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_ComplexSpeciesType(self):
# Test constructor
complex1 = core.ComplexSpeciesType()
# Generate test proteins from Mycoplasma Genintalium Genome
dna1 = core.DnaSpeciesType(id='chromosome',
sequence_path='tests/fixtures/seq.fna')
cell1 = dna1.cell = core.Cell()
cell1.knowledge_base = core.KnowledgeBase(
translation_table=4) # Table 4 is for mycoplasma
# Protein 1, MPN001
gene1 = prokaryote_schema.GeneLocus(id='gene1',
cell=cell1,
polymer=dna1,
start=692,
end=1834)
tu1 = prokaryote_schema.TranscriptionUnitLocus(id='tu1',
genes=[gene1],
polymer=dna1)
prot1 = prokaryote_schema.ProteinSpeciesType(id='prot1',
gene=gene1,
cell=cell1)
# Protein 2, MPN011
gene2 = prokaryote_schema.GeneLocus(id='gene2',
cell=cell1,
polymer=dna1,
start=12838,
end=13533,
strand=core.PolymerStrand.negative)
tu2 = prokaryote_schema.TranscriptionUnitLocus(id='tu2',
genes=[gene2],
polymer=dna1)
prot2 = prokaryote_schema.ProteinSpeciesType(id='prot2',
gene=gene2,
cell=cell1)
# Test adding complexation
# Add formation reaction: (2) prot1 + (3) prot2 ==> complex1
species_coeff1 = core.SpeciesTypeCoefficient(species_type=prot1,
coefficient=2)
species_coeff2 = core.SpeciesTypeCoefficient(species_type=prot2,
coefficient=3)
complex1.subunits = [species_coeff1, species_coeff2]
self.assertEqual(complex1.get_charge(), 38)
self.assertAlmostEqual(
complex1.get_mol_wt(),
(2 * prot1.get_mol_wt() + 3 * prot2.get_mol_wt()))
self.assertEqual(complex1.get_empirical_formula(),
chem.EmpiricalFormula('C7698H12076N1938O2248S23'))
def test_ComplexSpeciesType(self):
self.tmp_dirname = tempfile.mkdtemp()
sequence_path = os.path.join(self.tmp_dirname, 'test_seq.fasta')
with open(sequence_path, 'w') as f:
f.write(
'>dna1\nTTTATGAARGTNCTCATHAAYAARAAYGARCTCTAGTTTATGAARTTYAARTTYCTCCTCACNCCNCTCTAATTT\n'
)
dna1 = core.DnaSpeciesType(id='dna1', sequence_path=sequence_path)
# Protein subunit 1
gene1 = eukaryote_schema.GeneLocus(polymer=dna1, start=1, end=36)
rna1 = eukaryote_schema.PreRnaSpeciesType(gene=gene1)
exon1 = eukaryote_schema.ExonLocus(start=4, end=36)
transcript1 = eukaryote_schema.TranscriptSpeciesType(rna=rna1,
exons=[exon1])
cds1 = eukaryote_schema.CdsLocus(start=4, end=36)
prot1 = eukaryote_schema.ProteinSpeciesType(transcript=transcript1,
coding_region=cds1)
# Protein subunit 2
gene2 = eukaryote_schema.GeneLocus(polymer=dna1, start=37, end=75)
rna2 = eukaryote_schema.PreRnaSpeciesType(gene=gene2)
exon2 = eukaryote_schema.ExonLocus(start=40, end=72)
transcript2 = eukaryote_schema.TranscriptSpeciesType(rna=rna2,
exons=[exon2])
cds2 = eukaryote_schema.CdsLocus(start=40, end=72)
prot2 = eukaryote_schema.ProteinSpeciesType(transcript=transcript2,
coding_region=cds2)
# Complex formation: (2) prot1 + (3) prot2 ==> complex1
species_coeff1 = core.SpeciesTypeCoefficient(species_type=prot1,
coefficient=2)
species_coeff2 = core.SpeciesTypeCoefficient(species_type=prot2,
coefficient=3)
complex1 = core.ComplexSpeciesType(
subunits=[species_coeff1, species_coeff2])
self.assertEqual(complex1.get_charge(), 8)
self.assertAlmostEqual(
complex1.get_mol_wt(),
(2 * prot1.get_mol_wt() + 3 * prot2.get_mol_wt()))
self.assertEqual(complex1.get_empirical_formula(),
chem.EmpiricalFormula('C292H492N64O66S5'))
shutil.rmtree(self.tmp_dirname)
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_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_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')