def test_ComplexSpeciesType(self): # Test constructor complex1 = core.ComplexSpeciesType() self.assertEqual(complex1.region, '') self.assertEqual(complex1.binding, '') self.assertEqual(complex1.complex_type, '') self.assertEqual(complex1.composition_in_uniprot, '') self.assertEqual(complex1.formation_process, None) self.assertEqual(complex1.subunits, []) cofactor1 = core.MetaboliteSpeciesType( id='cofactor1', structure= 'InChI=1S/C8H7NO3/c10-6-1-4-5(2-7(6)11)9-3-8(4)12/h1-2,8-9,12H,3H2' ) cofactor2 = core.MetaboliteSpeciesType(id='cofactor2', structure='InChI=1S/Zn/q+2') # Test adding subunit composition # Add subunit composition: (2) cofactor1 + (3) cofactor2 ==> complex1 species_type_coeff1 = core.SpeciesTypeCoefficient( species_type=cofactor1, coefficient=2) species_type_coeff2 = core.SpeciesTypeCoefficient( species_type=cofactor2, coefficient=3) complex1.subunits = [species_type_coeff1, species_type_coeff2] self.assertEqual(complex1.get_charge(), 6) self.assertAlmostEqual( complex1.get_mol_wt(), (2 * cofactor1.get_mol_wt() + 3 * cofactor2.get_mol_wt())) self.assertEqual(complex1.get_empirical_formula(), chem.EmpiricalFormula('C16H14N2O6Zn3'))
def test_observable_coefficient(self): cell = core.Cell() comp1 = core.Compartment(id='c') met1 = core.MetaboliteSpeciesType(id='met1') dna1 = core.DnaSpeciesType(id="dna1") species1 = core.Species(species_type=met1, compartment=comp1) species2 = core.Species(species_type=dna1, compartment=comp1) speciesCoefficient1 = core.SpeciesCoefficient(species=species1, coefficient=2.5) speciesCoefficient2 = core.SpeciesCoefficient(species=species2, coefficient=3) observable1 = core.Observable( id='test', cell=cell, species=[speciesCoefficient1, speciesCoefficient2]) observableCoefficient1 = core.ObservableCoefficient( observable=observable1, coefficient=2.3) self.assertIsInstance(observableCoefficient1, core.ObservableCoefficient) self.assertIsInstance(observableCoefficient1.observable, core.Observable) self.assertIsInstance(observableCoefficient1.coefficient, float) self.assertEqual(observableCoefficient1.observable.id, 'test')
def test_serialize(self): comp = core.Compartment(id='c') met = core.MetaboliteSpeciesType(id='met') spec = core.Species(species_type=met, compartment=comp) spec_coeff = core.SpeciesCoefficient(species=spec, coefficient=3) self.assertEqual(spec_coeff.serialize(), '(3) met[c]') self.assertEqual( core.SpeciesCoefficient._serialize(species=spec, coefficient=3), '(3) met[c]') self.assertEqual( core.SpeciesCoefficient._serialize(species=spec, coefficient=1), 'met[c]') self.assertEqual( core.SpeciesCoefficient._serialize(species=spec, coefficient=2000), '(2.000000e+03) met[c]') self.assertEqual( core.SpeciesCoefficient._serialize(species=spec, coefficient=3, show_compartment=False), '(3) met') self.assertEqual( core.SpeciesCoefficient._serialize(species=spec, coefficient=-1), '(-1) met[c]') self.assertEqual( core.SpeciesCoefficient._serialize(species=spec, coefficient=-1, show_coefficient_sign=False), 'met[c]')
def test_constructor(self): met = core.MetaboliteSpeciesType(id='met') species_type_coeff = core.SpeciesTypeCoefficient(species_type=met, coefficient=3) self.assertEqual(species_type_coeff.species_type.id, 'met') self.assertEqual(species_type_coeff.coefficient, 3)
def test_constructor(self): comp = core.Compartment(id='c') met = core.MetaboliteSpeciesType(id='met') spec = core.Species(species_type=met, compartment=comp) spec_coeff = core.SpeciesCoefficient(species=spec, coefficient=3) self.assertEqual(spec_coeff.species.species_type.id, 'met') self.assertEqual(spec_coeff.species.compartment.id, 'c') self.assertEqual(spec_coeff.coefficient, 3)
def test_constructor(self): comp = core.Compartment(id='c') met = core.MetaboliteSpeciesType(id='met') spec = core.Species(species_type=met, compartment=comp) conc = core.Concentration(species=spec, value=0.2) self.assertEqual(conc.serialize(), 'met[c]') self.assertEqual(conc.value, 0.2) self.assertEqual(conc.units, 2)
