def test_compounds_exist(self):
reader = sbml.SBMLReader(self.doc, ignore_boundary=False)
species = {entry.id: entry for entry in reader.species}
self.assertEqual(len(species), 5)
gluc_species = species['M_Glucose_LPAREN_c_RPAREN_']
self.assertEqual(gluc_species.id, 'M_Glucose_LPAREN_c_RPAREN_')
self.assertEqual(gluc_species.name, 'Glucose')
self.assertEqual(gluc_species.compartment, 'C_c')
self.assertFalse(gluc_species.boundary)
self.assertEqual(gluc_species.formula, 'C6H12O6')
self.assertEqual(gluc_species.charge, 0)
g6p_species = species['M_Glucose_6_DASH_P_LPAREN_c_RPAREN_']
self.assertEqual(g6p_species.id, 'M_Glucose_6_DASH_P_LPAREN_c_RPAREN_')
self.assertEqual(g6p_species.name, 'Glucose-6-P')
self.assertEqual(g6p_species.compartment, 'C_c')
self.assertFalse(g6p_species.boundary)
self.assertEqual(g6p_species.formula, 'C6H11O9P')
self.assertEqual(g6p_species.charge, -2)
h2o_species = species['M_H2O_LPAREN_c_RPAREN_']
self.assertEqual(h2o_species.id, 'M_H2O_LPAREN_c_RPAREN_')
self.assertEqual(h2o_species.name, 'H2O')
self.assertEqual(h2o_species.compartment, 'C_c')
self.assertFalse(h2o_species.boundary)
self.assertEqual(h2o_species.formula, 'H2O')
self.assertEqual(h2o_species.charge, 0)
self.assertFalse(species['M_Phosphate_LPAREN_c_RPAREN_'].boundary)
self.assertTrue(species['M_Biomass'].boundary)
self.assertIsNone(species['M_Biomass'].formula)
self.assertIsNone(species['M_Biomass'].charge)
def test_compounds_exist(self):
reader = sbml.SBMLReader(self.doc, ignore_boundary=False)
species = {entry.id: entry for entry in reader.species}
self.assertEqual(len(species), 5)
self.assertEqual(species['Glucose'].id, 'Glucose')
self.assertEqual(species['Glucose'].name, 'Glucose')
self.assertEqual(species['Glucose'].compartment, 'cell')
self.assertFalse(species['Glucose'].boundary)
self.assertEqual(species['Glucose'].charge, 0)
self.assertEqual(species['Glucose_6_P'].id, 'Glucose_6_P')
self.assertEqual(species['Glucose_6_P'].name, 'Glucose_6_P')
self.assertEqual(species['Glucose_6_P'].compartment, 'cell')
self.assertFalse(species['Glucose_6_P'].boundary)
self.assertEqual(species['Glucose_6_P'].charge, -2)
self.assertEqual(species['H2O'].id, 'H2O')
self.assertEqual(species['H2O'].name, 'H2O')
self.assertEqual(species['H2O'].compartment, 'cell')
self.assertFalse(species['H2O'].boundary)
self.assertEqual(species['H2O'].charge, 0)
self.assertFalse(species['Phosphate'].boundary)
self.assertTrue(species['Biomass'].boundary)
def test_compartment_exists(self):
reader = sbml.SBMLReader(self.doc, ignore_boundary=False)
compartments = {entry.id: entry for entry in reader.compartments}
self.assertEqual(len(compartments), 2)
self.assertEqual(compartments['C_c'].id, 'C_c')
self.assertEqual(compartments['C_c'].name, 'cell')
self.assertEqual(compartments['C_b'].id, 'C_b')
self.assertEqual(compartments['C_b'].name, 'boundary')
def test_parse_reaction_cobra_objective(self):
reader = sbml.SBMLReader(self.doc)
reaction = reader.get_reaction('R_G6Pase')
coeff = sbml.parse_objective_coefficient(reaction)
self.assertIsNone(coeff)
reaction = reader.get_reaction('R_Biomass')
coeff = sbml.parse_objective_coefficient(reaction)
self.assertEqual(coeff, 1)
def test_objective_exists(self):
reader = sbml.SBMLReader(self.doc)
objectives = {entry.id: entry for entry in reader.objectives}
self.assertEqual(len(objectives), 1)
objective = objectives['obj1']
self.assertEqual(objective.name, 'Objective 1')
self.assertEqual(objective.type, 'maximize')
self.assertEqual(dict(objective.reactions), {'R_Biomass': 1})
def test_glucose_parse_notes(self):
reader = sbml.SBMLReader(self.doc)
species = reader.get_species('M_Glucose_LPAREN_c_RPAREN_')
notes_dict = sbml.parse_xhtml_species_notes(species)
self.assertEqual(notes_dict, {
'formula': 'C6H12O6',
'kegg': 'C00031',
'charge': 0
})
def setUp(self):
doc = BytesIO('''<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1"
