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 = {}