def test_SpeciesType(self): comp1 = core.Compartment(id='c') met1 = core.MetaboliteSpeciesType(id='met1') species1 = core.Species(species_type=met1, compartment=comp1) self.assertEqual(core.Species.gen_id(met1, comp1), 'met1[c]') self.assertEqual(core.Species.gen_id('met1', 'c'), 'met1[c]') with self.assertRaisesRegex(ValueError, 'incorrect species type'): core.Species.gen_id(None, 'c') with self.assertRaisesRegex(ValueError, 'incorrect compartment type'): core.Species.gen_id('met1', None) self.assertEqual(species1.id(), 'met1[c]')
def test_constructor(self): met = core.MetaboliteSpeciesType(structure=( 'InChI=1S' '/C10H14N5O7P' '/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20' '/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)' '/p-2/t4-,6-,7-,10-' '/m1' '/s1')) self.assertEqual(met.get_structure(), met.structure) self.assertEqual(met.get_empirical_formula(), chem.EmpiricalFormula('C10H12N5O7P')) self.assertEqual(met.get_charge(), -2) self.assertAlmostEqual(met.get_mol_wt(), 345.20530, places=4)
def test_serialize(self): met = core.MetaboliteSpeciesType(id='met') species_type_coeff = core.SpeciesTypeCoefficient(species_type=met, coefficient=3) self.assertEqual(species_type_coeff.serialize(), '(3) met') self.assertEqual( core.SpeciesTypeCoefficient._serialize(species_type=met, coefficient=3), '(3) met') self.assertEqual( core.SpeciesTypeCoefficient._serialize(species_type=met, coefficient=1), 'met') self.assertEqual( core.SpeciesTypeCoefficient._serialize(species_type=met, coefficient=2000), '(2.000000e+03) met')
def test_deserialize(self): comp1 = core.Compartment(id='c') met1 = core.MetaboliteSpeciesType(id='met1') dna1 = core.DnaSpeciesType(id='dna1') objects = { core.Compartment: { 'c': comp1, }, core.MetaboliteSpeciesType: { 'met1': met1, }, core.DnaSpeciesType: { 'dna1': dna1, }, } attr = core.SpeciesCoefficient.species result = core.Species.deserialize(attr, 'met1[c]', objects) self.assertEqual(result[0].species_type, met1) self.assertEqual(result[0].compartment, comp1) self.assertEqual(result[1], None) result2 = core.Species.deserialize(attr, 'met1[c]', objects) self.assertEqual(result2[0], result[0]) self.assertIn(core.Species, objects) self.assertIn('met1[c]', objects[core.Species]) self.assertNotIn('dna1[c]', objects[core.Species]) self.assertEqual( core.Species.deserialize(attr, 'dna1[c]', objects)[1], None) self.assertIn('dna1[c]', objects[core.Species]) self.assertNotEqual( core.Species.deserialize(attr, 'met2[c]', objects)[1], None) self.assertNotEqual( core.Species.deserialize(attr, 'met1[e]', objects)[1], None) self.assertNotEqual( core.Species.deserialize(attr, 'met1', objects)[1], None)
def test_observables(self): cell = core.Cell() comp1 = core.Compartment(id='c') met1 = core.MetaboliteSpeciesType(id='met1') dna1 = core.DnaSpeciesType(id="dna1") species1 = core.Species(species_type=met1, compartment=comp1) species2 = core.Species(species_type=dna1, compartment=comp1) speciesCoefficient1 = core.SpeciesCoefficient(species=species1, coefficient=2) speciesCoefficient2 = core.SpeciesCoefficient(species=species2, coefficient=3.3) observable1 = core.Observable( cell=cell, species=[speciesCoefficient1, speciesCoefficient2]) observableCoefficient1 = core.ObservableCoefficient( observable=observable1, coefficient=2) observable2 = core.Observable( cell=cell, species=[speciesCoefficient1, speciesCoefficient2], observables=[observableCoefficient1]) self.assertIsInstance(observable1, core.Observable) self.assertIsInstance(observable2, core.Observable) with self.assertRaisesRegex(AttributeError, ""): observable3 = core.Observable(cell=cell, species=[species1, species2]) self.assertIsInstance(observable1.species[0], core.SpeciesCoefficient) self.assertIsInstance(observable2.observables[0], core.ObservableCoefficient) self.assertIsInstance(observable1.species[0].species, core.Species) self.assertEqual(observable1.species[0].species.id(), 'met1[c]') self.assertEqual(observable1.species[1].species.species_type.id, 'dna1') self.assertIsInstance(observable2.observables[0].observable, core.Observable)
