Hi Yoolhee
If this is something you need fixed *now*, you have access to the RDKit
source code and you're confident to build a new version of RDKit, then try
the following.
1. from the root folder of the RDkit distribution, find the folder
Code/GraphMol/
2. in that folder, copy atomic_data.cpp to atomic_data.cpp.bak (so you can
restore things if necessary)
3. edit atomic_data.cpp as follows
- find the line for phosphorus that starts '15 P' (probably line 42
in the file)
- note that the line ends '3 5 7 \n \'
- find the line for arsenic, starting '33 As' (probably line 60)
- this line ends '3 5 \n \'
- change the line by inserting <tab>7 immediately after the 5 (that's a
tab character)
- the end of the arsenic line should now look like the end of the
phosphorus line
- save the file
4. rebuild RDKit
I wouldn't recommend trying this if you haven't previously built RDKit from
source.
@Greg - is it worth adding higher valence states for the halogens as well
while fixing As and Sb? At the moment we have
Cl 1
Br 1
I 1 2 5
Shouldn't these all be '1 3 5 7' ?
Best regards,
Chris
On 24 November 2017 at 21:31, Yoolhee Kim <yoolh...@andrew.cmu.edu> wrote:
> Chris,
>
> Thank you very much for your reply! I'm not very familiar with RDKIT, and
> I was wondering if you could elaborate how to fix the problem of adding '7'
> in the As entry so that the valence state is recognized.
>
> Best regards,
> Yoolhee Kim
>
> On Tue, Nov 21, 2017 at 8:22 AM, 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
>> >
>> > ------------------------------------------------------------
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>>
>
>
>
> --
> Yoolhee Kim
> M.S. in Energy Science Technology and Policy
> Carnegie Mellon University
> (714) 326-5820 | yoolh...@andrew.cmu.edu
>
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