[Rdkit-discuss] RDkit: While converting sdf file to fingerprint, facing several error

[Pitanti C. <ch...@gm...>]

Respected Altruistic Researcher,
While converting one sdf file to fingerprint, I am facing several errors.

My code

suppl = Chem.SDMolSupplier('1.sdf')for mol in suppl:
  if mol is None: continue
  # print(mol.GetNumAtoms())

fps = [Chem.RDKFingerprint(x) for x in supply]

I am facing many errors

ERROR: Problems encountered parsing Mol data, M  END missing around
line 16739...
ERROR: Explicit valence for atom # 0 O, 3, is greater than permitted...
ERROR: Could not sanitize molecule ending on line 78558...
ERROR: Post-condition ViolationRDKit ERROR: Element 'Alkyl' not
foundRDKit ERROR: Violation occurred on line 91 in file
/home/conda/feedstock_root/build_artifacts/rdkit_1593788763912/work/Code/GraphMol/PeriodicTable.hRDKit
ERROR: Failed Expression: anum > -1
...
WARNING: not removing hydrogen atom without neighbors

RDKit WARNING: atom 0 has specified valence (4) smaller than the drawn
valence 6.

Please direct me to the references. How can I correct them?