Hi Greg,
I want to get pharmacophore feature for each atom on the molecule using
GetFeaturesForMol().
It seems that sanitization is a must before running GetFeaturesForMol().
Many Thanks.
Best,
Changge
On Tue, Jul 11, 2017 at 7:31 AM, Greg Landrum <greg.land...@gmail.com>
wrote:
> Hi Changge,
>
> Is there any particular reason that you're calling updatePropertyCache on
> the molecule? That's not an operation that's normally necessary.
>
> Best,
> -greg
>
>
>
> On Mon, Jul 10, 2017 at 8:37 PM, Chicago Ji <chicago...@gmail.com> wrote:
>
>> Dear all,
>>
>> I met a problem with Aromatic N atoms.
>>
>> Here is the code:
>> ----------------------------
>>
>> sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]-!@[#7]-@1-@
>> [#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[
>> #7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1:
>> [#6]:[#6]:[#6]:[#6]:[#6]:1'
>>
>> mc = Chem.MolFromSmarts(sa,False)
>>
>> mc.UpdatePropertyCache()
>>
>> ------------------------------
>>
>> The error info says " Explicit valence for atom # 16 N, 4, is greater
>> than permitted"
>>
>> I also tried sanifix3.AdjustAromaticNs, but that doesn't work.
>>
>> Is there an easy way to solve this problem?
>>
>> Many thanks.
>>
>>
>> Best Regards,
>> Changge
>>
>>
>>
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