Thanks Hongbin and Pavel for the suggestions. I am now confident that the
approach Hongbin proposed to remove duplicate counts is a robust one. Now I
need to revisit/recheck all my SMARTS definitions.
One last question I have is do you guys have convenient online or local
documents to look up desired SMARTS.
Greg mentioned $RDBASE/Data/Functional_Group_Hierarchy.txt, which comes
with the installation of RDKIT.
Brian suggested daylight website,
http://www.daylight.com/dayhtml_tutorials/languages/
smarts/smarts_examples.html, which is a good place as well.
Best,
Chenyang
On Thu, Mar 9, 2017 at 1:09 AM, 杨弘宾 <yanyangh...@163.com> wrote:
> Hi Chemyang,
>
> Your issue was caused by the definition of "-OH(phenol)", I think. If
> you define this pattern as "cO", the atom *3* will be matched since it is
> the aromatic carbon bond to an oxygen. I guess you just wanted to match
> exactly the oxygen and restrict it with "bonding with an aromatic carbon".
> So the SMARTS should ber "[$(Oc)]", which indicates an oxygen with the
> environment of "bonding with an aromatic carbon".
>
> m = Chem.MolFromSmiles('CC1=CC(=C(C=C1)C(=O)O)O')
> m.GetSubstructMatches(Chem.MolFromSmiles('[$(Oc)]'))
> >>> ((10,),)
>
> Then only atom *10* will be matched and it won't interfere with other
> counts.
>
> Reference: http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
> 4.4
>
> ------------------------------
> Hongbin Yang
>
>
> *From:* Chenyang Shi <cs3...@columbia.edu>
> *Date:* 2017-03-09 01:32
> *To:* Greg Landrum <greg.land...@gmail.com>
> *CC:* rdkit-discuss <rdkit-discuss@lists.sourceforge.net>; 杨弘宾
> <yanyangh...@163.com>
> *Subject:* Re: [Rdkit-discuss] delete a substructure
> Dear Hongbin,
>
> I tried your method on a molecule, 4-Methylsalicylic acid
> (CC1=CC(=C(C=C1)C(=O)O)O). I looped through all groups defined in Joback
> method (using SMARTS), and used m.GetSubstructMatches to print out all
> atom positions. The result is summarized in the table.
>
> We can see there are duplicated counts--coming from COOH group. As
> suggested by Hongbin, we can remove duplicated atoms by looking at their
> positions--in this case, ((9),), ((7,8,),), ((7,),), and ((8,),) are
> subsets of ((7,8,9)) from -COOH. Indeed we can get rid of these duplicates.
> However, I also noticed that Atom (3,) from =C< (ring) group is also a part
> of -OH (phenol) ((10,3),). If we apply the same algorithm to remove
> duplicates, the =C<(ring) group will be only counted twice instead of three
> times.
>
> Greg, you mentioned as an alternative I can delete substructure using
> chemical reaction method. It would be greatly appreciated if you could show
> me (point me to) a simple example code, perhaps on a simple molecule? I
> find myself at a loss when browsing the manual. I would like to try also in
> that direction.
>
> Thanks,
> Chenyang
>
>
> [image: Inline image 1]
>
>
> On Mon, Mar 6, 2017 at 1:52 AM, Greg Landrum <greg.land...@gmail.com>
> wrote:
>
>> 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
>>>
>>>
>>
> [image: 提示图标] 邮件带有附件预览链接，若您转发或回复此邮件时不希望对方预览附件，建议您手动删除链接。
> 共有 *1* 个附件
> 4-Methylsalicyclic acid.png(54K) 极速下载
> <http://preview.mail.163.com/xdownload?filename=4-Methylsalicyclic+acid.png&mid=1tbiDxmVPlUL-6hHbgAAsd&part=4&sign=85ee2cc8065ae7029195ca0a123a4dbd&time=1489027421&uid=yanyanghong%40163.com>
> 在线预览
> <http://preview.mail.163.com/preview?mid=1tbiDxmVPlUL-6hHbgAAsd&part=4&sign=85ee2cc8065ae7029195ca0a123a4dbd&time=1489027421&uid=yanyanghong%40163.com>
>
>
------------------------------------------------------------------------------
Announcing the Oxford Dictionaries API! The API offers world-renowned
dictionary content that is easy and intuitive to access. Sign up for an
account today to start using our lexical data to power your apps and
projects. Get started today and enter our developer competition.
http://sdm.link/oxford
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
