def select_and_evaluate_decoys(f, target, file_loc='./', output_loc='./',
dataset='ALL', num_cand_dec_per_act=100,
num_dec_per_act=50, max_idx_cmpd=10000):
print("Processing: ", f)
dec_results = [f]
dec_results.append(dataset)
# Read data
data = decoy_utils.read_paired_file(file_loc+f)
# Filter dupes and actives that are too small
dec_results.append(len(set([d[0] for d in data])))
tmp = [Chem.MolFromSmiles(d[0]) for d in data]
data = [d for idx, d in enumerate(data) if tmp[idx] is not None \
and tmp[idx].GetNumHeavyAtoms()>min_active_size]
data = pd.DataFrame(data, columns=['act', 'dec'])
pss = get_pss_from_smiles(
data['act'].values, data['dec'].values)
data['pss'] = pss.mean(0)
data['score'] = data['pss']
result = []
for key, tmp_df in data.groupby('act'):
tmp_df = tmp_df.sort_values('score', ascending=False)
tmp_df = tmp_df.reset_index(drop=True)
for i in range(min([5, tmp_df.shape[0]])):
result.append([key, tmp_df['dec'].values[i]])
result = pd.DataFrame(result, columns=['act', 'dec'])
result.to_csv('tmp.smi', index=False, header=None, sep=' ')
# =============================================================================
#
# =============================================================================
decoy_smis_gen = list(set(result['dec']))
decoy_mols_gen = [Chem.MolFromSmiles(smi) for smi in decoy_smis_gen]
active_smis_gen = list(set(result['act']))
active_mols_gen = [Chem.MolFromSmiles(smi) for smi in active_smis_gen]
dataset = 'dude'
print('Calc props for chosen decoys')
actives_feat = decoy_utils.calc_dataset_props_dude(active_mols_gen)
decoys_feat = decoy_utils.calc_dataset_props_dude(decoy_mols_gen)
print('ML model performance')
print(actives_feat.shape)
print(decoys_feat.shape)
dec_results.extend(list(decoy_utils.calc_xval_performance(
actives_feat, decoys_feat, n_jobs=1)))
print('DEKOIS paper metrics (LADS, DOE, Doppelganger score)')
dec_results.append(decoy_utils.doe_score(actives_feat, decoys_feat))
lads_scores = decoy_utils.lads_score_v2(active_mols_gen, decoy_mols_gen)
dec_results.append(np.mean(lads_scores))
dg_scores, dg_ids = decoy_utils.dg_score(active_mols_gen, decoy_mols_gen)
dec_results.extend([np.mean(dg_scores), max(dg_scores)])
print('Save decoy mols')
print(dec_results)
return dec_results
def select_and_evaluate_decoys(f,
target,
file_loc='./',
output_loc='./',
dataset='ALL',
num_cand_dec_per_act=100,
num_dec_per_act=50,
max_idx_cmpd=10000):
print("Processing: ", f)
dec_results = [f]
dec_results.append(dataset)
# Read data
data = decoy_utils.read_paired_file(file_loc + f)
# Filter dupes and actives that are too small
dec_results.append(len(set([d[0] for d in data])))
tmp = [Chem.MolFromSmiles(d[0]) for d in data]
data = [d for idx, d in enumerate(data) if tmp[idx] is not None \
and tmp[idx].GetNumHeavyAtoms()>min_active_size]
result = pd.DataFrame(data, columns=['act', 'dec'])
decoy_smis_gen = list(set(result['dec']))
decoy_mols_gen = [Chem.MolFromSmiles(smi) for smi in decoy_smis_gen]
active_smis_gen = list(set(result['act']))
active_mols_gen = [Chem.MolFromSmiles(smi) for smi in active_smis_gen]
dataset = 'dude'
print('Calc props for chosen decoys')
actives_feat = decoy_utils.calc_dataset_props_dude(active_mols_gen)
decoys_feat = decoy_utils.calc_dataset_props_dude(decoy_mols_gen)
print('ML model performance')
print(actives_feat.shape)
print(decoys_feat.shape)
dec_results.extend(
list(
decoy_utils.calc_xval_performance(actives_feat,
decoys_feat,
n_jobs=1)))
print('DEKOIS paper metrics (LADS, DOE, Doppelganger score)')
dec_results.append(decoy_utils.doe_score(actives_feat, decoys_feat))
