Hi,
Without seeing the SDF itself it's hard to be specific, but here's what the
error messages are telling you, in general:
the first one normally indicates a badly formed record in the SDF. If you
look at around that line in the file you will, hopefully, see a misformed
record.
The next one, "Explicit valence" indicates that the molecule has an atom
(in this case an "O") that has the equivalent of three bonds to it. That's
not chemically reasonable, so the software complains
The error about "Alkyl" is self explanatory: there's a molecule in the SDF
which has an atom with symbol "Alkyl".
The rest are warnings.
In order to provide more specific help, we'll need to see the SDF you're
using (or at least the SDF for the molecules that are failing) as well as
information about which version of the RDKit you're using.
-greg
On Wed, Aug 5, 2020 at 11:43 PM Pitanti Chalowa <ch1...@gmail.com> wrote:
> 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?
> _______________________________________________
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> Rdkit-discuss@lists.sourceforge.net
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>
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