def test_ReactionParticipantAttribute(self): compart1 = core.Compartment(id='c') compart2 = core.Compartment(id='m') met1 = core.MetaboliteSpeciesType(id='met1') met2 = core.MetaboliteSpeciesType(id='met2') complex1 = core.ComplexSpeciesType(id='complex1') species1 = core.Species(species_type=met1, compartment=compart1) species2 = core.Species(species_type=met2, compartment=compart1) species3 = core.Species(species_type=complex1, compartment=compart1) species4 = core.Species(species_type=complex1, compartment=compart2) species_coeff1 = core.SpeciesCoefficient(species=species1, coefficient=-2) species_coeff2 = core.SpeciesCoefficient(species=species2, coefficient=-3) species_coeff3 = core.SpeciesCoefficient(species=species3, coefficient=5) species_coeff4 = core.SpeciesCoefficient(species=species4, coefficient=7) self.assertEqual( core.ReactionParticipantAttribute().serialize(participants=[]), '') self.assertEqual( core.ReactionParticipantAttribute().serialize( participants=[species_coeff1]), '[c]: (2) met1 ==> ') self.assertEqual( core.ReactionParticipantAttribute().serialize( participants=[species_coeff1, species_coeff2]), '[c]: (2) met1 + (3) met2 ==> ') self.assertEqual( core.ReactionParticipantAttribute().serialize( participants=[species_coeff1, species_coeff2, species_coeff3]), '[c]: (2) met1 + (3) met2 ==> (5) complex1') self.assertEqual( core.ReactionParticipantAttribute().serialize( participants=[species_coeff1, species_coeff2, species_coeff4]), '(2) met1[c] + (3) met2[c] ==> (7) complex1[m]') objects = { core.DnaSpeciesType: {}, core.MetaboliteSpeciesType: { 'met1': met1, 'met2': met2 }, core.ComplexSpeciesType: { 'complex1': complex1 }, core.Compartment: { 'c': compart1, 'm': compart2 }, core.Species: { 'met1[c]': species1, 'met2[c]': species2, 'complex1[c]': species3, 'complex[m]': species4 }, } result = core.ReactionParticipantAttribute().deserialize( value='[c]: met1 ==> met2', objects=objects) self.assertEqual(result[0][0].species.species_type, met1) self.assertEqual(result[0][1].species.species_type, met2) self.assertEqual(result[0][0].coefficient, -1) self.assertEqual(result[0][1].coefficient, 1) self.assertEqual(result[0][0].species.compartment, compart1) self.assertEqual(result[0][1].species.compartment, compart1) self.assertEqual(result[0][0].species.id(), 'met1[c]') self.assertEqual(result[0][1].species.id(), 'met2[c]') self.assertEqual(result[1], None) result = core.ReactionParticipantAttribute().deserialize( value='(2) met1[c] + (3) met2[c] ==> (7) complex1[m]', objects=objects) self.assertEqual(result[0][0].species.species_type, met1) self.assertEqual(result[0][1].species.species_type, met2) self.assertEqual(result[0][2].species.species_type, complex1) self.assertEqual(result[0][0].coefficient, -2) self.assertEqual(result[0][1].coefficient, -3) self.assertEqual(result[0][2].coefficient, 7.0) self.assertEqual(result[0][0].species.compartment, compart1) self.assertEqual(result[0][1].species.compartment, compart1) self.assertEqual(result[0][2].species.compartment, compart2) self.assertEqual(result[0][0].species.id(), 'met1[c]') self.assertEqual(result[0][1].species.id(), 'met2[c]') self.assertEqual(result[0][2].species.id(), 'complex1[m]') self.assertEqual(result[1], None) result = core.ReactionParticipantAttribute().deserialize( value='met2[c] ==>', objects=objects) self.assertEqual(result[0], None) self.assertEqual(result[1].messages[0], 'Incorrectly formatted participants: met2[c] ==>') result = core.ReactionParticipantAttribute().deserialize( value='==> met1[c]', objects=objects) self.assertEqual(result[0], None) self.assertEqual(result[1].messages[0], 'Incorrectly formatted participants: ==> met1[c]')
