Smells

Author: DaniDelHoyo

autodock/scripts/convertToSMIs.py

@@ -29,12 +29,12 @@
 
 from utils import parseMoleculeFile
 
-def pdbqt_to_smi(pdbqt_file):
+def pdbqtToSMI(pdbqtFile):
     obConversion = openbabel.OBConversion()
     obConversion.SetInAndOutFormats("pdbqt", "can")
 
     mol = openbabel.OBMol()
-    success = obConversion.ReadFile(mol, pdbqt_file)
+    success = obConversion.ReadFile(mol, pdbqtFile)
 
     if success:
         smiles = obConversion.WriteString(mol).strip()
@@ -59,12 +59,12 @@ def pdbqt_to_smi(pdbqt_file):
                 for line in f:
                     molFile = line.split(',')[0].strip()
                     if molFile.endswith('.pdbqt'):
-                        smi = pdbqt_to_smi(molFile)
+                        smi = pdbqtToSMI(molFile)
                         mol = Chem.MolFromSmiles(smi)
                     else:
                         mol = parseMoleculeFile(molFile)
 
-                    canonical_smiles = Chem.MolToSmiles(mol, canonical=True)
-                    fMap.write(f'{molFile},{canonical_smiles}\n')
-                    fo.write(line.replace(molFile, canonical_smiles))
+                    canonicalSMI = Chem.MolToSmiles(mol, canonical=True)
+                    fMap.write(f'{molFile},{canonicalSMI}\n')
+                    fo.write(line.replace(molFile, canonicalSMI))
 

autodock/scripts/meeko_preparation.py

@@ -53,7 +53,7 @@ def getBiggestFrag(mol):
     for mol in frags:
         if mol.GetNumAtoms() > maxi:
             maxi, bMol = mol.GetNumAtoms(), mol
-    return mol
+    return bMol
 
 if __name__ == "__main__":
     '''Use: python <scriptName> <paramsFile> 

autodock/scripts/utils.py

@@ -60,15 +60,15 @@ def getMolFilesDic(molFiles):
 def parsePDBQT(pdbqtFile):
   from rdkit import Chem
   with open(pdbqtFile, "r") as f:
-    pdb_lines = [line for line in f if not line.startswith(("REMARK", "TORSDO"))]  # Filtra líneas no estándar
+    pdbLines = [line for line in f if not line.startswith(("REMARK", "TORSDO"))]  # Filtra líneas no estándar
 
   # Guardamos el PDB temporalmente
-  temp_pdb = pdbqtFile.replace('.pdb', '.pdbqt')
-  with open(temp_pdb, "w") as f:
-    f.writelines(pdb_lines)
+  tempPDB = pdbqtFile.replace('.pdb', '.pdbqt')
+  with open(tempPDB, "w") as f:
+    f.writelines(pdbLines)
 
   # Leer la molécula desde el PDB
-  mol = Chem.MolFromPDBFile(temp_pdb, removeHs=False)
+  mol = Chem.MolFromPDBFile(tempPDB, removeHs=False)
 
   if mol:
     return Chem.MolToSmiles(mol)

autodock/utils/utils.py

@@ -57,7 +57,7 @@ def getMolName(molText):
       if confId is not None:
         oFile = oFile.replace('.sdf', f'-{confId}.sdf')
 
-      if not molName in molDic:
+      if molName not in molDic:
         molDic[molName] = []
       with open(oFile, 'w') as fo:
         fo.write(f'{molText}\n\n$$$$')

autodock/wizards/wizard_select.py

@@ -31,11 +31,15 @@
 Then, it will load the structure and will take all chain related
 information such as name and number of residues.
 """
+import os, json
+
+from pwchem.utils import runOpenBabel
 
 from pwchem.wizards import *
 from pwchem.utils import RESIDUES1TO3
 
-from autodock.protocols import *
+from autodock.protocols import ProtChemADTPrepareReceptor, ProtChemAutodock, ProtChemVinaDocking, ProtChemAutodockGPU, \
+  ProtEncoderDockScoring, ProtRingtailFilter, ProtChemAutoSiteGenPharmacophore
 from autodock.viewers import ViewerRingtail
 from autodock import Plugin as autodockPlugin
 
@@ -173,7 +177,7 @@ def getModels(self):
     return models
 
   def show(self, form, *params):
-    inputParams, outputParam = self.getInputOutput(form)
+    _, outputParam = self.getInputOutput(form)
     try:
       models = self.getModels()
     except Exception as e: