="False"/>
</enzymeml:format>
</enzymeml:formats>
<enzymeml:listOfMeasurements>
<enzymeml:measurement file="file0" id="m0" name="SomeMeasurement" temperature_unit="u2" temperature_value="4.0" ph="7.0">
<enzymeml:initConc protein="p0" value="10.0" unit="u1"/>
<enzymeml:initConc reactant="s0" value="10.0" unit="u1"/>
</enzymeml:measurement>
</enzymeml:listOfMeasurements>
<enzymeml:files>
<enzymeml:file file="./data/m0.csv" format="format0" id="file0"/>
</enzymeml:files>
</enzymeml:data>
</annotation>
<reaction metaid="METAID_R0" sboTerm="SBO:0000176" id="r0" name="string" reversible="true">
<annotation>
<enzymeml:reaction xmlns:enzymeml="http://sbml.org/enzymeml/version2">
<enzymeml:conditions>
<enzymeml:temperature value="200.0" unit="u2"/>
<enzymeml:ph value="7.0"/>
</enzymeml:conditions>
</enzymeml:reaction>
</annotation>
<listOfReactants>
<speciesReference sboTerm="SBO:0000015" species="s0" stoichiometry="1" constant="false"/>
</listOfReactants>
<listOfProducts>
<speciesReference sboTerm="SBO:0000011" species="s1" stoichiometry="1" constant="false"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference sboTerm="SBO:0000013" species="p0"/>
</listOfModifiers>
<kineticLaw name="Menten">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> s0 </ci>
<ci> x </ci>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="x" value="10" units="u3">
<annotation>
<enzymeml:parameter xmlns:enzymeml="http://sbml.org/enzymeml/version2">
<enzymeml:initialValue>10.0</enzymeml:initialValue>
<enzymeml:stdev>0.1</enzymeml:stdev>
</enzymeml:parameter>
</annotation>
</localParameter>
</listOfLocalParameters>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

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