def test_SubunitAttribute(self): compart1 = core.Compartment(id='c') met1 = core.MetaboliteSpeciesType(id='met1') dna1 = core.DnaSpeciesType(id='dna1') complex1 = core.ComplexSpeciesType(id='complex1') species1 = core.Species(species_type=complex1, compartment=compart1) species_type_coeff1 = core.SpeciesTypeCoefficient(species_type=met1, coefficient=2) species_type_coeff2 = core.SpeciesTypeCoefficient(species_type=dna1, coefficient=3) species_type_coeff3 = core.SpeciesTypeCoefficient( species_type=complex1, coefficient=5) self.assertEqual(core.SubunitAttribute().serialize(subunits=[]), '') self.assertEqual( core.SubunitAttribute().serialize(subunits=[species_type_coeff1]), '(2) met1') self.assertEqual( core.SubunitAttribute().serialize( subunits=[species_type_coeff1, species_type_coeff2]), '(3) dna1 + (2) met1') self.assertEqual( core.SubunitAttribute().serialize(subunits=[ species_type_coeff1, species_type_coeff2, species_type_coeff3 ]), '(5) complex1 + (3) dna1 + (2) met1') objects = { core.DnaSpeciesType: { 'dna1': dna1 }, core.MetaboliteSpeciesType: { 'met1': met1 }, core.ComplexSpeciesType: { 'complex1': complex1 }, } result = core.SubunitAttribute().deserialize(value='met1 + (2) dna1', objects=objects) self.assertEqual(result[0][0].species_type, met1) self.assertEqual(result[0][1].species_type, dna1) self.assertEqual(result[0][0].coefficient, 1) self.assertEqual(result[0][1].coefficient, 2) self.assertEqual(result[0][0].species_type.id, 'met1') self.assertEqual(result[0][1].species_type.id, 'dna1') self.assertEqual(result[1], None) result = core.SubunitAttribute().deserialize( value='(2) met1 + (7) complex1', objects=objects) self.assertEqual(result[0][0].species_type, met1) self.assertEqual(result[0][1].species_type, complex1) self.assertEqual(result[0][0].coefficient, 2) self.assertEqual(result[0][1].coefficient, 7) self.assertEqual(result[0][0].species_type.id, 'met1') self.assertEqual(result[0][1].species_type.id, 'complex1') self.assertEqual(result[1], None) result = core.SubunitAttribute().deserialize( value='[c]met1 + (2) dna1', objects=objects) self.assertEqual(result[0], None) self.assertEqual( result[1].messages[0], 'Incorrectly formatted participants: [c]met1 + (2) dna1')
def test_deserialize(self): comp = core.Compartment(id='c') dna = core.DnaSpeciesType(id='dna') met = core.MetaboliteSpeciesType(id='met') spec = core.Species(species_type=dna, compartment=comp) objects = { core.Compartment: { 'c': comp, }, core.DnaSpeciesType: { 'dna': dna, }, core.MetaboliteSpeciesType: { 'met': met, }, core.Species: { 'dna[c]': spec, }, } attr = core.Reaction.participants result = core.SpeciesCoefficient.deserialize(attr, '(3) dna[c]', objects) self.assertEqual(result[0].species, spec) self.assertEqual(result[0].coefficient, 3) self.assertEqual(result[1], None) self.assertEqual(len(objects[core.Species]), 1) self.assertEqual(len(objects[core.SpeciesCoefficient]), 1) result2 = core.SpeciesCoefficient.deserialize(attr, '(3) dna[c]', objects) self.assertEqual(result2[0], result[0]) self.assertEqual(result2[1], None) self.assertEqual(len(objects[core.Species]), 1) self.assertEqual(len(objects[core.SpeciesCoefficient]), 1) result = core.SpeciesCoefficient.deserialize(attr, '(-2) dna[c]', objects) self.assertEqual(result[0].species, spec) self.assertEqual(result[0].coefficient, -2) self.assertEqual(result[1], None) self.assertEqual(len(objects[core.Species]), 1) self.assertEqual(len(objects[core.SpeciesCoefficient]), 2) result = core.SpeciesCoefficient.deserialize(attr, 'dna[c]', objects) self.assertEqual(result[0].species, spec) self.assertEqual(result[0].coefficient, 1) self.assertEqual(result[1], None) self.assertEqual(len(objects[core.Species]), 1) self.assertEqual(len(objects[core.SpeciesCoefficient]), 