lads_scores = decoy_utils.lads_score_v2(active_mols_gen, decoy_mols_gen)
dec_results.append(np.mean(lads_scores))
dg_scores, dg_ids = decoy_utils.dg_score(active_mols_gen, decoy_mols_gen)
dec_results.extend([np.mean(dg_scores), max(dg_scores)])
print('Save decoy mols')
print(dec_results)
return dec_results
def select_and_evaluate_decoys(data):
dec_results = []
# Filter dupes and actives that are too small
dec_results.append(len(set([d[0] for d in data])))
seen = set()
data = [d for d in data if Chem.MolFromSmiles(d[0]) is not None and Chem.MolFromSmiles(d[0]).GetNumHeavyAtoms()>min_active_size]
unique_data = [x for x in data if not (tuple(x) in seen or seen.add(tuple(x)))]
in_smis = [d[0] for d in data]
gen_smis = [d[1] for d in data]
dec_results.extend([len(set(in_smis)), len(data), len(unique_data)])
print('Calculate properties of in_smis and gen_mols')
used = set([])
in_smis_set = [x for x in in_smis if x not in used and (used.add(x) or True)]
active_mols_gen = [Chem.MolFromSmiles(smi) for smi in in_smis_set]
decoy_mols_gen = [Chem.MolFromSmiles(smi) for smi in gen_smis]
print('Calc props for chosen decoys')
actives_feat = decoy_utils.calc_dataset_props_dude(active_mols_gen)
decoys_feat = decoy_utils.calc_dataset_props_dude(decoy_mols_gen)
print('ML model performance')
dec_results.extend(list(decoy_utils.calc_xval_performance(actives_feat, decoys_feat, n_jobs=1)))
print('DEKOIS paper metrics (LADS, DOE, Doppelganger score)')
dec_results.append(decoy_utils.doe_score(actives_feat, decoys_feat))
lads_scores = decoy_utils.lads_score_v2(active_mols_gen, decoy_mols_gen)
dec_results.append(np.mean(lads_scores))
dg_scores, dg_ids = decoy_utils.dg_score(active_mols_gen, decoy_mols_gen)
dec_results.extend([np.mean(dg_scores), max(dg_scores)])
# Save intermediate performance results in unique file
#with open(output_loc+'results_'+f+'.csv', 'w') as csvfile:
# writer = csv.writer(csvfile, delimiter=',', quotechar='|', quoting=csv.QUOTE_MINIMAL)
# writer.writerow(dec_results)
return dec_results
def select_and_evaluate_decoys(f, target, idx, file_loc='./', output_loc='./',
dataset='ALL', num_cand_dec_per_act=100,
num_dec_per_act=50, max_idx_cmpd=10000):
print("Processing: ", f)
dec_results = [f]
dec_results.append(dataset)
# Read data
data = decoy_utils.read_paired_file(file_loc+f)
# =============================================================================
#
# =============================================================================
data = [d+[Chem.MolFromSmiles(d[1])] for d in data]
lads_scores = decoy_utils.lads_score_v2(
[Chem.MolFromSmiles(smi) for smi in list(set([d[0] for d in data]))],
[d[2] for d in data])
data = [d for idx, d in enumerate(data) if lads_scores[idx]<0.5]
# =============================================================================
# data = [d for d in data if AllChem.EmbedMolecule(
# Chem.AddHs(d[2]), randomSeed=42) != -1]
# =============================================================================
data = [d[:2] for d in data]
# =============================================================================
#
# =============================================================================
# Filter dupes and actives that are too small
dec_results.append(len(set([d[0] for d in data])))
seen = set()
tmp = [Chem.MolFromSmiles(d[0]) for d in data]
data = [d for idx, d in enumerate(data) if tmp[idx] is not None \
and tmp[idx].GetNumHeavyAtoms()>min_active_size]
unique_data = [x for x in data if not (tuple(x) in seen or seen.add(tuple(x)))]
in_smis = [d[0] for d in data]
