[Rdkit-discuss] how to handle a chiral flag failure

[Mike Mazanetz]

Hi RDKit gurus.

 

I noted that compound 4 in the sdf, a poorly represented aryl system fails
with this error.

 

Any ideas on how to try/catch this error, or skip the molecule with an
error, as the script dies painfully when it gets this far.  Snippet enclosed
of the python call.

 

Best - and thanks,

 

mike

 



 

 

 

def calc_SDF(file_name_list):

  print("")  

  print("SDF Chunking Completed")  

  print("")

 

  calc_values = []

  calc_values.append(str("ORIG_SMI SMILES InChi HAC HBD HBA molWt nRotB nAr
TPSA nChr"))

 

  for j in range(len(file_name_list)):

      assert os.path.isfile(file_name_list[j]), "File %s does not exist!" %
file_name_list[j]

      

      mols = file_name_list[j]

      suppl = Chem.SDMolSupplier(mols)

      lensuppl = len(suppl)

      remover = SaltRemover() 

      

 

      for i in range(lensuppl):

          if suppl[i] is None:

              with open('.//test_out.csv', 'w', newline='') as csvfile:

                  output = csv.writer(csvfile, delimiter=',', quoting =
csv.QUOTE_ALL)

                  output.writerow(['Compound: ', i, ' failed.'])

          else:

              orig = Chem.MolToSmiles(suppl[i])

              Chem.rdmolops.SanitizeMol(suppl[i],268435455)

              y = Chem.MolToSmiles(remover.StripMol(suppl[i]))

              HAC = Chem.Lipinski.HeavyAtomCount(Chem.MolFromSmiles(y))

              HBD = Chem.Lipinski.NumHDonors(Chem.MolFromSmiles(y))

              HBA = Chem.Lipinski.NumHAcceptors(Chem.MolFromSmiles(y))

              molwt = Chem.Descriptors.MolWt(Chem.MolFromSmiles(y)) 

              nRotB = Chem.Lipinski.NumRotatableBonds(Chem.MolFromSmiles(y))

              nAr = Chem.Lipinski.NumAromaticRings(Chem.MolFromSmiles(y))

              InChi = Chem.MolToInchi(Chem.MolFromSmiles(y))

              TPSA = Chem.Descriptors.TPSA(Chem.MolFromSmiles(y))

              nChr =
len(Chem.FindMolChiralCenters(Chem.MolFromSmiles(y),includeUnassigned=True))

              calc_values.append(str('{} {} {} {} {} {} {:.2f} {} {} {:.0f}
{}'.format(orig, y, InChi, HAC, HBD, HBA, molwt, nRotB, nAr, TPSA, nChr)))

              print(j, i)

 

  now = datetime.datetime.now()

  print("")

  print("Job ended at", now.strftime("%H:%M"), "on",
now.strftime("%Y-%m-%d"))

  log.close()

  sys.stderr = save_std_err

  return calc_values

 

 

 

enamine_fail.sdf
Description: Binary data

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