3) result = core.SpeciesCoefficient.deserialize(attr, 'met[c]', objects) self.assertEqual(result[0].species.species_type, met) self.assertEqual(result[0].species.compartment, comp) self.assertEqual(result[0].coefficient, 1) self.assertEqual(result[1], None) self.assertEqual(len(objects[core.Species]), 2) self.assertEqual(len(objects[core.SpeciesCoefficient]), 4) result = core.SpeciesCoefficient.deserialize(attr, 'dna2[c]', objects) self.assertEqual(result[0], None) self.assertNotEqual(result[1], None) result = core.SpeciesCoefficient.deserialize(attr, 'dna', objects) self.assertEqual(result[0], None) self.assertNotEqual(result[1], None) result = core.SpeciesCoefficient.deserialize(attr, 'dna', objects, compartment=comp) self.assertEqual(result[0].species.species_type, dna) self.assertEqual(result[0].species.compartment, comp) self.assertEqual(result[0].coefficient, 1) self.assertEqual(result[1], None) result = core.SpeciesCoefficient.deserialize(attr, '(2) dna', objects, compartment=comp) self.assertEqual(result[0].species.species_type, dna) self.assertEqual(result[0].species.compartment, comp) self.assertEqual(result[0].coefficient, 2) self.assertEqual(result[1], None) result = core.SpeciesCoefficient.deserialize(attr, '(-3) dna', objects, compartment=comp) self.assertEqual(result[0].species.species_type, dna) self.assertEqual(result[0].species.compartment, comp) self.assertEqual(result[0].coefficient, -3) self.assertEqual(result[1], None)
def test_serialize(self): comp1 = core.Compartment(id='c') met1 = core.MetaboliteSpeciesType(id='met1') species1 = core.Species(species_type=met1, compartment=comp1) self.assertEqual(species1.serialize(), 'met1[c]')
def setUp(self): self.cell_1 = cell_1 = core.Cell() self.compartment_1 = compartment_1 = core.Compartment(cell=cell_1, id='c') self.species_type_1 = species_type_1 = core.MetaboliteSpeciesType( id='species_type_1') self.species_type_2 = species_type_2 = core.MetaboliteSpeciesType( id='species_type_2') self.species_1 = species_1 = core.Species(species_type=species_type_1, compartment=compartment_1) self.species_2 = species_2 = core.Species(species_type=species_type_2, compartment=compartment_1) self.participant_1 = participant_1 = core.SpeciesCoefficient( species=species_1, coefficient=1) self.participant_2 = participant_2 = core.SpeciesCoefficient( species=species_2, coefficient=1) self.reaction_1 = reaction_1 = core.Reaction( id='reaction_1', name='test_reaction', cell=cell_1, participants=[participant_1, participant_2], reversible=False) self.rate_law_equation_1 = rate_law_equation_1 = core.RateLawEquation( expression=species_1.id()) self.rate_law_1 = rate_law_1 = core.RateLaw( reaction=reaction_1, direction=core.RateLawDirection.forward, k_m=0.1, k_cat=0.5, equation=rate_law_equation_1) self.reaction_2 = reaction_2 = core.Reaction( id='reaction_2', name='test_reaction2', cell=cell_1, participants=[participant_1, participant_2], reversible=False) self.parameter_1 = parameter_1 = core.Parameter(id='p1', name='test_parameter1', value=0.7, error=0.01, units='s^-1') self.parameter_2 = parameter_2 = core.Parameter(id='p2', name='test_parameter2', value=2., error=0.1, units='M') self.parameter_3 = parameter_3 = core.Parameter(id='p3', name='test_parameter3', value=2.3, error=0.15, units='M') self.rate_law_equation_2 = rate_law_equation_2 = core.RateLawEquation( expression= 'p1*species_type_1[c]*species_type_2[c]/(p2+species_type_2[c]+(species_type_2[c]^2/p3))', modifiers=[species_1, species_2], parameters=[parameter_1, parameter_2]) self.rate_law_2 = rate_law_2 = core.RateLaw( reaction=reaction_2, direction=core.RateLawDirection.backward, equation=rate_law_equation_2) self.objects = { core.Species: { species_1.id(): species_1, species_2.id(): species_2 }, core.Parameter: { parameter_1.id: parameter_1, parameter_2.id: parameter_2, parameter_3.id: parameter_3 } }