def test_ngram_3(data):
ngram = NGram(sample_order=5)
ngram.fit(data['pg'][0][:20], train_order=5)
def on_errors(self, error):
if isinstance(error, MolConvertError):
raise error
else:
return error.old_smi
np.random.seed(123456)
ngram.on_errors = types.MethodType(on_errors, ngram)
with pytest.raises(MolConvertError):
old_smis = ['CC(=S)C([*])(C)=CCC([*])']
ngram.proposal(old_smis)
def on_errors(self, error):
if isinstance(error, GetProbError):
raise error
else:
return error.old_smi
np.random.seed(654321)
ngram.on_errors = types.MethodType(on_errors, ngram)
with pytest.raises(GetProbError):
old_smis = ['C([*])C([*])(C1=C(OCCC)C=CC(Br)C1)']
ngram.proposal(old_smis)
def learn_n_gram2(smiles):
# Method 2: expand n-gram training set with randomly reordered SMILES
# (we show one of the many possible ways of doing it)
n_reorder = 10 # pick a fixed number of re-ordering
# convert the SMILES to canonical SMILES in RDKit (not necessary in general)
cans = []
for smi in smiles:
# remove some molecules in the full SMILES list that may lead to error
try:
cans.append(Chem.MolToSmiles(Chem.MolFromSmiles(smi)))
except:
print(smi)
pass
mols = [Chem.MolFromSmiles(smi) for smi in cans]
smi_reorder = []
for mol in mols:
idx = list(range(mol.GetNumAtoms()))
np.random.shuffle(idx)
tmp = [Chem.MolToSmiles(mol, rootedAtAtom=x) for x in range(min(len(idx), n_reorder))]
smi_reorder.append(list(set(tmp)))
# flatten out the list and train the N-gram
flat_list = [item for sublist in smi_reorder for item in sublist]
n_gram_reorder = NGram(reorder_prob=0.5)
n_gram_reorder.fit(flat_list)
# save results
# with open('ngram_reorder_full.obj', 'wb') as f:
# pk.dump(n_gram_reorder, f)
return n_gram_reorder
def learn_n_gram0(smiles):
# initialize a new n-gram
n_gram = NGram()
# train the n-gram with SMILES of available molecules
n_gram.fit(smiles, train_order=5)
return n_gram
def _learn_n_gram2(smiles, reorder_prob=0.5, paraphrased_smiles_number=10):
# Method 2: expand n-gram training set with randomly reordered SMILES
# (we show one of the many possible ways of doing it)
mols = _smiles_to_mol(smiles)
generated_smiles = []
gen_smi_append = generated_smiles.append
for mol in mols:
number_of_atom = mol.GetNumAtoms()
sample_number = min(number_of_atom, paraphrased_smiles_number)
shuffled_index = np.random.permutation(number_of_atom)
tmp = [
Chem.MolToSmiles(mol, rootedAtAtom=int(x))
for x in shuffled_index[:sample_number]
]
gen_smi_append(list(set(tmp)))
flat_list = [item for sublist in generated_smiles for item in sublist]
n_gram = NGram(reorder_prob=reorder_prob)
n_gram.fit(flat_list)
return n_gram
def _learn_n_gram1(smiles):
# Method 1: use canonical SMILES in RDKit with no reordering
cans = _canonicalize_smiles(smiles)
n_gram = NGram(reorder_prob=0)
n_gram.fit(cans)
return n_gram
def learn_n_gram1(smiles):
# Method 1: use canonical SMILES in RDKit with no reordering
cans = [Chem.MolToSmiles(Chem.MolFromSmiles(smi)) for smi in smiles]
n_gram_cans = NGram(reorder_prob=0)
n_gram_cans.fit(cans)
# save results
# with open('ngram_cans.obj', 'wb') as f:
# pk.dump(n_gram_cans, f)
return n_gram_cans
def test_iqspr_1(data):
np.random.seed(0)
ecfp = ECFP(n_jobs=1, input_type='smiles')
bre = BayesianRidgeEstimator(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_iqspr_1(data):
np.random.seed(0)
ecfp = data['ecfp']
bre = GaussianLogLikelihood(descriptor=ecfp)
ngram = NGram()
iqspr = IQSPR(estimator=bre, modifier=ngram)
X, y = data['pg']
bre.fit(X, y)