xmlns:html="http://www.w3.org/1999/xhtml"
level="3" version="1"
fbc:required="false">
<model id="test_model" name="Test model">
<listOfCompartments>
<compartment id="C_c" name="cell" constant="true"/>
<compartment id="C_b" name="boundary" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="M_Glucose" name="Glucose" compartment="C_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" fbc:charge="0" fbc:chemicalFormula="C6H12O6"/>
<species id="M_Glucose_6_P" name="Glucose-6-P" compartment="C_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" fbc:charge="-2" fbc:chemicalFormula="C6H11O9P"/>
<species id="M_H2O" name="H2O" compartment="C_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" fbc:charge="0" fbc:chemicalFormula="H2O"/>
<species id="M_Phosphate" name="Phosphate" compartment="C_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" fbc:charge="-2" fbc:chemicalFormula="HO4P"/>
<species id="M_Biomass" name="Biomass" compartment="C_b" constant="false" boundaryCondition="true" hasOnlySubstanceUnits="false"/>
</listOfSpecies>
<listOfReactions>
<reaction id="R_G6Pase" reversible="true" fast="false">
<listOfReactants>
<speciesReference species="M_Glucose" stoichiometry="2" constant="true"/>
<speciesReference species="M_Phosphate" stoichiometry="2" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_H2O" stoichiometry="2" constant="true"/>
<speciesReference species="M_Glucose_6_P" stoichiometry="2" constant="true"/>
</listOfProducts>
</reaction>
<reaction id="R_Biomass" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="M_Glucose_6_P" stoichiometry="0.56" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_Biomass" stoichiometry="1" constant="true"/>
</listOfProducts>
</reaction>
</listOfReactions>
<fbc:listOfObjectives fbc:activeObjective="obj1">
<fbc:objective fbc:id="obj1" fbc:name="Objective 1" fbc:type="maximize">
<fbc:listOfFluxObjectives>
<fbc:fluxObjective fbc:reaction="R_Biomass" fbc:coefficient="1"/>
</fbc:listOfFluxObjectives>
</fbc:objective>
</fbc:listOfObjectives>
<fbc:listOfFluxBounds>
<fbc:fluxBound fbc:reaction="R_G6Pase" fbc:operation="greaterEqual" fbc:value="-10"/>
<fbc:fluxBound fbc:reaction="R_G6Pase" fbc:operation="lessEqual" fbc:value="1000"/>
<fbc:fluxBound fbc:reaction="R_Biomass" fbc:operation="greaterEqual" fbc:value="0"/>
<fbc:fluxBound fbc:reaction="R_Biomass" fbc:operation="lessEqual" fbc:value="1000"/>
</fbc:listOfFluxBounds>
</model>
</sbml>'''.encode('utf-8'))
reader = sbml.SBMLReader(doc)
self._model = reader.create_model()
def test_reaction_xml_notes(self):
reader = sbml.SBMLReader(self.doc)
reaction = reader.get_reaction('R_G6Pase')
notes = reaction.xml_notes
notes_tags = list(notes)
self.assertEqual(len(notes_tags), 1)
self.assertEqual(notes_tags[0].tag, '{http://www.w3.org/1999/xhtml}p')
self.assertEqual(notes_tags[0].text, 'Glucose 6-phosphatase')
def test_parse_reaction_cobra_flux_bounds(self):
reader = sbml.SBMLReader(self.doc)
reaction = reader.get_reaction('R_G6Pase')
lower, upper = sbml.parse_flux_bounds(reaction)
self.assertIsNone(lower)
self.assertIsNone(upper)
reaction = reader.get_reaction('R_Biomass')
lower, upper = sbml.parse_flux_bounds(reaction)
self.assertEqual(lower, 0)
self.assertEqual(upper, 1000)
def test_g6pase_parse_notes(self):
reader = sbml.SBMLReader(self.doc)
reaction = reader.get_reaction('R_G6Pase')
notes = sbml.parse_xhtml_reaction_notes(reaction)
self.assertEqual(
notes, {
'subsystem': 'Glycolysis / Gluconeogenesis',
'genes': 'b0822',
'ec': '3.1.3.9',
'confidence': 3,
'authors': ['Jane Doe', 'John Doe']
})
def test_biomass_reaction_exists(self):
reader = sbml.SBMLReader(self.doc, ignore_boundary=False)
reaction = reader.get_reaction('Biomass')
self.assertFalse(reaction.reversible)
# Compare equation of reaction
actual_equation = Reaction(
Direction.Forward,
[(Compound('Glucose_6_P', 'cell'), Fraction(56, 100)),
