Atom hybridization matching

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Atom hybridization matching

Nina Jeliazkova
Dear All,

We are looking to pointers/examples, explaining atom hybridization matching "^"  , implemented in OpenBabel . Is there additional information to the one found at http://openbabel.org/wiki/SMARTS page?

In addition to the Daylight Toolkit syntax, Open Babel also offers the following extensions to SMARTS which are not currently supported by Daylight:

    • Atom hybridization matching "^". For example [#6^3] matches a carbon atom (atomic number 6) with sp3 hybridization. Accepted hybridizations include:
      • 1 - sp e.g., [#6^1][#7]
      • 2 - sp2 e.g., [#6^2][#6^2]
      • 3 - sp3 e.g., [#8^3]
Best regards,
Nina Jeliazkova

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Re: Atom hybridization matching

Geoffrey Hutchison
> We are looking to pointers/examples, explaining atom hybridization matching "^"  , implemented in OpenBabel . Is there additional information to the one found at http://openbabel.org/wiki/SMARTS page?

I suspect your question is "how do you determine hybridization?" The rules are given in data/atomtyp.txt.

e.g.

> INTHYB  [C]                       3       #sp3 carbon
> INTHYB  [c,$(C=*)]                2       #sp2 carbon
> INTHYB  [$([#6]([#8D1])[#8D1])]   2       #sp2 carbon
> INTHYB  [$(C#*),$(C(=*)=*)]       1       #sp  carbon
>
> INTHYB  [N]                       3       #sp3 nitrogen
> INTHYB  [n,$(N=*),$(N[#6,#7,#8]=,:,#*)] 2 #sp2 nitrogen
> INTHYB  [ND1,ND2,ND3]a            2       #sp2 nitrogen
> INTHYB  [$(N#*),$([ND2](=*)=*)]   1       #sp  nitrogen
> ...


Hope that helps,
-Geoff
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Re: Atom hybridization matching

Nina Jeliazkova
Geoffrey Hutchison wrote:
We are looking to pointers/examples, explaining atom hybridization matching "^"  , implemented in OpenBabel . Is there additional information to the one found at http://openbabel.org/wiki/SMARTS page? 
    

I suspect your question is "how do you determine hybridization?" The rules are given in data/atomtyp.txt.

e.g.
  
INTHYB  [C]                       3       #sp3 carbon
INTHYB  [c,$(C=*)]                2       #sp2 carbon
INTHYB  [$([#6]([#8D1])[#8D1])]   2       #sp2 carbon
INTHYB  [$(C#*),$(C(=*)=*)]       1       #sp  carbon

INTHYB  [N]                       3       #sp3 nitrogen
INTHYB  [n,$(N=*),$(N[#6,#7,#8]=,:,#*)] 2 #sp2 nitrogen
INTHYB  [ND1,ND2,ND3]a            2       #sp2 nitrogen
INTHYB  [$(N#*),$([ND2](=*)=*)]   1       #sp  nitrogen
...
    

  
Thank you, this is helpful indeed.

Nina
Hope that helps,
-Geoff
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