bre.update_targets(reset=True, bandgap=(0.1, 0.2), density=(0.9, 1.2))
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):
assert np.abs(np.sum(p) - 1.0) < 1e-5
assert np.sum(f) == 5
def test_ngram_1(data):
ngram = NGram()
assert ngram.ngram_table is None
assert ngram.max_len == 1000
assert ngram.del_range == (1, 10)
assert ngram.reorder_prob == 0
assert ngram.sample_order == (1, 10)
assert ngram._train_order is None
ngram.set_params(max_len=500, reorder_prob=0.2)
assert ngram.max_len == 500
assert ngram.del_range == (1, 10)
assert ngram.reorder_prob == 0.2
def test_ngram_4():
smis1 = ['CCCc1ccccc1', 'CC(CCc1ccccc1)CC', 'Cc1ccccc1CC', 'C(CC(C))CC', 'CCCC']
n_gram1 = NGram() # base case
n_gram1.fit(smis1, train_order=3)
assert n_gram1._train_order == (1, 3)
tmp_tab = n_gram1._table
assert (len(tmp_tab),len(tmp_tab[0][0])) == (3,2)
check_close = [[(4, 5), (2, 2)], [(6, 5), (3, 2)], [(8, 4), (4, 2)]]
check_open = [[(5, 5), (2, 2)], [(6, 5), (3, 2)], [(6, 5), (4, 2)]]
for ii, x in enumerate(tmp_tab):
for i in range(len(x[0])):
assert x[0][i].shape == check_close[ii][i]
assert x[1][i].shape == check_open[ii][i]
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', target_col=0)
rdkitfp = RDKitFP(n_jobs=1, input_type='smiles', target_col=0)
bre = GaussianLogLikelihood(descriptor=ecfp)
bre2 = GaussianLogLikelihood(descriptor=rdkitfp)
bre.fit(X, y[['bandgap', 'glass_transition_temperature']])
bre2.fit(X, y[['density', 'refractive_index']])
bre.update_targets(bandgap=(1, 2), glass_transition_temperature=(200, 300))
bre2.update_targets(refractive_index=(2, 3), density=(0.9, 1.2))
class MyLogLikelihood(BaseLogLikelihoodSet):
def __init__(self):
super().__init__()
self.loglike = bre
self.loglike = bre2
like_mdl = MyLogLikelihood()
ngram = NGram()
ngram.fit(X[0:20], train_order=5)
iqspr = IQSPR(estimator=bre, modifier=ngram)
# prepare test data
yield dict(ecfp=ecfp,
rdkitfp=rdkitfp,
bre=bre,
bre2=bre2,
like_mdl=like_mdl,
ngram=ngram,
iqspr=iqspr,
pg=(X, y))
print('test over')
def test_ngram_6(data):
smis0 = ['CCCc1ccccc1', 'CC(CCc1ccccc1)CC', 'Cc1ccccc1CC', 'C(CC(C))CC', 'CCCC']
n_gram0 = NGram() # base case
n_gram0.fit(smis0, train_order=5)
n_gram1, n_gram2 = n_gram0.split_table(cut_order=2)
assert n_gram1._train_order == (1, 2)
assert n_gram1.min_len == 1
assert n_gram2._train_order == (3, 5)
assert n_gram2.min_len == 3
n_gram3 = n_gram2.merge_table(n_gram1, weight=1, overwrite=False)
assert n_gram3._train_order == (1, 5)
assert n_gram3.min_len == 3
assert np.all(n_gram3._table[3][0][1] == n_gram0._table[3][0][1])
assert np.all(n_gram3._table[2][1][0] == n_gram0._table[2][1][0])
n_gram1.merge_table(n_gram2, weight=1)
assert n_gram1._train_order == (1, 5)
assert n_gram1.min_len == 1
assert np.all(n_gram1._table[3][0][1] == n_gram0._table[3][0][1])
assert np.all(n_gram1._table[2][1][0] == n_gram0._table[2][1][0])
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 = BayesianRidgeEstimator(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_ngram_2(data):
ngram = NGram()
with pytest.warns(RuntimeWarning, match='<sample_order>'):
ngram.fit(data['pg'][0][:20], train_order=5)
assert ngram._train_order == (1, 5)
assert ngram.sample_order == (1, 5)
assert ngram.ngram_table is not None
np.random.seed(123456)
with pytest.warns(RuntimeWarning, match='can not convert'):
old_smis = ['CC(=S)C([*])(C)=CCC([*])']
tmp = ngram.proposal(old_smis)
assert tmp == old_smis
np.random.seed(654321)
with pytest.warns(RuntimeWarning, match='get_prob: '):
old_smis = ['C([*])C([*])(C1=C(OCCC)C=CC(Br)C1)']
