Using the pharmacophore search code on molecules constructed from SMARTS
is, in many circumstances, unlikely to yield the results that you are
looking for. Query-Query matching is different than Query-Atom matching.

It's more common to look for ph4 features in molecules constructed from
SMILES or from a mol file. Is there a particular reason that you need to
use SMARTS?

-greg


On Tue, Jul 11, 2017 at 8:54 AM, Chicago Ji <chicago...@gmail.com> wrote:

> 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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>>
>
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