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SMART notation to select diamine molecule

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SMART notation to select diamine molecule

alfredoq
Dear all:

I am trying to select all compounds containing two amine moieties among a set of monoamine and diamine compounds. I am using the following SMART pattern:

[N;*N]

however this pattern hits borth monoamine and diamine compounds. I can't figure out by reading the available SMART documentation how to set this search. I would greatly appreacite if anyone can give me any hint,

thank you very much in advance,

best regards

Alfredo
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Re: SMART notation to select diamine molecule

Stefano Forli
Alfredo,
take a look at this page [1] for the best definition of amines that fits your dataset.

In theory, the SMARTS standard supports multiple patterns definition (see "Two primary or
secondary amines" in the page), but unfortunately OpenBabel doesn't support it.

I guess the most straightforward way is to count occurrences per molecule (i.e., 2, in
your case), unless somebody with more experience knows a more elegant way.

Best,

S

[1] http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html#N


On 05/12/2016 04:10 PM, alfredoq wrote:

> Dear all:
>
> I am trying to select all compounds containing two amine moieties among a
> set of monoamine and diamine compounds. I am using the following SMART
> pattern:
>
> [N;*N]
>
> however this pattern hits borth monoamine and diamine compounds. I can't
> figure out by reading the available SMART documentation how to set this
> search. I would greatly appreacite if anyone can give me any hint,
>
> thank you very much in advance,
>
> best regards
>
> Alfredo
>
>
>
> --
> View this message in context: http://forums.openbabel.org/SMART-notation-to-select-diamine-molecule-tp4659297.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
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--

  Stefano Forli, PhD

  Assistant Professor of Integrative
  Structural and Computational Biology,
  Molecular Graphics Laboratory

  Dept. of Integrative Structural
   and Computational Biology, MB-112A
  The Scripps Research Institute
  10550  North Torrey Pines Road
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Re: SMART notation to select diamine molecule

alfredoq
Thank you very much Stefano for your kind reply. As you suggested, as part of my several attempts I used the "disconnection symbol" (.) to hit the second amine in the molecule, but I couldnt figure out why it wasnt being recognized by obabel. From your answer, I know now that the problem is that this pattern is not supported.
From your suggestion, is there a way of counting functional group occurrencies within obabel?

kind regards

Alfredo
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Re: SMART notation to select diamine molecule

Geoff Hutchison
>> From your suggestion, is there a way of counting functional group
> occurrencies within obabel?

With the command-line? No. But you can use C++ or Pybel to do that, e.g.
http://baoilleach.blogspot.com/2007/07/pybel-hack-that-sd-file.html

import pybel

amine = pybel.Smarts("[N]")

for mol in pybel.readfile("sdf", "NoRules.sdf"):
        # how many amines are there?
        print len(amine.findall(mol))


Hope that helps,
-Geoff

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Re: SMART notation to select diamine molecule

alfredoq
Thank you very much Geoff for the hint,

best regards

Alfredo
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