Upload AggregatorAdvisor Preprocessing Script.py

AggregatorAdvisor Preprocessing Script.py

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+## Script to sanitize and split AggregatorAdvisor dataset
+
+# 1. Load modules
+
+pip install rdkit
+pip install molvs
+import pandas as pd
+import numpy as np
+import urllib.request
+import tqdm
+import rdkit
+from rdkit import Chem
+import molvs
+
+standardizer = molvs.Standardizer()
+fragment_remover = molvs.fragment.FragmentRemover()
+
+#3. Resolve SMILES parse error
+
+# Smiles is 'None', found the compound on ChemSpider
+# Smiles displayed 'Explicit valence for atom # 2 O, 3, is greater than permitted'
+# https://www.chemspider.com/Chemical-Structure.17588253.html?rid=026abd00-5d7b-4c7a-b279-3ba43ab46203
+AA.loc[AA['smiles'] == '[O-][N+](=[O-])C1=CC=CC(=C1)C2=NC(CO2)C3=CC=CC=C3' , 'smiles'] = 'c1ccc(cc1)C2COC(=N2)c3cccc(c3)[N+](=O)[O-]'
+
+# Smiles is 'None', found the compound on ChemSpider
+# Smiles displayed 'Explicit valence for atom # 2 O, 3, is greater than permitted'
+# https://www.chemspider.com/Chemical-Structure.17588254.html?rid=0f94ced5-dee6-4274-b0c5-796500b40be7
+AA.loc[AA['smiles'] == '[O-][N+](=[O-])C1=CC=CC(=C1)C2=NCCC(O2)C3=CC=CC=C3', 'smiles'] = 'c1ccc(cc1)C2CCN=C(O2)c3cccc(c3)[N+](=O)[O-]'
+
+#4. Sanitize with MolVS and print problems
+
+AA['X'] = [ \
+    rdkit.Chem.MolToSmiles(
+        fragment_remover.remove(
+        standardizer.standardize(
+        rdkit.Chem.MolFromSmiles(
+        smiles))))
+    for smiles in AA['smiles']]
+
+problems = []
+for index, row in tqdm.tqdm(AA.iterrows()):
+    result = molvs.validate_smiles(row['X'])
+    if len(result) == 0:
+        continue
+    problems.append( (row['substance_id'], result) )
+
+# most are because it includes the salt form and/or it is not neutralized
+for substance_id, alert in problems:
+    print(f"substance_id: {substance_id}, problem: {alert[0]}")
+
+#5. Select columns and rename the dataset
+
+AA.rename(columns={'X': 'new SMILES'}, inplace=True)
+AA[['new SMILES', 'substance_id', 'aggref_index', 'logP']].to_csv('AggregatorAdvisor.csv', index=False)