Re: [Ambit-users] [URGENT] Issues with my SMIRKS reaction. Need help

Yannick,

Could you please file an issue https://sourceforge.net/p/ambit/bugs/ if not
already.

SMIRKS processing has number of updates and cleanups since this spring, do
try to use the version in trunk 3.0.3-SNAPSHOT.

Best regards,
Nina

On 12 September 2016 at 22:29, Yannick .Djoumbou <y.d...@gm...>
wrote:

>
>
> On Sun, Jul 10, 2016 at 7:57 PM, Yannick .Djoumbou <y.d...@gm...>
> wrote:
>
>> Hi all,
>>
>> I have some issues with my SMIRKS manager.
>> have written the SMIKRS below that I am applying on one compounds:
>>
>> [#6;A;H2X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5][P;X4:4]([#8;X2:2])
>> ([#8;A;X2H1,X1-:3])=[O;X1:1]>>[#8;X2:2][P;X4:4]1(=[O;X1:1])[
>> #8;A;X:3][#6;A;H1X4:7]!@-[#6;A;H2X4:6]!@-[#8;X2:5]1
>>
>>
>> I am trying to join two atoms here to form a cycle, The C7 and the O3.  In
>>  the reactant, O3 can be linked to a Hydrogen atom (case 1)  or can be
>> negatively charged (case 2). The problem is that in the product, the O3 has
>> a valence of 3 (with an implicit H) (case 1), or a valence of 2 (case 2).
>>
>> The examples are illustrated in the attached file.
>>
>>
>> Could anyone help?
>>
>>
>> Thanks.
>>
>>
>> Regards,
>>
>
>