Hi, Greg,
The SMARTS comes from MCS.FindMCS() analysis. It seems that MCS can only
output the result as SMARTS.
Maybe I can calculate atom features of the "mother molecule', and then
extract those belonging to the common substructure.
Or I can delete some atoms of the 'mother molecule', and output as SMILES.
Many thanks for your help.
Best,
Changge
On Tue, Jul 11, 2017 at 8:26 AM, Greg Landrum <greg.land...@gmail.com>
wrote:
> 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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