The solution that Hongbin proposes to the double-counting problem is a good
one. Just be sure to sort your substructure queries in the right order so
that the more complex ones come first.
Another thing you might think about is making your queries more specific.
For example, as you pointed out "[OH]" is very general and matches parts of
carboxylic acids and a number of other functional groups. The RDKit has a
set of fairly well tested (though certainly not perfect) functional group
definitions in $RDBASE/Data/Functional_Group_Hierarchy.txt. The alcohol
definition from there looks like this:
[O;H1;$(O-!@[#6;!$(C=!@[O,N,S])])]
-greg
On Mon, Mar 6, 2017 at 7:20 AM, 杨弘宾 <yanyangh...@163.com> wrote:
> Hi, Chenyang,
> You don't need to delete the substructure from the molecule. Just
> check whehter the mapped atoms have been matched. For example:
>
> m = Chem.MolFromSmiles('CC(=O)O')
> OH = Chem.MolFromSmarts('[OH]')
> COOH = Chem.MolFromSmarts('C(O)=O')
>
> m.GetSubstructMatches(OH)
> >> ((3,),)
> m.GetSubstructMatchs(COOH)
> >> ((1, 3, 2),)
>
> Since atom "3" has been already matched, it should be ignored.
> So you can create a "set" to record the matched atoms to avoid repetitive
> count.
>
> ------------------------------
> Hongbin Yang 杨弘宾
>
>
> *From:* Chenyang Shi <cs3...@columbia.edu>
> *Date:* 2017-03-06 14:04
> *To:* Greg Landrum <greg.land...@gmail.com>
> *CC:* RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
> *Subject:* Re: [Rdkit-discuss] delete a substructure
> Hi Greg,
>
> Thanks for a prompt reply. I did try "GetSubstructMatches()" and it
> returns correct numbers of substructures for CH3COOH. The potential problem
> with this approach is that if the molecule is getting complicated, it will
> possibly generate duplicate numbers for certain functional groups. For
> example, --OH (alcohol) group will be likely also counted in --COOH. A
> safer way, in my mind, is to remove the substructure that has been counted.
>
> Greg, you mentioned "chemical reaction functionality", can you show me a
> demo script with that using CH3COOH as an example. I will definitely delve
> into the manual to learn more. But reading your code will be a good start.
>
> Thanks,
> Chenyang
>
>
>
> On Sun, Mar 5, 2017 at 10:15 PM, Greg Landrum <greg.land...@gmail.com>
> wrote:
>
>> Hi Chenyang,
>>
>> If you're really interested in counting the number of times the
>> substructure appears, you can do that much quicker with
>> `GetSubstructMatches()`:
>>
>> In [2]: m = Chem.MolFromSmiles('CC(C)CCO')
>> In [3]: len(m.GetSubstructMatches(Chem.MolFromSmarts('[CH3;X4]')))
>> Out[3]: 2
>>
>> Is that sufficient, or do you actually want to sequentially remove all of
>> the groups in your list?
>>
>> If you actually want to remove them, you are probably better off using
>> the chemical reaction functionality instead of DeleteSubstructs(), which
>> recalculates the number of implicit Hs on atoms after each call.
>>
>> -greg
>>
>>
>> On Mon, Mar 6, 2017 at 4:21 AM, Chenyang Shi <cs3...@columbia.edu> wrote:
>>
>>> I am new to rdkit but I am already impressed by its vibrant community. I
>>> have a question regarding deleting substructure. In the RDKIT
>>> documentation, this is a snippet of code describing how to delete
>>> substructure:
>>>
>>> >>>m = Chem.MolFromSmiles("CC(=O)O")
>>> >>>patt = Chem.MolFromSmarts("C(=O)[OH]")
>>> >>>rm = AllChem.DeleteSubstructs(m, patt)
>>> >>>Chem.MolToSmiles(rm)
>>> 'C'
>>>
>>> This block of code first loads a molecule CH3COOH using SMILES code,
>>> then defines a substructure COOH using SMARTS code which is to be deleted.
>>> After final line of code, the program outputs 'C', in SMILES form.
>>>
>>> I had wanted to develop a method for detecting number of groups in a
>>> molecule. In CH3COOH case, I can search number of --CH3 and --COOH group by
>>> using their respective SMARTS code with no problem. However, when molecule
>>> becomes more complicated, it is preferred to delete the substructure that
>>> has been searched before moving to next search using SMARTS code. Well, in
>>> current case, after searching -COOH group and deleting it, the leftover is
>>> 'C' which is essentially CH4 instead of --CH3. I cannot proceed with
>>> searching with SMARTS code for --CH3 ([CH3;A;X4!R]).
>>>
>>> Is there any way to work around this?
>>> Thanks,
>>> Chenyang
>>>
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>>
>>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
