import pytest
import stk
from .case_data import CaseData
@pytest.fixture(
params=(
CaseData(
key_maker=stk.Inchi(),
molecule=stk.BuildingBlock('NCCN'),
key_name='InChI',
key='InChI=1S/C2H8N2/c3-1-2-4/h1-4H2',
),
CaseData(
key_maker=stk.InchiKey(),
molecule=stk.BuildingBlock('NCCN'),
key_name='InChIKey',
key='PIICEJLVQHRZGT-UHFFFAOYSA-N',
),
CaseData(
key_maker=stk.Smiles(),
molecule=stk.BuildingBlock('NCCN'),
key_name='SMILES',
key='NCCN',
),
CaseData(
key_maker=stk.Smiles(),
molecule=stk.BuildingBlock('C(N)CN'),
key_name='SMILES',
key='NCCN',
def test_get_all(mongo_client):
"""
Test iteration over all molecules.
"""
database_name = '_test_get_entries_constructed_molecule'
mongo_client.drop_database(database_name)
key_maker = stk.Inchi()
jsonizer = stk.ConstructedMoleculeJsonizer(
key_makers=(key_maker, )
)
database = stk.ConstructedMoleculeMongoDb(
mongo_client=mongo_client,
database=database_name,
jsonizer=jsonizer,
put_lru_cache_size=0,
get_lru_cache_size=0,
)
molecules = [
stk.ConstructedMolecule(
topology_graph=stk.polymer.Linear(
building_blocks=(stk.BuildingBlock(
smiles='BrCCCBr',
functional_groups=[stk.BromoFactory()]),
),
repeating_unit='A',
num_repeating_units=3,
),
),
stk.ConstructedMolecule(
topology_graph=stk.polymer.Linear(
building_blocks=(
stk.BuildingBlock(
smiles='BrCCBr',
functional_groups=[stk.BromoFactory()]
),
stk.BuildingBlock(
smiles='BrCNCBr',
functional_groups=[stk.BromoFactory()]
),
),
repeating_unit='AB',
num_repeating_units=2,
),
),
]
molecules_by_key = {
key_maker.get_key(molecule): molecule
for molecule in molecules
}
for molecule in molecules:
database.put(molecule)
for i, retrieved in enumerate(database.get_all()):
key = key_maker.get_key(retrieved)
molecule = molecules_by_key[key]
is_equivalent_constructed_molecule(
molecule.with_canonical_atom_ordering(),
retrieved.with_canonical_atom_ordering(),
)
# Check number of molecules.
assert i+1 == len(molecules)
import stk
import numpy as np
import pytest
from .case_data import CaseData
@pytest.fixture(
params=(
CaseData(
jsonizer=stk.MoleculeJsonizer(key_makers=(
stk.Inchi(),
stk.InchiKey(),
)),
molecule=stk.BuildingBlock(
smiles='Br[C+2][C+2]Br', ).with_position_matrix(
np.array([
[0, 0, 0],
[1, 1, 1],
[2, 2, 2],
[3, 3, 3],
],
dtype=np.float64)),
json={
'molecule': {
'a': (
(35, 0),
(6, 2),
(6, 2),
(35, 0),
),
def get_inchis(batch):
inchi = stk.Inchi()
return tuple(inchi.get_key(record.get_molecule()) for record in batch)
