Cleaned up getSmilesFromFile.py.

src/MolecularDockingKit/getSmilesFromFile.py

@@ -1,29 +1,43 @@
-#This script extracts the smiles from the file named as drugs.txt
 import os
-def getSmilesFromFile(fileName):
-    INF = open(fileName,'r').readlines()
-    tmp1  = [i.strip().split() for i in INF][1:]
-    molNames, smiles = [], []
-    for i in tmp1:
-        if (i[-1] == 'TRUE') or (i[-1] == 'FALSE'):
+from typing import List, Tuple
+
+
+def get_smiles_from_file(file_name: str) -> Tuple[List[str], List[str]]:
+    """
+    Extracts smiles from the given file.
+
+    Args:
+        file_name (str): The name of the file containing smiles.
+
+    Returns:
+        Tuple[List[str], List[str]]: A tuple containing lists of molecule names and smiles.
+    """
+    with open(file_name, 'r') as file:
+        lines = file.readlines()[1:]
+
+    mol_names, smiles = [], []
+
+    for line in lines:
+        elements = line.strip().split()
+        if elements[-1] in {'TRUE', 'FALSE'}:
             continue
         else:
-            if len(i) > 3:
-                molNames.append('_'.join([j.replace('/','-') for j in i[:-2]]))
-                smiles.append(i[-1])
-            elif len(i) == 3:
-                molNames.append(i[0])
-                smiles.append(i[2])
+            if len(elements) > 3:
+                mol_names.append('_'.join([element.replace('/', '-') for element in elements[:-2]]))
+                smiles.append(elements[-1])
+            elif len(elements) == 3:
+                mol_names.append(elements[0])
+                smiles.append(elements[2])
             else:
-                print('something wrong with ', i, '.')
-
-    #Writing the names of molecules in a file inside a separate directory
-    #for future calculations
-    if not os.path.exists('../../moleculeLists'):
-        os.mkdir('../../moleculeLists')
-    os.chdir('../../moleculeLists')
-    with open("fileList.txt", 'w') as file:
-        file.write('\n'.join(molNames))
+                print(f'Something wrong with {elements}.')
 
-    return [molNames, smiles]
+    # Writing the names of molecules in a file inside a separate directory for future calculations
+    molecule_lists_dir = '../../moleculeLists'
+    if not os.path.exists(molecule_lists_dir):
+        os.mkdir(molecule_lists_dir)
+    os.chdir(molecule_lists_dir)
+
+    with open("fileList.txt", 'w') as file:
+        file.write('\n'.join(mol_names))
 
+    return mol_names, smiles