(Compound('Glucose', 'cell'), Fraction(88, 100))],
[(Compound('Biomass', 'boundary'), 1)])
self.assertEqual(reaction.equation, actual_equation)
def test_g6pase_reaction_exists(self):
reader = sbml.SBMLReader(self.doc)
reaction = reader.get_reaction('G6Pase')
self.assertTrue(reaction.reversible)
# Compare equation of reaction
actual_equation = Reaction(Direction.Both,
[(Compound('Glucose', 'cell'), 2),
(Compound('Phosphate', 'cell'), 2)],
[(Compound('H2O', 'cell'), 2),
(Compound('Glucose_6_P', 'cell'), 2)])
self.assertEqual(reaction.equation, actual_equation)
def test_biomass_reaction_exists(self):
reader = sbml.SBMLReader(self.doc, ignore_boundary=False)
reaction = reader.get_reaction('R_Biomass')
self.assertFalse(reaction.reversible)
# Compare equation of reaction
actual_equation = Reaction(
Direction.Forward,
[(Compound('M_Glucose_6_DASH_P_LPAREN_c_RPAREN_',
'C_c'), Decimal('0.56')),
(Compound('M_Glucose_LPAREN_c_RPAREN_', 'C_c'), Decimal('0.88'))],
[(Compound('M_Biomass', 'C_b'), 1)])
self.assertEqual(reaction.equation, actual_equation)
def test_create_and_convert_model(self):
reader = sbml.SBMLReader(self.doc)
model = reader.create_model()
sbml.convert_sbml_model(model)
self.assertEqual({entry.id
for entry in model.compounds},
{'Glucose', 'Glucose_6_P', 'H2O', 'Phosphate'})
self.assertEqual({entry.id
for entry in model.reactions}, {'G6Pase', 'Biomass'})
self.assertEqual({entry.id for entry in model.compartments}, {'cell'})
self.assertEqual(set(model.model), {'Biomass', 'G6Pase'})
def test_g6pase_reaction_exists(self):
reader = sbml.SBMLReader(self.doc)
reaction = reader.get_reaction('R_G6Pase')
self.assertTrue(reaction.reversible)
# Compare equation of reaction
actual_equation = Reaction(
Direction.Both,
[(Compound('M_Glucose_LPAREN_c_RPAREN_', 'C_c'), 2),
(Compound('M_Phosphate_LPAREN_c_RPAREN_', 'C_c'), 2)],
[(Compound('M_H2O_LPAREN_c_RPAREN_', 'C_c'), 2),
(Compound('M_Glucose_6_DASH_P_LPAREN_c_RPAREN_', 'C_c'), 2)])
self.assertEqual(reaction.equation, actual_equation)
def test_flux_bounds_exists(self):
reader = sbml.SBMLReader(self.doc)
flux_bounds = list(reader.flux_bounds)
self.assertEqual(len(flux_bounds), 4)
biomass_bounds = set((b.operation, b.value) for b in flux_bounds
if b.reaction == 'R_Biomass')
self.assertEqual(biomass_bounds, {('greaterEqual', 0),
('lessEqual', 1000)})
g6pase_bounds = set((b.operation, b.value) for b in flux_bounds
if b.reaction == 'R_G6Pase')
self.assertEqual(g6pase_bounds, {('greaterEqual', -10),
('lessEqual', 1000)})
def test_g6pase_reaction_exists(self):
reader = sbml.SBMLReader(self.doc, ignore_boundary=False)
reaction = reader.get_reaction('R_G6Pase')
self.assertTrue(reaction.reversible)
# Compare equation of reaction
actual_equation = Reaction(
Direction.Both,
[(Compound('M_Glucose_LPAREN_c_RPAREN_', 'C_c'), 2),
(Compound('M_Phosphate_LPAREN_c_RPAREN_', 'C_c'), 2)],
[(Compound('M_H2O_LPAREN_c_RPAREN_', 'C_c'), 2),
(Compound('M_Glucose_6_DASH_P_LPAREN_c_RPAREN_', 'C_c'), 2)])
self.assertEqual(reaction.equation, actual_equation)
self.assertEqual(reaction.properties['lower_flux'], -10)
self.assertEqual(reaction.properties['upper_flux'], 1000)
def test_create_and_convert_model(self):
reader = sbml.SBMLReader(self.doc)
model = reader.create_model()
sbml.convert_sbml_model(model)
self.assertEqual(
{entry.id
for entry in model.compounds},
{'Glucose(c)', 'Glucose_6-P(c)', 'H2O(c)', 'Phosphate(c)'})
self.assertEqual({entry.id
for entry in model.reactions}, {'G6Pase', 'Biomass'})
self.assertEqual({entry.id for entry in model.compartments}, {'c'})
self.assertEqual(model.limits['Biomass'], ('Biomass', 0, 1000))
self.assertEqual(model.biomass_reaction, 'Biomass')
self.assertEqual(set(model.model), {'Biomass', 'G6Pase'})
def setUp(self):
s = StringIO('''<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level1"
xmlns:html="http://www.w3.org/1999/xhtml"
level="1" version="2">
<model name="Test model">
