Hi Christos, thank you so much!
Your approach is much simpler and quicker than what I had, and it now works
with polycyclic compounds. I did try your approach at first but I could not
have an image representation in ChemDraw of the SMARTS I was creating with
the "a" labels. I thought I was doing something wrong and thought the only
way was to use the more complicated “:[*]” notation… Your script provides
valid SMARTS even if ChemDraw does not recognize them. You saved me a lot
of time.
Thanks again,
Alexis
On 19 May 2017 at 14:38, Christos Kannas <chriskan...@gmail.com> wrote:
> Hi Alexis,
>
> In SMARTS you can define an aromateic atom with "a".
> So I'm thinking that something like the following, might produce more
> correct generalised SMARTS patterns.
>
> https://gist.github.com/CKannas/7a9e2768461260461155257fd30c2152
>
> *Note: Please check if the chemistry is correct.*
>
> Best,
>
> Christos
>
> Christos Kannas
>
> Researcher
> Ph.D Student
>
> [image: View Christos Kannas's profile on LinkedIn]
> <http://cy.linkedin.com/in/christoskannas>
>
> On 19 May 2017 at 12:52, Alexis Parenty <alexis.parenty.h...@gmail.com>
> wrote:
>
>> Hi everyone,
>>
>>
>> I need a function that could generalize any aromatic rings from a SMARTS:
>>
>> [image: Inline images 1]
>>
>>
>> I have noticed that it is possible to rearrange most of SMARTS strings
>> into a general aromatic SMARTS strings by following those simple rules:
>>
>> 1 Exchange any lower case of a SMARTS string with
>> “:[*]”
>>
>> 2 Catch the two cycle junctions of the SMARTS:
>>
>> a. Where a number(1-9) appears a first time in the string: insert
>> a colon after the digit (for example “[*]1” to “[*]1:”
>>
>> b. Where the same number appears a second time, move the semi colon
>> before the digit (for example “[*]1:” to “[*]:1 the
>>
>>
>> I have written a function (see under) that works fine with any SMART
>> containing a single aromatic ring. But it does get buggy when I have a
>> SMARTS with more than one aromatic ring:
>>
>>
>>
>> [image: Inline images 2]
>>
>>
>>
>> def get_aromatic_generalised_smarts(smarts):
>> for arom_atom in ("c", "o", "n", "s"):
>> smarts = smarts.replace(arom_atom, "x")
>> smarts = smarts.replace("[xH]", "x") # to take care of explicit hydrogen
>> atoms
>>
>> for char in smarts:
>> if char == 'x':
>> smarts = smarts.replace(char, ":[*]")
>>
>> for char in smarts:
>> if char.isdigit():
>> if ("[*]"+char) in smarts:
>> for cycle_junction in ("[*]1", "[*]2", "[*]3", "[*]4", "[*]5",
>> "[*]6", "[*]7", "[*]8", "[*]9"):
>> smarts = smarts.replace(cycle_junction, "[*]:" +
>> cycle_junction[-1]) # that make the second cycle junction OK but introduce
>> an error in the first cycle jonction that is corrected next line
>> smarts = smarts.replace(":[*]:"+char, "[*]"+char, 1) # to
>> correct the first cycle junction.
>> break
>> return smarts
>>
>>
>> print(get_aromatic_generalised_smarts("[*]c1coc(Cl)n1"))
>> print(get_aromatic_generalised_smarts("[*]c1coc(Cl)c1"))
>>
>> print(get_aromatic_generalised_smarts("[*]c1coc(Cl)c1Cc2ccccc2")
>>
>>
>> Am I heading in the right direction? I can't make my heads around SMARTS
>> with more than one aromatic rings...
>>
>> Maybe regular expressions would be more appropriate? Maybe there is an
>> RDKit function that does the trick from a mol object?
>>
>>
>> Thanks,
>>
>>
>> Alexis
>>
>>
>>
>>
>>
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>
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