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?
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
