Re: [Rdkit-discuss] Unwanted explicit Hs
Thank you WIm for your clarification: so the library is not inferring the
valence, it's "choosing" one.
I think I've found the solution to my issue: I should probably use
rdkit.MolFromSmarts()
mol = chem.rdkit.MolFromSmarts('CCS=O')
chem.rdkit.MolToSmiles(mol)
'CCS=O'
Sometimes, just explaining your problem to others, helps finding the
solution.
Thomas
Il giorno sab 29 apr 2023 alle ore 20:45 Wim Dehaen
ha scritto:
> THe reason for this is that it will prevent ambiguities due to
> nonstandard, higher valences. Because of this, it is not possible to infer
> the implicit hydrogen count, so it must be specified explicitly. For S and
> P the standard valence would be 2 and 3 respectively, just like for O and
> N. But S has nonstandard valences available: 4 and 6 as in sulfones and
> sulfoxides. P can commonly have valence of 5, as in phosphoranes.
> Your provided SMILES has a valence of at least 3, exceeding the standard
> valence of 2. This creates and ambiguity, where the SMILES parser has to
> decide whether the S has a valence of 4 or 6. Likewise, with the SMILES
> "FP(F)(F)F" a roundtrip through rdkit will convert this into
> "F[PH](F)(F)F", this means the notation is consistent with F[PH2](F)F and
> distinguishable from FP(F)F. In general when higher valence states are not
> possible rdkit will throw a valence error but there are some more examples
> available. For example "CIC" will become C[IH]C.
>
> best wishes
> wim
>
>
> On Sat, Apr 29, 2023 at 12:20 PM Thomas wrote:
>
>> I am not a chemist, so it can be a silly question, but I am interested in
>> the logic behind it, also because other libraries (like OpenBabel) behave
>> differently.
>>
>> Why sometimes RDKit writes hydrogens explicitly?
>>
>> mol = rdkit.MolFromSmiles('CCS=O', sanitize=False)
>> rdkit.MolToSmiles(mol)
>> 'CC[SH]=O'
>>
>> The input SMILES is intended as a pattern, not a molecule. I make a mol
>> out of it only to get the canonical SMILES, that will be then used as
>> SMARTS.
>> Logically, I don't understand how the number of H attached to the S can
>> be "guessed" by the library, still it cannot be left implicit.
>>
>> Furthermore, I have seen this behaviour only with S and P. I was
>> wondering if it's a confined issue, or it can happen with any element.
>> Thank you
>> ___
>> Rdkit-discuss mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
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Re: [Rdkit-discuss] Unwanted explicit Hs
THe reason for this is that it will prevent ambiguities due to nonstandard,
higher valences. Because of this, it is not possible to infer the implicit
hydrogen count, so it must be specified explicitly. For S and P the
standard valence would be 2 and 3 respectively, just like for O and N. But
S has nonstandard valences available: 4 and 6 as in sulfones and
sulfoxides. P can commonly have valence of 5, as in phosphoranes.
Your provided SMILES has a valence of at least 3, exceeding the standard
valence of 2. This creates and ambiguity, where the SMILES parser has to
decide whether the S has a valence of 4 or 6. Likewise, with the SMILES
"FP(F)(F)F" a roundtrip through rdkit will convert this into
"F[PH](F)(F)F", this means the notation is consistent with F[PH2](F)F and
distinguishable from FP(F)F. In general when higher valence states are not
possible rdkit will throw a valence error but there are some more examples
available. For example "CIC" will become C[IH]C.
best wishes
wim
On Sat, Apr 29, 2023 at 12:20 PM Thomas wrote:
> I am not a chemist, so it can be a silly question, but I am interested in
> the logic behind it, also because other libraries (like OpenBabel) behave
> differently.
>
> Why sometimes RDKit writes hydrogens explicitly?
>
> mol = rdkit.MolFromSmiles('CCS=O', sanitize=False)
> rdkit.MolToSmiles(mol)
> 'CC[SH]=O'
>
> The input SMILES is intended as a pattern, not a molecule. I make a mol
> out of it only to get the canonical SMILES, that will be then used as
> SMARTS.
> Logically, I don't understand how the number of H attached to the S can be
> "guessed" by the library, still it cannot be left implicit.
>
> Furthermore, I have seen this behaviour only with S and P. I was wondering
> if it's a confined issue, or it can happen with any element.
> Thank you
> ___
> Rdkit-discuss mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
___
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[Rdkit-discuss] Unwanted explicit Hs
I am not a chemist, so it can be a silly question, but I am interested in
the logic behind it, also because other libraries (like OpenBabel) behave
differently.
Why sometimes RDKit writes hydrogens explicitly?
mol = rdkit.MolFromSmiles('CCS=O', sanitize=False)
rdkit.MolToSmiles(mol)
'CC[SH]=O'
The input SMILES is intended as a pattern, not a molecule. I make a mol out
of it only to get the canonical SMILES, that will be then used as SMARTS.
Logically, I don't understand how the number of H attached to the S can be
"guessed" by the library, still it cannot be left implicit.
Furthermore, I have seen this behaviour only with S and P. I was wondering
if it's a confined issue, or it can happen with any element.
Thank you
___
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[email protected]
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