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def test_iqspr_1(data):
np.random.seed(0)
ecfp = ECFP(n_jobs=1, input_type='smiles')
bre = GaussianLogLikelihood(descriptor=ecfp)
ngram = NGram()
iqspr = IQSPR(estimator=bre, modifier=ngram)
X, y = data['pg']
bre.fit(X, y)
ngram.fit(data['pg'][0][0:20], train_order=10)
beta = np.linspace(0.05, 1, 10)
for s, ll, p, f in iqspr(data['pg'][0][:5], beta, yield_lpf=True, bandgap=(0.1, 0.2), density=(0.9, 1.2)):
assert np.abs(np.sum(p) - 1.0) < 1e-5
assert np.sum(f) == 5, print(f)
def test_ecfp_4(data):
fps = ECFP(n_jobs=1, input_type='any')
with pytest.raises(ValueError):
fps.transform(data['err_smis'])
fps = ECFP(n_jobs=1, input_type='any', on_errors='nan')
ret = fps.transform(data['err_smis'])
assert pd.DataFrame(data=ret).shape == (4, 2048)
assert np.isnan(ret[1][10])
assert np.isnan(ret[2][20])
def test_ecfp_2(data):
fps = ECFP(n_jobs=1, input_type='smiles')
with pytest.raises(TypeError):
fps.transform(data['mols'])
fps.transform(data['smis'])
def data():
# ignore numpy warning
import warnings
print('ignore NumPy RuntimeWarning\n')
warnings.filterwarnings("ignore", message="numpy.dtype size changed")
warnings.filterwarnings("ignore", message="numpy.ndarray size changed")
pwd = Path(__file__).parent
pg_data = pd.read_csv(str(pwd / 'polymer_test_data.csv'))
X = pg_data['smiles']
y = pg_data.drop(['smiles', 'Unnamed: 0'], axis=1)
ecfp = ECFP(n_jobs=1, input_type='smiles')
bre = GaussianLogLikelihood(descriptor=ecfp)
ngram = NGram()
iqspr = IQSPR(estimator=bre, modifier=ngram)
# prepare test data
yield dict(ecfp=ecfp, bre=bre, ngram=ngram, iqspr=iqspr, pg=(X, y))
print('test over')
def test_ecfp_3(data):
fps = ECFP(n_jobs=1, input_type='any')
fps.transform(data['mols'] + data['smis'])
def test_ecfp_1(data):
fps = ECFP(n_jobs=1)
fps.transform(data['mols'])
with pytest.raises(TypeError):
fps.transform(data['smis'])
def test_ecfp_4(data):
fps = ECFP(n_jobs=1, input_type='any')
with pytest.raises(ValueError):
fps.transform(data['err_smis'])
fps = ECFP(n_jobs=1, input_type='any', on_errors='nan')
ret = fps.transform(data['err_smis'])
assert pd.DataFrame(data=ret).shape == (4, 2048)
assert np.isnan(ret[1][10])
assert np.isnan(ret[2][20])
def __init__(self, n_jobs=-1, *, elements=None, include=None,
exclude=None):
super().__init__()
self.n_jobs = n_jobs
self.rdkit_fp = FPsCalc(n_jobs)
# self.rdkit_fp = MACCS_MOLS(n_jobs)