def test_template_repository(template_mols, model_sort_key):
template_repo = repo.create_template_repository()
ids = template_repo.save(template_mols)
data = list(template_repo.load(ids))
data.sort(key=model_sort_key)
assert data == template_mols
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_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_template_importer(json_importer):
template_importer = importers.TemplateImporter(json_importer)
ids = template_importer.import_data()
template_repo = repo.create_template_repository()
data = list(template_repo.load(ids))
docs = json_importer.load(template_importer.saver.TYPE.STRING)
kekules = [doc['kekule'] for doc in docs]
assert(len(data) == 3)
for mol in data:
assert(mol._id != None)
assert(mol.kekule in kekules)
kekules.remove(mol.kekule)
def _match_reactions(self, key):
templates = repo.create_template_repository().load()
ps_capable_templates = tuple(template._id for template in filter(lambda x: x.pictet_spangler_kekule, templates))
for template_peptide in self.template_peptide_repo.load(key):
reactions = []
sidechain_data = set(monomer['sidechain'] for monomer in template_peptide.monomers if
monomer['sidechain'] is not None)
monomer_data = set(
monomer['_id'] for monomer in template_peptide.monomers if monomer['sidechain'] is None)
for mol_id in chain(sidechain_data, monomer_data):
reactions.extend(filter(lambda x: x.template == template_peptide.template, self.reactions[mol_id]))
first_monomer = template_peptide.monomers[0]['sidechain']
is_proline = template_peptide.monomers[0]['proline']
# can apply pictet_spangler reactions or template_only_reactions because
# 1. Template 2 and 3 has unmasked aldehyde
# 2. First monomer has a sidechain which comes from a set of aromatic heterocycles (either the sidechain
# undergo pictet_spangler or the template can undergo pictet_spangler/aldehyde cyclization)
# 3. First monomer doesnt contain any aromatic atoms and is not a proline thus the template will be able
# to undergo the template_only_reactions
if template_peptide.template in ps_capable_templates and \
((first_monomer is not None) or (first_monomer is None and not is_proline)):
# get pictet_spangler reactions involving only the first monomer or any other type of reaction
reactions = filter(lambda x: ((x.type == self.PS and x.reacting_mol['_id'] == first_monomer)
or x.type in (self.FC, self.TT, self.PI)), reactions)
# sort reactions based on if they are pictet_spangler or not
pictet, other = [], []
for rxn in reactions:
other.append(rxn) if rxn.type != self.PS else pictet.append(rxn)
if not pictet or first_monomer is None:
rxn_combinations = product(self.template_only_reactions[template_peptide.template], other)
else:
# if pictet_spangler fails because template is not oligomerized to the peptide at the first monomer
# (as may occur with lysine in the peptide) then template_only_reaction will be applied. Otherwise
# pictet_spangler will occur, blocking the template_only_reaction from taking place
rxn_combinations = product(pictet, self.template_only_reactions[template_peptide.template], other)
yield MacrocycleDataHandlerTuple(template_peptide, rxn_combinations)
else: # friedel_crafts, tsuji_trost, pyrrolo_indolene
yield MacrocycleDataHandlerTuple(template_peptide,
[[rxn] for rxn in filter(lambda x: x.type != self.PS, reactions)])
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.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()
self.template_repo = repo.create_template_repository()
super().__init__(repo.create_reaction_repository())
def __init__(self):
self.template_repo = repo.create_template_repository()
self.peptide_repo = repo.create_peptide_repository()
super().__init__(repo.create_template_peptide_repository())
def test_template_repository_fail():
template_repo = repo.create_template_repository()
_ = template_repo.save(['dne'])
assert len(template_repo.failed_instances) == 1
def __init__(self, loader):
self.loader = loader
self.saver = repo.create_template_repository()