improved xyzFromSmiles.py

src/MolecularDockingKit/xyzFromSmiles.py

@@ -1,24 +1,34 @@
+import numpy as np
 from rdkit import Chem
 from rdkit.Chem import AllChem
 
-###########################################################
-#                                                         #
-# This program generates the xyz coordinates for the      #
-# molecules using SMILES. It tries for upto 20 iterations #
-# inside the rdkit MM force field optimizer and only      #
-# returns a geometry if converged. Most of the molecules  #
-# were converged with an exception of four to five.       #
-#                                                         #
-###########################################################
-def xyzFromSmiles(smiles, fileName):
+
+def xyz_from_smiles(smiles: str, file_name: str) -> None:
+    """
+    Generates the xyz coordinates for molecules using SMILES.
+
+    Parameters:
+    smiles (str): The SMILES string of the molecule.
+    file_name (str): The name of the output file to save the molecule coordinates.
+
+    Returns:
+    None. Saves the coordinates to a file in SD format.
+    """
+
+    # Convert SMILES to RDKit molecule object
     mol = Chem.MolFromSmiles(smiles)
+
+    # Add hydrogen atoms to the molecule
     mol = Chem.AddHs(mol)
+
+    # Embed the molecule and optimize using the MMFF force field
     AllChem.EmbedMolecule(mol, useRandomCoords=True)
     try:
         AllChem.MMFFOptimizeMolecule(mol, maxIters=20)
-        writer = Chem.rdmolfiles.SDWriter(fileName + '.sd')
+
+        # Write the molecule to an SD file
+        writer = Chem.rdmolfiles.SDWriter(file_name + '.sd')
         writer.write(mol)
     except:
-        print('Skipping ', fileName)
+        print('Skipping ', file_name)
         return
-