Hi

A quick follow-up to my last message, w.r.t. halogens. The issue is
not that higher oxidation state halogen ions can't be constructed at
all, but they end up with bizarre charges on the halogen which are
frequently not recognised by other software.

Chris

On 21 November 2017 at 08:22, Chris Earnshaw <cgearns...@gmail.com> wrote:
> Hi
>
> The entries for P and As in RDKit's atomic_data.cpp are -
> 15      P       0.75    0.89    2.08    30.974  5       31
> 30.97376163     3       5       7
> 33      As      1.21    1.2     1.85    74.922  5       75
> 74.9215965       3       5
>
> So the required 'connectivities' for PF6- are present in the file
> (final 3 values, '7' being the relevant one here), but not for As. I'm
> not quite sure why this should be so as the phosphorus is P(V) in PF6,
> but this appears to be the cause. You'll have to add the '7' in the As
> entry and rebuild RDKit to allow AsF6- to be processed. A similar fix
> would be needed for antimony too. Someone please let me know if
> there's a more convenient solution!
>
> There are similar issues for the halogens as well. Only iodine has
> values > 1, so by default it's not possible to construct e.g.
> chlorates, or bromates, and no perhalates are allowed.
>
> Regards,
> Chris Earnshaw
>
> On 20 November 2017 at 23:03, Yoolhee Kim <yoolh...@andrew.cmu.edu> wrote:
>> Hello,
>>
>> I'm trying to get RDKIT to recognize LiAsF6 from the SMILES Formula
>> "[Li+].F[As-](F)(F)(F)(F)F" but it seems that RDKIT will not read it
>> correctly and is unable to create a molecule object.
>>
>> RDKIT is able to understand LiPF6 from the SMILES formula
>> "[Li+].F[P-](F)(F)(F)(F)F" so I tried using that and replacing P with As
>> using both replaceatom and replacesubstruct functions, but that had some
>> issues as well.
>>
>> Has anyone faced a similar issue or have any suggestions?
>>
>> Thanks!
>>
>> -Yoolhee
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Reply via email to