in_mols = [Chem.MolFromSmiles(smi) for smi in in_smis]
set_in_smis = list(set(in_smis))
set_in_mols = [Chem.MolFromSmiles(smi) for smi in set_in_smis]
gen_smis = [d[1] for d in data]
gen_mols = [Chem.MolFromSmiles(smi) for smi in gen_smis]
dec_results.extend([len(set(in_smis)), len(data), len(unique_data)])
print('Calculate properties of in_smis and gen_mols')
used = set([])
in_smis_set = [x for x in in_smis if x not in used and (used.add(x) or True)]
in_mols_set = [Chem.MolFromSmiles(smi) for smi in in_smis_set]
if dataset == "dude_ext":
in_props_temp = decoy_utils.calc_dataset_props_dude_extended(in_mols_set, verbose=True)
gen_props = decoy_utils.calc_dataset_props_dude_extended(gen_mols, verbose=True)
elif dataset == "dekois":
in_props_temp = decoy_utils.calc_dataset_props_dekois(in_mols_set, verbose=True)
gen_props = decoy_utils.calc_dataset_props_dekois(gen_mols, verbose=True)
elif dataset == "MUV":
in_props_temp = decoy_utils.calc_dataset_props_muv(in_mols_set, verbose=True)
gen_props = decoy_utils.calc_dataset_props_muv(gen_mols, verbose=True)
elif dataset == "ALL":
in_props_temp = decoy_utils.calc_dataset_props_all(in_mols_set, verbose=True)
gen_props = decoy_utils.calc_dataset_props_all(gen_mols, verbose=True)
elif dataset == "dude":
in_props_temp = decoy_utils.calc_dataset_props_dude(in_mols_set, verbose=True)
gen_props = decoy_utils.calc_dataset_props_dude(gen_mols, verbose=True)
else:
print("Incorrect dataset")
exit()
in_mols_temp = list(in_smis_set) # copy
in_props = []
for i, smi in enumerate(in_smis):
in_props.append(in_props_temp[in_mols_temp.index(smi)])
in_basic_temp = decoy_utils.calc_dataset_props_basic(in_mols_set, verbose=True)
in_mols_temp = list(in_smis_set) # copy
in_basic = []
for i, smi in enumerate(in_smis):
in_basic.append(in_basic_temp[in_mols_temp.index(smi)])
gen_basic_props = decoy_utils.calc_dataset_props_basic(gen_mols, verbose=True)
print('Scale properties based on in_mols props')
active_props_scaled_all = []
decoy_props_scaled_all = []
active_min_all = []
active_max_all = []
active_scale_all = []
active_props = in_props_temp
print('Exclude errors from min/max calc')
act_prop = np.array(active_props)
active_maxes = np.amax(act_prop, axis=0)
active_mins = np.amin(act_prop, axis=0)
active_max_all.append(active_maxes)
active_min_all.append(active_mins)
scale = []
for (a_max, a_min) in zip(active_maxes,active_mins):
if a_max != a_min:
scale.append(a_max - a_min)
else:
scale.append(a_min)
scale = np.array(scale)
scale[scale == 0.0] = 1.0
active_scale_all.append(scale)
active_props_scaled = (active_props - active_mins) / scale
active_props_scaled_all.append(active_props_scaled)
# Calc SA scores
in_sa_temp = [sascorer.calculateScore(mol) for mol in set_in_mols]
in_smis_temp = list(set(in_smis))
in_sa = []
for i, smi in enumerate(in_smis):
in_sa.append(in_sa_temp[in_smis_temp.index(smi)])
gen_sa_props = [sascorer.calculateScore(mol) for mol in gen_mols]
print('Calc Morgan fingerprints')
in_fps = []
for i, mol in enumerate(in_mols):
in_fps.append(
AllChem.GetMorganFingerprintAsBitVect(mol,2,nBits=1024))
gen_fps = []
for i, mol in enumerate(gen_mols):
gen_fps.append(
AllChem.GetMorganFingerprintAsBitVect(mol,2,nBits=1024))
print('Calc DG scores')
dg_scores, dg_ids = decoy_utils.dg_score_rev(set_in_mols, gen_mols)
print('Calc LADS scores')
lads_scores = decoy_utils.lads_score_v2(set_in_mols, gen_mols)
print('Construct dictionary of results')
results_dict = {}
for i in range(len(in_smis)):
# Get scaling
in_props_scaled = (in_props[i] - active_min_all) / active_scale_all
