Update inference.py

inference.py

@@ -113,7 +113,7 @@ class Inference(object):
 
     def decoder_load(self, dictionary_name):
         ''' Loading the atom and bond decoders'''
-        with open("DrugGEN/data/decoders/" + dictionary_name + "_" + self.dataset_name + '.pkl', 'rb') as f:
+        with open("data/decoders/" + dictionary_name + "_" + self.dataset_name + '.pkl', 'rb') as f:
             return pickle.load(f)
 
 
@@ -139,16 +139,16 @@ class Inference(object):
         self.restore_model(self.submodel, self.inference_model)
 
         # smiles data for metrics calculation.
-        chembl_smiles = [line for line in open("DrugGEN/data/chembl_train.smi", 'r').read().splitlines()]
-        chembl_test = [line for line in open("DrugGEN/data/chembl_test.smi", 'r').read().splitlines()]
-        drug_smiles = [line for line in open("DrugGEN/data/akt_inhibitors.smi", 'r').read().splitlines()]
+        chembl_smiles = [line for line in open("data/chembl_train.smi", 'r').read().splitlines()]
+        chembl_test = [line for line in open("data/chembl_test.smi", 'r').read().splitlines()]
+        drug_smiles = [line for line in open("data/akt_inhibitors.smi", 'r').read().splitlines()]
         drug_mols = [Chem.MolFromSmiles(smi) for smi in drug_smiles]
         drug_vecs = [AllChem.GetMorganFingerprintAsBitVect(x, 2, nBits=1024) for x in drug_mols if x is not None]
 
 
         # Make directories if not exist.
-        if not os.path.exists("DrugGEN/experiments/inference/{}".format(self.submodel)):
-            os.makedirs("DrugGEN/experiments/inference/{}".format(self.submodel))
+        if not os.path.exists("experiments/inference/{}".format(self.submodel)):
+            os.makedirs("experiments/inference/{}".format(self.submodel))
 
 
         self.G.eval()
@@ -197,7 +197,7 @@ class Inference(object):
                             if molecules is None:
                                 none_counter += 1
 
-                with open("DrugGEN/experiments/inference/{}/inference_drugs.txt".format(self.submodel), "a") as f:
+                with open("experiments/inference/{}/inference_drugs.txt".format(self.submodel), "a") as f:
                     for molecules in inference_drugs:
                         if molecules is not None:
                             molecules = molecules.replace("*", "C") 
@@ -245,9 +245,9 @@ if __name__=="__main__":
 
     # Data configuration.
     parser.add_argument('--inf_dataset_file', type=str, default='chembl45_test.pt')
-    parser.add_argument('--inf_raw_file', type=str, default='DrugGEN/data/chembl_test.smi')
+    parser.add_argument('--inf_raw_file', type=str, default='data/chembl_test.smi')
     parser.add_argument('--inf_batch_size', type=int, default=1, help='Batch size for inference')
-    parser.add_argument('--mol_data_dir', type=str, default='DrugGEN/data')
+    parser.add_argument('--mol_data_dir', type=str, default='data')
     parser.add_argument('--features', type=str2bool, default=False, help='features dimension for nodes')
 
     # Model configuration.