def test_annotation(): st = Phosphorylation(Agent('BRAF', db_refs = {'UP': 'P15056'}), Agent('MAP2K2', db_refs = {'HGNC': '6842'})) pa = PysbAssembler() pa.add_statements([st]) pa.make_model() assert(len(pa.model.annotations) == 4)
def test_pysb_assembler_actsub(): stmt = ActiveForm(Agent('BRAF', mutations=[MutCondition('600', 'V', 'E')]), 'activity', True) pa = PysbAssembler() pa.add_statements([stmt]) model = pa.make_model(policies='two_step') assert(len(model.rules)==0) assert(len(model.monomers)==1)
def test_pysb_assembler_autophos1(): enz = Agent('MEK1') stmt = Autophosphorylation(enz, 'serine', '222') pa = PysbAssembler() pa.add_statements([stmt]) model = pa.make_model() assert(len(model.rules)==1) assert(len(model.monomers)==1)
def test_non_python_name_phos(): st = Phosphorylation(Agent('14-3-3'), Agent('BRAF kinase')) pa = PysbAssembler() pa.add_statements([st]) pa.make_model() names = [m.name for m in pa.model.monomers] assert('BRAF_kinase' in names) assert('p14_3_3' in names) bng.generate_equations(pa.model)
def test_pysb_assembler_complex1(): member1 = Agent('BRAF') member2 = Agent('MEK1') stmt = Complex([member1, member2]) pa = PysbAssembler() pa.add_statements([stmt]) model = pa.make_model() assert(len(model.rules)==2) assert(len(model.monomers)==2)
def test_pysb_assembler_dephos_noenz(): enz = None sub = Agent('MEK1') stmt = Phosphorylation(enz, sub, 'serine', '222') pa = PysbAssembler() pa.add_statements([stmt]) model = pa.make_model() assert(len(model.rules)==0) assert(len(model.monomers)==0)
def test_pysb_assembler_transphos1(): egfr = Agent('EGFR') enz = Agent('EGFR', bound_conditions=[BoundCondition(egfr, True)]) stmt = Transphosphorylation(enz, 'tyrosine') pa = PysbAssembler() pa.add_statements([stmt]) model = pa.make_model() assert(len(model.rules)==1) assert(len(model.monomers)==1)
def test_activity_activity3(): subj = Agent('Vemurafenib') obj = Agent('BRAF') stmt = Inhibition(subj, obj) pa = PysbAssembler(policies='one_step') pa.add_statements([stmt]) model = pa.make_model() assert(len(model.rules)==1) assert(len(model.monomers)==2)
def test_pysb_assembler_dephos_twostep1(): phos = Agent('PP2A') sub = Agent('MEK1') stmt = Dephosphorylation(phos, sub, 'serine', '222') pa = PysbAssembler(policies='two_step') pa.add_statements([stmt]) model = pa.make_model() assert(len(model.rules)==3) assert(len(model.monomers)==2)
def test_activity_activity(): subj = Agent('KRAS') obj = Agent('BRAF') stmt = Activation(subj, obj) pa = PysbAssembler(policies='interactions_only') pa.add_statements([stmt]) model = pa.make_model() assert(len(model.rules)==1) assert(len(model.monomers)==2)
def test_pysb_assembler_phos_twostep_local(): enz = Agent('BRAF') sub = Agent('MEK1') stmt = Phosphorylation(enz, sub, 'serine', '222') pa = PysbAssembler() pa.add_statements([stmt]) model = pa.make_model(policies='two_step') assert(len(model.rules)==3) assert(len(model.monomers)==2)
def test_pysb_assembler_rasgap1(): gap = Agent('NF1') ras = Agent('HRAS') stmt = RasGap(gap, ras) pa = PysbAssembler() pa.add_statements([stmt]) model = pa.make_model() assert(len(model.rules)==1) assert(len(model.monomers)==2)
def test_agent_loc(): st = Phosphorylation(Agent('BRAF', location='cytoplasm'), Agent('MEK')) pa = PysbAssembler() pa.add_statements([st]) pa.make_model() assert(len(pa.model.rules) == 1) r = pa.model.rules[0] braf = r.reactant_pattern.complex_patterns[0].monomer_patterns[0] assert(braf.site_conditions == {'loc': 'cytoplasm'})
