Hi, Greg.
Thanks a lot for your code.
I met another error. I don't know whether it's Normal.
I have a correct SMILES, and read it through MolFromSmarts:
--------------------------------------------------------
sa = 'CC(C)(C)c1ccc(cc1)C(O)CCCN1CCC(CC1)C(O)(c1ccccc1)c1ccccc1'
Chem.MolFromSmarts(sa)
--------------------------------------------------------
Is there something wrong with my input?
Many Thanks.
Best,
Changge
On Tue, Jul 11, 2017 at 4:53 PM, Greg Landrum <greg.land...@gmail.com>
wrote:
> 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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>>>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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