tmp = ngram.proposal(old_smis)
assert tmp == old_smis
def test_ngram_5():
smis1 = ['CCCc1ccccc1', 'CC(CCc1ccccc1)CC', 'Cc1ccccc1CC', 'C(CC(C))CC', 'CCCC']
smis2 = ['C(F)(F)C', 'CCCF', 'C(F)C=C']
smis3 = ['c123c(cc(ccc(N)ccc3)cccc2)cccc1', 'c1cncc1', 'CC(=O)CN']
n_gram1 = NGram() # base case
n_gram1.fit(smis1, train_order=3)
n_gram2 = NGram() # higher order but lower num of rings
n_gram2.fit(smis2, train_order=4)
n_gram3 = NGram() # lower order but higher num of rings
n_gram3.fit(smis3, train_order=2)
tmp_ngram = n_gram1.merge_table(n_gram2, weight=1, overwrite=False)
assert tmp_ngram._train_order == (1, 4)
tmp_tab = tmp_ngram._table
assert (len(tmp_tab), len(tmp_tab[0][0])) == (4,2)
tmp_ngram = n_gram1.merge_table(n_gram3, weight=1, overwrite=False)
assert tmp_ngram._train_order == (1, 3)
tmp_tab = tmp_ngram._table
assert (len(tmp_tab), len(tmp_tab[0][0])) == (3, 4)
n_gram1.merge_table(n_gram2, n_gram3, weight=[0.5, 1])
tmp_tab = n_gram1._table
assert n_gram1._train_order == (1, 4)
assert (len(tmp_tab), len(tmp_tab[0][0])) == (4, 4)
assert tmp_tab[0][0][0].loc["['C']","C"] == 11.0
assert tmp_tab[0][1][0].loc["['(']", "C"] == 3.0
def combine_fragments(self, smis_base, smis_frag):
"""
combine two SMILES strings with '*' as connection points
Parameters
----------
smis_base: str
SMILES for combining.
If no '*', assume connection point at the end.
If more than one '*', the first will be picked if it's not the 1st character.
smis_frag: str
SMILES for combining.
If no '*', assume connection point at the front.
If more than one '*', the first will be picked.
"""
# prepare NGram object for use of ext. SMILES
ngram = NGram()
# check position of '*'
mols_base = Chem.MolFromSmiles(smis_base)
if mols_base is None:
raise RuntimeError('Invalid base SMILES!')
idx_base = [
i for i in range(mols_base.GetNumAtoms())
if mols_base.GetAtomWithIdx(i).GetSymbol() == '*'
]
# rearrange base SMILES to avoid 1st char = '*'
if len(idx_base) == 1 and idx_base[0] == 0:
smis_base_head = Chem.MolToSmiles(mols_base, rootedAtAtom=1)
elif len(idx_base) == 0:
smis_base_head = smis_base + '*'
else:
smis_base_head = smis_base
# converge base to ext. SMILES and pick insertion location
esmi_base = ngram.smi2esmi(smis_base_head)
esmi_base = esmi_base[:-1]
idx_base = esmi_base.index[esmi_base['esmi'] == '*'].tolist()
if idx_base[0] == 0:
idx_base = idx_base[1]
else:
idx_base = idx_base[0]
# rearrange fragment to have 1st char = '*' and convert to ext. SMILES
mols_frag = Chem.MolFromSmiles(smis_frag)
if mols_frag is None:
raise RuntimeError('Invalid frag SMILES!')
idx_frag = [
i for i in range(mols_frag.GetNumAtoms())
if mols_frag.GetAtomWithIdx(i).GetSymbol() == '*'
]
if len(idx_frag) == 0:
esmi_frag = ngram.smi2esmi(smis_frag)
# remove last '!'
esmi_frag = esmi_frag[:-1]
else:
esmi_frag = ngram.smi2esmi(
Chem.MolToSmiles(mols_frag, rootedAtAtom=idx_frag[0]))
# remove leading '*' and last '!'
esmi_frag = esmi_frag[1:-1]
# check open rings of base SMILES
nRing_base = esmi_base['n_ring'].loc[idx_base]
# re-number rings in fragment SMILES
esmi_frag['n_ring'] = esmi_frag['n_ring'] + nRing_base
# delete '*' at the insertion location
esmi_base = esmi_base.drop(idx_base).reset_index(drop=True)
# combine base with the fragment
ext_smi = pd.concat(
[esmi_base.iloc[:idx_base], esmi_frag,
esmi_base.iloc[idx_base:]]).reset_index(drop=True)
new_pd_row = {'esmi': '!', 'n_br': 0, 'n_ring': 0, 'substr': ['!']}
ext_smi.append(new_pd_row, ignore_index=True)
return ngram.esmi2smi(ext_smi)