def test_pysb_assembler_rasgef1(): gef = Agent('SOS1') ras = Agent('HRAS') stmt = RasGef(gef, ras) pa = PysbAssembler() pa.add_statements([stmt]) model = pa.make_model() assert(len(model.rules)==1) assert(len(model.monomers)==2)
def test_pysb_assembler_autophos2(): raf1 = Agent('RAF1') enz = Agent('MEK1', bound_conditions=[BoundCondition(raf1, True)]) stmt = Autophosphorylation(enz, 'serine', '222') pa = PysbAssembler() pa.add_statements([stmt]) model = pa.make_model() assert(len(model.rules)==1) assert(len(model.monomers)==2)
def test_pysb_assembler_complex3(): hras = Agent('HRAS') member1 = Agent('BRAF', bound_conditions=[BoundCondition(hras, True)]) member2 = Agent('MEK1') stmt = Complex([member1, member2]) pa = PysbAssembler() pa.add_statements([stmt]) model = pa.make_model() assert(len(model.rules)==2) assert(len(model.monomers)==3)
def test_set_context_monomer_notfound(): st = Phosphorylation(Agent('MAP2K1'), Agent('XYZ')) pa = PysbAssembler() pa.add_statements([st]) pa.make_model() assert(pa.model.parameters['MAP2K1_0'].value < 1000) assert(pa.model.parameters['XYZ_0'].value < 1000) pa.set_context('A375_SKIN') assert(pa.model.parameters['MAP2K1_0'].value > 10000) assert(pa.model.parameters['XYZ_0'].value < 1000)
def test_pysb_assembler_twostep_mixed(): member1 = Agent('BRAF') member2 = Agent('RAF1') st1 = Complex([member1, member2]) st2 = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3')) pa = PysbAssembler() pa.add_statements([st1, st2]) pa.make_model(policies='two_step') assert(len(pa.model.rules)==5) assert(len(pa.model.monomers)==4)
def test_pysb_assembler_dephos2(): phos = Agent('PP2A') raf1 = Agent('RAF1') sub = Agent('MEK1', bound_conditions=[BoundCondition(raf1, True)]) stmt = Dephosphorylation(phos, sub, 'serine', '222') pa = PysbAssembler() pa.add_statements([stmt]) model = pa.make_model() assert(len(model.rules)==1) assert(len(model.monomers)==3)
def test_pysb_assembler_act1(): egfr = Agent('EGFR') subj = Agent('GRB2', bound_conditions=[BoundCondition(egfr, True)]) obj = Agent('SOS1') stmt = Activation(subj, obj) pa = PysbAssembler() pa.add_statements([stmt]) model = pa.make_model() assert(len(model.rules)==1) assert(len(model.monomers)==3)
def test_synthesis_one_step(): subj = Agent('KRAS') obj = Agent('BRAF') st1 = Synthesis(subj, obj) st2 = Synthesis(None, obj) pa = PysbAssembler(policies='one_step') pa.add_statements([st1, st2]) model = pa.make_model() assert(len(model.rules)==2) assert(len(model.monomers)==2)
def test_pysb_assembler_phos2(): hras = Agent('HRAS') enz = Agent('BRAF', bound_conditions=[BoundCondition(hras, True)]) sub = Agent('MEK1') stmt = Phosphorylation(enz, sub, 'serine', '222') pa = PysbAssembler() pa.add_statements([stmt]) model = pa.make_model() assert(len(model.rules)==1) assert(len(model.monomers)==3)
def test_activeform_site(): a = Agent('A', db_refs={'HGNC': '1234'}) b = Agent('B', db_refs={'HGNC': '5678'}) b_phos = Agent('B', mods=[ModCondition('phosphorylation', 'Y', '200')], db_refs={'HGNC': '5678'}) st1 = Phosphorylation(a, b, 'S', '100') st2 = ActiveForm(b_phos, 'kinase', True) pa = PysbAssembler(policies='one_step') pa.add_statements([st1, st2]) model = pa.make_model()
def test_increaseamount_interactions_only(): subj = Agent('KRAS') obj = Agent('BRAF') st1 = IncreaseAmount(subj, obj) st2 = IncreaseAmount(None, obj) pa = PysbAssembler(policies='interactions_only') pa.add_statements([st1, st2]) model = pa.make_model() assert(len(model.rules)==1) assert(len(model.monomers)==2)
