decoys from ligands

post/decoys_from_ligands.py

+"""
+    Build set of decoys for each ligand using DecoyFinder.
+"""
+import sys
+import os
+import pickle
+import tempfile
+
+from pybel import *
+
+if __name__ == "__main__":
+    sys.path.append('..')
+
+from data_processor.pybel_fp import index_to_vec
+
+from decoy_finder import *
+
+def build_decoy_dict(lig_dict, decoy_dict=None):
+    """ Build decoys for ligand dictionary.
+        Dictionary contains SMILES (value) for each ligand ID (key)
+    """
+    #dict: {'lig_code': [(lig_fp, [decoy_fps])]}
+    if not decoy_dict:
+        decoy_dict = {}
+    for name, sm in lig_dict.items():
+        if name in decoy_dict:
+            print(f">>> already did {name}")
+            continue
+        try:
+            os.remove('decoys.sdf')
+            os.remove('lig.txt')
+        except:
+            pass
+        #call decoy finder
+        print(f">>> decoy generation for {name}, {sm}")
+        with open('lig.txt', 'w') as l:
+            l.write(sm)
+        for _ in find_decoys(query_files=['lig.txt'], db_files=['../data/in-vitro.csv'], outputfile='decoys.sdf'):
+            pass
+
+        # parse output SDF.
+        try:
+            mols = readfile("sdf", "decoys.sdf")
+        except:
+            continue
+        ligand_fp = index_to_vec(readstring('smi', sm).calcfp(fptype='maccs').bits, nbits=166)
+        decoys = []
+        for mol in mols:
+            fp = mol.calcfp(fptype="maccs").bits
+            fp = index_to_vec(fp, nbits=166)
+            decoys.append(fp)
+        decoy_dict[name] = (ligand_fp, decoys)
+
+        os.remove('decoys.sdf')
+        os.remove('lig.txt')
+
+        pickle.dump(decoy_dict, open('decoys_zinc.p', 'wb'))
+    return decoy_dict
+
+if __name__ == "__main__":
+    lig_dict = pickle.load(open('../data/smiles_ligs_dict.p', 'rb'))
+    decoy_dict = pickle.load(open('decoys_zinc.p', 'rb'))
+    decs = build_decoy_dict(lig_dict, decoy_dict=decoy_dict)
+    pickle.dump(decs, open('decoys_zinc.p', 'wb'))
+    pass