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import numpy as np |
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import pandas as pd |
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from rdkit import Chem |
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from rdkit.Chem import Descriptors |
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mw_list=[] |
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logp_list=[] |
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TPSA_list=[] |
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HBD_list=[] |
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HBA_list=[] |
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rot_bond_list=[] |
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ring_count_list=[] |
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frac_sp3_list=[] |
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df=pd.read_parquet("./ecfp/all_data_merged-cleaned-ecfp4.parquet") |
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for smi in df["Smiles_molvs"]: |
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mol = Chem.MolFromSmiles(smi) |
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if mol is None: |
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mw_list.append(np.nan) |
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logp_list.append(np.nan) |
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TPSA_list.append(np.nan) |
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HBD_list.append(np.nan) |
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HBA_list.append(np.nan) |
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rot_bond_list.append(np.nan) |
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ring_count_list.append(np.nan) |
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frac_sp3_list.append(np.nan) |
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print(smi,"this smile failed") |
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continue |
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mw_list.append( Descriptors.MolWt(mol) ) |
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logp_list.append( Descriptors.MolLogP(mol) ) |
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TPSA_list.append( Descriptors.TPSA(mol) ) |
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HBD_list.append( Descriptors.NumHDonors(mol) ) |
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HBA_list.append( Descriptors.NumHAcceptors(mol) ) |
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rot_bond_list.append(Descriptors.NumRotatableBonds(mol) ) |
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ring_count_list.append(Descriptors.RingCount(mol) ) |
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frac_sp3_list.append(Descriptors.FractionCSP3(mol) ) |
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df["MolWt"] = mw_list |
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df["ClogP"] = logp_list |
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df["TPSA"] = TPSA_list |
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df["HBD"] = HBD_list |
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df["HBA"] = HBA_list |
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df["NumRotatableBonds"] = rot_bond_list |
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df["RingCount"] = ring_count_list |
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df["FractionCSP3"] = frac_sp3_list |
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output_file="./ecfp_and_properties/all_data_merged-cleaned-ecfp4-properties.parquet" |
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df.to_parquet(output_file, index=False) |
