Here's a simple bit of code that shows how to get only pharmacophore
features whose atoms are contained completely in the MCS:
https://gist.github.com/greglandrum/faf47bd161d9b3af5374c358d0a0786d
An interesting extension to this, which I may do for a blog post later, is
to further filter things to get the "maximum common pharmacophore"
-greg
On Tue, Jul 11, 2017 at 1:41 PM, Greg Landrum <greg.land...@gmail.com>
wrote:
> 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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