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import pandas as pd |
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import numpy as np |
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from rdkit import Chem |
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from rdkit.Chem import Descriptors |
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df_train = pd.read_csv("./intermediate/train.csv") |
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df_test = pd.read_csv("./intermediate/test.csv") |
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df_train = df_train.drop(['SMILES'], axis=1) |
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df_test = df_test.drop(['SMILES'], axis=1) |
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descriptor_names = [desc_name for desc_name, _ in Descriptors.descList] |
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len(descriptor_names) |
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def calculate_rdkit_descriptors(smiles): |
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mol = Chem.MolFromSmiles(smiles) |
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if mol is None: |
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return None |
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return {desc_name: func(mol) for desc_name, func in Descriptors.descList} |
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df_train_descriptors = df_train["Standardized_SMILES"].apply(calculate_rdkit_descriptors) |
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df_test_descriptors = df_test["Standardized_SMILES"].apply(calculate_rdkit_descriptors) |
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df_train_descriptors = pd.DataFrame(df_train_descriptors.tolist()) |
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df_test_descriptors = pd.DataFrame(df_test_descriptors.tolist()) |
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df_train_final = pd.concat([df_train, df_train_descriptors], axis=1) |
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df_test_final = pd.concat([df_test, df_test_descriptors], axis=1) |
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df_train_final.to_csv("./intermediate/train_rdkit_descriptors.csv", index=False) |
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df_test_final.to_csv("./intermediate/test_rdkit_descriptors.csv", index=False) |