<listOfCompartments>
<compartment name="cell"/>
</listOfCompartments>
<listOfSpecies>
<species name="Glucose" compartment="cell" initialAmount="1"/>
<species name="Glucose_6_P" compartment="cell" initialAmount="1"/>
<species name="H2O" compartment="cell" initialAmount="1"/>
<species name="Phosphate" compartment="cell" initialAmount="1" boundaryCondition="false"/>
<species name="Biomass" compartment="cell" initialAmount="1" boundaryCondition="true"/>
</listOfSpecies>
<listOfReactions>
<reaction name="G6Pase" reversible="true">
<listOfReactants>
<speciesReference species="Glucose" stoichiometry="2"/>
<speciesReference species="Phosphate" stoichiometry="2"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="H2O" stoichiometry="2"/>
<speciesReference species="Glucose_6_P" stoichiometry="2"/>
</listOfProducts>
<notes>
<html:p>Glucose 6-phosphatase</html:p>
</notes>
</reaction>
<reaction name="Biomass" reversible="false">
<listOfReactants>
<speciesReference species="Glucose_6_P" stoichiometry="56" denominator="100"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="Biomass"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>''')
self.reader = sbml.SBMLReader(s)
def setUp(self):
s = StringIO('''<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
xmlns:html="http://www.w3.org/1999/xhtml"
level="3" version="1">
<model id="test_model" name="Test model">
<listOfCompartments>
<compartment id="C_c" name="cell" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="M_Glucose" name="Glucose" compartment="C_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false"/>
<species id="M_Glucose_6_P" name="Glucose-6-P" compartment="C_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false"/>
<species id="M_H2O" name="H2O" compartment="C_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false"/>
<species id="M_Phosphate" name="Phosphate" compartment="C_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false"/>
<species id="M_Biomass" name="Biomass" compartment="C_c" constant="false" boundaryCondition="true" hasOnlySubstanceUnits="false"/>
</listOfSpecies>
<listOfReactions>
<reaction id="R_G6Pase" reversible="true" fast="false">
<listOfReactants>
<speciesReference species="M_Glucose" stoichiometry="2" constant="true"/>
<speciesReference species="M_Phosphate" stoichiometry="2" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_H2O" stoichiometry="2" constant="true"/>
<speciesReference species="M_Glucose_6_P" stoichiometry="2" constant="true"/>
</listOfProducts>
<notes>
<html:p>Glucose 6-phosphatase</html:p>
</notes>
</reaction>
<reaction id="R_Biomass" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="M_Glucose_6_P" stoichiometry="0.56" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_Biomass" stoichiometry="1" constant="true"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>''')
self.reader = sbml.SBMLReader(s)
def test_compartment_exists_with_ignore_boundary(self):
reader = sbml.SBMLReader(self.doc, ignore_boundary=True)
compartments = {entry.id: entry for entry in reader.compartments}
self.assertEqual(len(compartments), 1)
self.assertEqual(compartments['cell'].id, 'cell')
self.assertEqual(compartments['cell'].name, 'cell')
def test_objective_not_present(self):
reader = sbml.SBMLReader(self.doc)
objectives = list(reader.objectives)
self.assertEqual(len(objectives), 0)
self.assertIsNone(reader.get_active_objective())
def test_flux_bounds_not_present(self):
reader = sbml.SBMLReader(self.doc)
flux_bounds = list(reader.flux_bounds)
self.assertEqual(len(flux_bounds), 0)
def test_model_name(self):
reader = sbml.SBMLReader(self.doc)
self.assertEqual(reader.id, 'test_model')
self.assertEqual(reader.name, 'Test model')
def test_active_objective(self):
reader = sbml.SBMLReader(self.doc)
objectives = {entry.id: entry for entry in reader.objectives}
self.assertEqual(reader.get_active_objective(), objectives['obj1'])
