Add utility functionality for checking for duplicates

Author: davidlmobley

scripts/utils.py

@@ -5,6 +5,7 @@
 
 #import cPickle as pickle
 import pickle
+from openeye.oechem import *
 
 def read_database():
     """Read the database from a pickle file and return it"""
@@ -23,3 +24,48 @@ def convert_to_json( database_pickle, database_json):
 
     with open(database_json,"w", encoding='utf-8') as fs:
         json.dump(freeSolv,fs)
+
+def check_for_duplicates( database_contents ):
+    """Take contents of database and re-generate all SMILES, checking for duplicates.
+
+    Parameters:
+    ----------
+    database_contents : dict
+        dictionary of FreeSolv database, keyed by compound ID
+
+    Returns:
+    ----------
+    num_dupes : int
+        Number of duplicated compound pairs found
+    keypairs : list
+        List containing tuples of pairs corresponding to the compound IDs of the duplicates
+    """
+
+    # Pull compound IDs
+    cids = [ item for item in database_contents ]
+
+    # Generate new OEMols from SMILES
+    oemols = []
+    for cid in cids:
+        mol = OEMol()
+        OEParseSmiles(mol, database_contents[cid]['smiles'])
+        oemols.append(mol)
+
+    # Generate new SMILES from OEMols, thereby standardizing
+    smiles = []
+    for mol in oemols:
+        smiles.append(OEMolToSmiles(mol))
+
+    # Build duplicate info
+    clean_smiles = []
+    keypairs = []
+    for idx,cid in enumerate(cids):
+        smi = smiles[idx]
+        if smi not in clean_smiles:
+            clean_smiles.append(smi)
+        else:
+            dupe_idx = smiles.index(smi)
+            keypairs.append( (cids[dupe_idx], cid) )
+
+    return len(keypairs), keypairs
+