def test_monomer_importer(json_importer, independent_importers):
monomer_importer = importers.MonomerImporter(json_importer)
ids = monomer_importer.import_data()
monomer_repo = repo.create_monomer_repository()
backbone_repo = repo.create_backbone_repository()
monomer_data = list(monomer_repo.load(ids))
monomer_docs = json_importer.load(monomer_importer.saver.TYPE.STRING)
backbone_data = list(backbone_repo.load())
kekules = [doc['kekule'] for doc in monomer_docs]
backbones = [mol.to_reduced_dict() for mol in backbone_data]
assert(len(monomer_data) == 4)
for mol in monomer_data:
rdkit_mol = mol.mol
assert(mol._id != None)
assert(mol.required == bool(AllChem.CalcNumAromaticRings(rdkit_mol)))
assert(mol.backbone in backbones)
assert(mol.sidechain is None)
assert(mol.connection is None)
assert(mol.proline == bool(AllChem.CalcNumAliphaticRings(
rdkit_mol) and rdkit_mol.HasSubstructMatch(PROLINE_N_TERM)))
assert(mol.imported == True)
assert(mol.kekule in kekules)
kekules.remove(mol.kekule)
def test_initialize(initialized_repository):
assert len(list(repo.create_backbone_repository().load())) == 3
assert len(list(repo.create_connection_repository().load())) == 2
assert len(list(repo.create_template_repository().load())) == 3
assert len(list(repo.create_sidechain_repository().load())) == 3
assert len(list(repo.create_monomer_repository().load())) == 4
assert len(list(repo.create_regiosqm_repository().load())) == 3
assert len(list(repo.create_pka_repository().load())) == 3
def test_monomer_repository(monomer_mols, model_sort_key):
monomer_repo = repo.create_monomer_repository()
ids = monomer_repo.save(monomer_mols)
data = list(monomer_repo.load(ids))
data.sort(key=model_sort_key)
for i, monomer in enumerate(monomer_mols):
monomer.index = i
assert data == monomer_mols
def test_initialize_predictions_only(partial_initialized_repository):
exporter = RegioSQMExporter()
exporter.export_regiosqm_smiles_file()
initializer = CPMGInitializer()
initializer._initialize_predictions_only()
assert len(list(repo.create_backbone_repository().load())) == 3
assert len(list(repo.create_connection_repository().load())) == 2
assert len(list(repo.create_template_repository().load())) == 3
assert len(list(repo.create_sidechain_repository().load())) == 3
assert len(list(repo.create_monomer_repository().load())) == 4
assert len(list(repo.create_regiosqm_repository().load())) == 3
assert len(list(repo.create_pka_repository().load())) == 3
def test_initialize_mol_only(partial_initialized_repository):
assert len(list(repo.create_backbone_repository().load())) == 3
assert len(list(repo.create_connection_repository().load())) == 2
assert len(list(repo.create_template_repository().load())) == 3
assert len(list(repo.create_sidechain_repository().load())) == 3
assert len(list(repo.create_monomer_repository().load())) == 4
def __init__(self):
self.plan_repo = repo.create_peptide_plan_repository()
self.monomer_repo = repo.create_monomer_repository()
super().__init__(repo.create_peptide_repository())
def __init__(self):
self.backbone_repo = repo.create_backbone_repository()
self.sidechain_repo = repo.create_sidechain_repository()
super().__init__(repo.create_monomer_repository())
def __init__(self):
self.sidechain_repo = repo.create_sidechain_repository()
self.monomer_repo = repo.create_monomer_repository()
self.template_repo = repo.create_template_repository()
super().__init__(repo.create_reaction_repository())
def __init__(self):
self.sidechain_repo = repo.create_sidechain_repository()
self.monomer_repo = repo.create_monomer_repository()
def test_monomer_repository_fail():
monomer_repo = repo.create_monomer_repository()
_ = monomer_repo.save(['dne'])
assert len(monomer_repo.failed_instances) == 1
def __init__(self, loader):
self.loader = loader
self.saver = repo.create_monomer_repository()
self.backbones = {}