def test_decreaseamount_one_step(): subj = Agent('KRAS') obj = Agent('BRAF') st1 = DecreaseAmount(subj, obj) st2 = DecreaseAmount(None, obj) pa = PysbAssembler(policies='one_step') pa.add_statements([st1, st2]) model = pa.make_model() assert(len(model.rules)==2) assert(len(model.monomers)==2)
def test_pysb_assembler_complex_multiway(): member1 = Agent('BRAF') member2 = Agent('MEK1') member3 = Agent('ERK1') stmt = Complex([member1, member2, member3]) pa = PysbAssembler() pa.add_statements([stmt]) model = pa.make_model(policies='multi_way') assert(len(model.rules)==2) assert(len(model.monomers)==3)
def test_set_context(): st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3')) pa = PysbAssembler() pa.add_statements([st]) pa.make_model() assert(pa.model.parameters['MAP2K1_0'].value == pa.default_initial_amount) assert(pa.model.parameters['MAPK3_0'].value == pa.default_initial_amount) pa.set_context('A375_SKIN') assert(pa.model.parameters['MAP2K1_0'].value > 10000) assert(pa.model.parameters['MAPK3_0'].value > 10000)
def test_export_model(): st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3')) pa = PysbAssembler() pa.add_statements([st]) pa.make_model() exp_str = pa.export_model('kappa') assert(exp_str) exp_str = pa.export_model('bngl') assert(exp_str) exp_str = pa.export_model('sbml', file_name='/dev/null') assert(exp_str)
def test_neg_agent_mod(): mc = ModCondition('phosphorylation', 'serine', '123', False) st = Phosphorylation(Agent('BRAF', mods=[mc]), Agent('MAP2K2')) pa = PysbAssembler(policies='one_step') pa.add_statements([st]) pa.make_model() assert(len(pa.model.rules) == 1) r = pa.model.rules[0] braf = r.reactant_pattern.complex_patterns[0].monomer_patterns[0] assert(braf.monomer.name == 'BRAF') assert(braf.site_conditions == {'S123': ('u', WILD)})
def test_mut(): mut = MutCondition('600', 'V', 'E') st = Phosphorylation(Agent('BRAF', mutations=[mut]), Agent('MEK')) pa = PysbAssembler() pa.add_statements([st]) pa.make_model() assert(len(pa.model.rules) == 1) r = pa.model.rules[0] braf = r.reactant_pattern.complex_patterns[0].monomer_patterns[0] assert(braf.monomer.name == 'BRAF') assert(braf.site_conditions == {'V600': 'E'})
def test_generate_equations(): st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3')) pa = PysbAssembler() pa.add_statements([st]) pa.make_model() bng.generate_equations(pa.model)
def test_deubiq_michaelis_menten(): stmt = Deubiquitination(Agent('MEK'), Agent('ERK')) pa = PysbAssembler() pa.add_statements([stmt]) pa.make_model(policies='michaelis_menten') assert (len(pa.model.parameters) == 4)
def test_phos_atpdep(): st = Phosphorylation(Agent('BRAF'), Agent('MEK'), 'S', '222') pa = PysbAssembler() pa.add_statements([st]) pa.make_model(policies='atp_dependent') assert (len(pa.model.rules) == 5)
def test_set_context_celltype_notfound(): st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3')) pa = PysbAssembler() pa.add_statements([st]) pa.make_model() pa.set_context('XYZ')
def test_print_model(): st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3')) pa = PysbAssembler() pa.add_statements([st]) pa.make_model() pa.save_model('/dev/null')
def test_non_python_name_bind(): st = Complex([Agent('14-3-3'), Agent('BRAF kinase')]) pa = PysbAssembler() pa.add_statements([st]) pa.make_model() bng.generate_equations(pa.model)