|
|
import os |
|
|
import pandas as pd |
|
|
import rdkit |
|
|
import molvs |
|
|
import tqdm |
|
|
import glob |
|
|
from rdkit import Chem |
|
|
|
|
|
standardizer = molvs.Standardizer() |
|
|
fragment_remover = molvs.fragment.FragmentRemover() |
|
|
|
|
|
|
|
|
|
|
|
filter_map = { |
|
|
"585": "584", |
|
|
"1476": "1478", |
|
|
"485341": "485294" |
|
|
} |
|
|
|
|
|
|
|
|
cid_sets = {} |
|
|
|
|
|
|
|
|
for target_aid in filter_map.values(): |
|
|
file_name = f"pubchem_aid_{target_aid}_active.csv" |
|
|
file_full_path = os.path.join("./active", file_name) |
|
|
|
|
|
if os.path.exists(file_full_path): |
|
|
df = pd.read_csv(file_full_path) |
|
|
cid_sets[target_aid] = set(df["CID"].tolist()) |
|
|
else: |
|
|
print(f"Warning: file for AID {target_aid} not found!") |
|
|
|
|
|
|
|
|
for target_aid, filter_aid in filter_map.items(): |
|
|
file_name = f"pubchem_aid_{target_aid}_active.csv" |
|
|
file_full_path = os.path.join("./active", file_name) |
|
|
|
|
|
if not os.path.exists(file_full_path): |
|
|
print(f"Skipping {target_aid}, file not found.") |
|
|
continue |
|
|
|
|
|
df = pd.read_csv(file_full_path) |
|
|
|
|
|
before = len(df) |
|
|
df = df[~df["CID"].isin(cid_sets[filter_aid])] |
|
|
after = len(df) |
|
|
|
|
|
output_path = f"./active/pubchem_aid_{target_aid}_active_filtered.csv" |
|
|
df.to_csv(output_path, index=False) |
|
|
|
|
|
print(f"{target_aid}: removed {before - after} compounds from {before}, saved to {output_path}") |
|
|
|
|
|
|
|
|
filtered_files = [ |
|
|
"pubchem_aid_585_active_filtered.csv", |
|
|
"pubchem_aid_1476_active_filtered.csv", |
|
|
"pubchem_aid_485341_active_filtered.csv" |
|
|
] |
|
|
|
|
|
|
|
|
for file in filtered_files: |
|
|
file_path = os.path.join("./active", file) |
|
|
file_name = os.path.splitext(file)[0] |
|
|
|
|
|
|
|
|
active_df = pd.read_csv(file_path) |
|
|
smiles_series = active_df["CanonicalSMILES"] |
|
|
active_df["curated_SMILES"] = None |
|
|
cid = active_df["CID"] |
|
|
|
|
|
valid_indices = [] |
|
|
invalid_smiles = [] |
|
|
warning_smiles = [] |
|
|
|
|
|
for idx, smiles in smiles_series.items(): |
|
|
mol = Chem.MolFromSmiles(smiles) |
|
|
compound_cid = cid.iloc[idx] |
|
|
|
|
|
if mol is None: |
|
|
invalid_smiles.append({ |
|
|
'CID': compound_cid, |
|
|
'SMILES': smiles, |
|
|
'Reason': "MolFromSmiles returned None" |
|
|
}) |
|
|
continue |
|
|
|
|
|
results = molvs.validate_smiles(smiles) |
|
|
if len(results) > 0: |
|
|
warning_smiles.append({ |
|
|
'CID': compound_cid, |
|
|
'SMILES': smiles, |
|
|
'Reason': results |
|
|
}) |
|
|
continue |
|
|
|
|
|
mol = standardizer.standardize(mol) |
|
|
mol = fragment_remover.remove(mol) |
|
|
standardized = Chem.MolToSmiles(mol) |
|
|
|
|
|
active_df.at[idx, "curated_SMILES"] = standardized |
|
|
valid_indices.append(idx) |
|
|
|
|
|
|
|
|
valid_df = active_df.loc[valid_indices].reset_index(drop=True) |
|
|
valid_df = valid_df.drop(columns=["CanonicalSMILES"]) |
|
|
valid_df = valid_df.rename(columns={"curated_SMILES": "SMILES"}) |
|
|
aid = file_name.replace("pubchem_aid_", "").replace("_active_filtered", "") |
|
|
valid_df.insert(0, "AID", aid) |
|
|
|
|
|
invalid_df = pd.DataFrame(invalid_smiles) |
|
|
warning_df = pd.DataFrame(warning_smiles) |
|
|
invalid_df.insert(0, "AID", aid) |
|
|
warning_df.insert(0, "AID", aid) |
|
|
|
|
|
valid_df.to_csv(f'./curated/{file_name}_curated.csv', index=False) |
|
|
invalid_df.to_csv(f'./curated/{file_name}_invalid_smiles.csv', index=False) |
|
|
warning_df.to_csv(f'./curated/{file_name}_molvs_validation.csv', index=False) |
|
|
|
|
|
print(f"Finished curation for {file_name}") |
|
|
print(f" Valid: {len(valid_df)}, Invalid: {len(invalid_df)}, Warnings: {len(warning_df)}\n") |