gen_props_scaled = (np.array(gen_props[i]) - active_min_all) / active_scale_all
prop_diff = np.linalg.norm(np.array(in_props_scaled)-np.array(gen_props_scaled))
# Get basic props diff
basic_diff = np.sum(abs(np.array(in_basic[i])-np.array(gen_basic_props[i])))
if in_smis[i] in results_dict:
sim = DataStructs.TanimotoSimilarity(in_fps[i], gen_fps[i])
results_dict[in_smis[i]].append(
[in_smis[i], gen_smis[i], in_props[i], gen_props[i], prop_diff,
sim, basic_diff, abs(gen_sa_props[i]-in_sa[i]),
dg_scores[i], lads_scores[i], gen_mols[i]])
else:
sim = DataStructs.TanimotoSimilarity(in_fps[i], gen_fps[i])
results_dict[in_smis[i]] = [
[in_smis[i], gen_smis[i], in_props[i], gen_props[i], prop_diff,
sim, basic_diff, abs(gen_sa_props[i]-in_sa[i]),
dg_scores[i], lads_scores[i], gen_mols[i]] ]
print('Get decoy matches')
results = []
results_success_only = []
sorted_mols_success = []
for key in results_dict:
# Set initial criteria - Note most of these are relatively weak
prop_max_diff = 5
max_basic_diff = 3
max_sa_diff = 1.51
max_dg_score = 0.35
max_lads_score = 0.2# 5# 0.1
while True:
count_success = sum([i[4]<prop_max_diff \
and i[6]<max_basic_diff and i[7]<max_sa_diff \
and i[8]<max_dg_score and i[9]<max_lads_score \
for i in results_dict[key][0:max_idx_cmpd]])
# Adjust criteria if not enough successes
if count_success < num_cand_dec_per_act and max_dg_score<1:
#print("Widening search", count_success)
prop_max_diff *= 1.1
max_basic_diff += 1
max_sa_diff *= 1.1
max_dg_score *= 1.1
max_lads_score *= 1.1
else:
#print("Reached threshold", count_success)
# Sort by sum of LADS and property difference (smaller better)
sorted_mols_success.append(
[(i[0], i[1], i[4], i[9], i[4]+i[9], i[10]) \
for i in sorted(results_dict[key][0:max_idx_cmpd],
key=lambda i: i[4]+i[9], reverse=False)
if i[4]<prop_max_diff \
and i[6]<max_basic_diff and i[7]<max_sa_diff \
and i[8]<max_dg_score and i[9]<max_lads_score])
#assert count_success == len(sorted_mols_success[-1])
break
print('Choose decoys')
# =============================================================================
# active_smis_gen = []
# =============================================================================
decoy_smis_gen = set()
embed_fails = 0
dupes_wanted = 0
for act_res in sorted_mols_success:
count = 0
# Greedy selection based on sum of LADS score and property difference (smaller better)
for ent in act_res:
# Check can gen conformer
if ent[1] not in decoy_smis_gen: # Check conf and not a decoy for another ligand
decoy_smis_gen.update([ent[1]])
count +=1
if count >= num_dec_per_act:
break
elif ent[1] in decoy_smis_gen:
dupes_wanted +=1
else:
embed_fails += 1
# =============================================================================
# active_smis_gen.append(act_res[0][0])
# =============================================================================
decoy_smis_gen = list(decoy_smis_gen)
decoy_mols_gen = [Chem.MolFromSmiles(smi) for smi in decoy_smis_gen]
# =============================================================================
# active_mols_gen = [Chem.MolFromSmiles(smi) for smi in active_smis_gen]
# =============================================================================
active_mols_gen = set_in_mols
dataset = 'dude'
print('Calc props for chosen decoys')
if dataset == "dude_ext":
actives_feat = decoy_utils.calc_dataset_props_dude_extended(active_mols_gen, verbose=True)
decoys_feat = decoy_utils.calc_dataset_props_dude_extended(decoy_mols_gen, verbose=True)
elif dataset == "dekois":
actives_feat = decoy_utils.calc_dataset_props_dekois(active_mols_gen, verbose=True)
