Hi Fredrik,
Can i determine the position of the fonctional groups within the molecules
with pybel _ openbabel ?
Thank you in advance for your help.
T-B
2011/2/24 NGUYEN Thanh Binh <thanhbin...@gmail.com>
> Hi again,
>
> I am preparing a file for you , but now it is not important. Indeed, i have
> used Findall() but unsuccessfully yet. Anyway, thank you very much.
>
> Best regards,
>
> T-B
>
>
> 2011/2/24 Fredrik Wallner <fred...@wallner.nu>
>
> Hi again,
>>
>> On looking at the Pybel code for findall I thought that what you probably
>> want is to use the openbabel backbone and call GetMapList instead of
>> GetUMapList as findall() does. However, that didn't work either for me (the
>> result was still only 1 set of atoms). I also tried MatchesSMARTS as
>> in: [x.OBAtom.MatchesSMARTS("C=C") for x in mol.atoms] (mol being C=C) but
>> that gave [True, False] and not [True, True] as I would have expected. So,
>> unfortunately, I don't have any idea how to solve this at the moment...
>>
>> Kind regards,
>> Fredrik
>> 24 feb 2011 kl. 10.52 skrev Fredrik Wallner:
>>
>> Hi again,
>>
>> Could you please send a small list of SMILES and the expected result along
>> with your code so that we can see what's happening. Please also cc the list.
>>
>> Kind regards,
>> Fredrik
>>
>> 24 feb 2011 kl. 10.45 skrev NGUYEN Thanh Binh:
>>
>> Thank you very much Mr. Fredrik. It is exactly my problem. How can i solve
>> this problem ?
>>
>> Best regards,
>>
>> Thanh Binh
>>
>>
>> ---------- Forwarded message ----------
>> From: NGUYEN Thanh Binh <thanhbin...@gmail.com>
>> Date: 2011/2/24
>> Subject: Re: [Open Babel] Asking about SMARTS
>> To: Noel O'Boyle <baoille...@gmail.com>
>>
>>
>> Dear,
>>
>> I have not tried the SMARTSWiewer yet. Thank you very much for this useful
>> link.
>>
>> An example SMILES is C=C and C=CC. I want to parse and to regconize two
>> groups such as -CH= and =CH2.
>>
>> Many thanks in advance for your advices.
>>
>> Thanh Binh.
>>
>>
>>
>>
>> 2011/2/24 Noel O'Boyle <baoille...@gmail.com>
>>
>> Did you try the SmartsViewer? http://smartsview.zbh.uni-hamburg.de/
>>>
>>> Can you give an example molecule (SMILES) where you do not get the
>>> expected result?
>>>
>>> - Noel
>>>
>>> On 23 February 2011 10:16, NGUYEN Thanh Binh <thanhbin...@gmail.com>
>>> wrote:
>>> > Dear,
>>> >
>>> > My name is NGUYEN Thanh Binh. I am working about the SMARTS parsing.
>>> > I have used the library OPENBABEL to do it.
>>> > But i have a problem that needs your help. My following problem is :
>>> >
>>> > When i have constructed SMARTS Formulas in order to parse and to count
>>> the
>>> > fonctional groups for the alpha alkene by using PYBEL, i can not count
>>> the
>>> > number of groups CH2= of the Ethylene. The rests are good except for
>>> > Ethylene. I have tried to correct the SMARTS but unsuccessfully yet.
>>> >
>>> > My SMARTS formula for CH2= is : [CX3H2]=[#6]
>>> >
>>> > I write to you for demande some advices about this problem.
>>> >
>>> > Many thanks in advance for your help,
>>> >
>>> > Best regards
>>> >
>>> > NGUYEN Thanh Binh
>>> >
>>> > P/S: please answer to me by this email adress: thanhbin...@gmail.com
>>> >
>>> >
>>> >
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>>
>>
>>
>>
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