Interesting use case.
I can send some sample code for this later this afternoon.
On Tue, Jul 11, 2017 at 11:43 AM, Chicago Ji <chicago...@gmail.com> wrote:
> 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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