decoys_feat = decoy_utils.calc_dataset_props_dekois(decoy_mols_gen, verbose=True)
elif dataset == "MUV":
actives_feat = decoy_utils.calc_dataset_props_muv(active_mols_gen, verbose=True)
decoys_feat = decoy_utils.calc_dataset_props_muv(decoy_mols_gen, verbose=True)
elif dataset == "ALL":
actives_feat = decoy_utils.calc_dataset_props_all(active_mols_gen, verbose=True)
decoys_feat = decoy_utils.calc_dataset_props_all(decoy_mols_gen, verbose=True)
elif dataset == "dude":
actives_feat = decoy_utils.calc_dataset_props_dude(active_mols_gen)
decoys_feat = decoy_utils.calc_dataset_props_dude(decoy_mols_gen)
else:
print("Incorrect dataset")
exit()
print('ML model performance')
print(actives_feat.shape)
print(decoys_feat.shape)
dec_results.extend(list(decoy_utils.calc_xval_performance(
actives_feat, decoys_feat, n_jobs=1)))
print('DEKOIS paper metrics (LADS, DOE, Doppelganger score)')
dec_results.append(decoy_utils.doe_score(actives_feat, decoys_feat))
lads_scores = decoy_utils.lads_score_v2(active_mols_gen, decoy_mols_gen)
dec_results.append(np.mean(lads_scores))
dg_scores, dg_ids = decoy_utils.dg_score(active_mols_gen, decoy_mols_gen)
dec_results.extend([np.mean(dg_scores), max(dg_scores)])
# Save intermediate performance results in unique file
#with open(output_loc+'results_'+f+'.csv', 'w') as csvfile:
# writer = csv.writer(csvfile, delimiter=',', quotechar='|', quoting=csv.QUOTE_MINIMAL)
# writer.writerow(dec_results)
print('Save decoy mols')
output_name = output_loc + \
f'/{target}_{idx}_selected_{num_dec_per_act}_{num_cand_dec_per_act}.smi'
with open(output_name, 'w') as outfile:
for i, smi in enumerate(decoy_smis_gen):
outfile.write(set_in_smis[i//num_dec_per_act] + ' ' + smi + '\n')
print(dec_results)
GM = np.mean(dec_results[7+1:7+1+3])
print(f'GM: {GM:.4f}')
dec_results.append(GM)
return dec_results
def select_and_evaluate_decoys(f,
file_loc='./',
dataset='dude',
num_cand_dec_per_act=100,
num_dec_per_act=50,
max_idx_cmpd=10000):
print("Processing: ", f)
dec_results = [f]
dec_results.append(dataset)
# Read data
data = decoy_utils.read_paired_file(file_loc + f)
# Filter dupes and actives that are too small
dec_results.append(len(set([d[0] for d in data])))
seen = set()
data = [
d for d in data if Chem.MolFromSmiles(d[0]) is not None
and Chem.MolFromSmiles(d[0]).GetNumHeavyAtoms() > min_active_size
]
unique_data = [
x for x in data if not (tuple(x) in seen or seen.add(tuple(x)))
]
in_smis = [d[0] for d in data]
gen_smis = [d[1] for d in data]
dec_results.extend([len(set(in_smis)), len(data), len(unique_data)])
print('Calculate properties of in_smis and gen_mols')
used = set([])
in_smis_set = [
x for x in in_smis if x not in used and (used.add(x) or True)
]
active_mols_gen = [Chem.MolFromSmiles(smi) for smi in in_smis_set]
decoy_mols_gen = [Chem.MolFromSmiles(smi) for smi in gen_smis]
dataset = 'dude'
print('Calc props for chosen decoys')
actives_feat = decoy_utils.calc_dataset_props_dude(active_mols_gen)
decoys_feat = decoy_utils.calc_dataset_props_dude(decoy_mols_gen)
print('ML model performance')
dec_results.extend(
list(
decoy_utils.calc_xval_performance(actives_feat,
decoys_feat,
n_jobs=1)))
print('DEKOIS paper metrics (LADS, DOE, Doppelganger score)')
dec_results.append(decoy_utils.doe_score(actives_feat, decoys_feat))
lads_scores = decoy_utils.lads_score_v2(active_mols_gen, decoy_mols_gen)
dec_results.append(np.mean(lads_scores))
dg_scores, dg_ids = decoy_utils.dg_score(active_mols_gen, decoy_mols_gen)
dec_results.extend([np.mean(dg_scores), max(dg_scores)])
print(dec_results)
return dec_results