subject:"\[Rdkit\-discuss\] Reaction changing bonds but not charges"

Re: [Rdkit-discuss] Reaction changing bonds but not charges

2017-10-09 Thread Chris Murphy

That works, thanks! I'll be sure to include an explicit +0 when converting
when I need the product to be neutral.

On Mon, Oct 9, 2017 at 11:15 AM, Chris Earnshaw 
wrote:

> Hi
>
> I don't think the reaction SMARTS does specify a change in the
> charges. The N and O have to be charged in order to match the reactant
> pattern but they won't be altered by the transformation. If you
> specify that the product atoms are explicitly neutral I think you'll
> get the result you want -
> [#8-:2]-[#7+:1]=[O:3]>>[O+0:2]=[N+0:1]=[O:3]
>
> Chris Earnshaw
>
> On 9 October 2017 at 15:57, Chris Murphy 
> wrote:
> > Hi,
> >
> > I am using rdChemReactions to perform substructure transformations as
> > defined by configurable reaction smarts. When I create the reaction and
> run
> > a mol through it that I expect to be transformed by the indicated
> reaction
> > smarts, I see that the bonds have been changed according to the smarts,
> but
> > the charges are not changed.
> >
> > I am using the following smarts to define the transformation:
> > [#8-:2]-[#7+:1]=[O:3]>>[O:2]=[N:1]=[O:3]
> >
> > The input molecule is as follows:
> >
> >   Mrv16c5 10061718252D
> >
> >   9  9  0  0  0  0999 V2000
> >-0.5916   -0.06780. C   0  0  0  0  0  0  0  0  0  0  0  0
> >-1.3060   -0.48030. C   0  0  0  0  0  0  0  0  0  0  0  0
> >-1.3060   -1.30540. C   0  0  0  0  0  0  0  0  0  0  0  0
> >-0.5916   -1.71790. C   0  0  0  0  0  0  0  0  0  0  0  0
> > 0.1229   -1.30540. C   0  0  0  0  0  0  0  0  0  0  0  0
> > 0.1229   -0.48030. C   0  0  0  0  0  0  0  0  0  0  0  0
> >-0.59160.75720. N   0  3  0  0  0  0  0  0  0  0  0  0
> >-1.30611.16970. O   0  5  0  0  0  0  0  0  0  0  0  0
> > 0.12291.16970. O   0  0  0  0  0  0  0  0  0  0  0  0
> >   1  2  2  0  0  0  0
> >   2  3  1  0  0  0  0
> >   3  4  2  0  0  0  0
> >   4  5  1  0  0  0  0
> >   5  6  2  0  0  0  0
> >   6  1  1  0  0  0  0
> >   1  7  1  0  0  0  0
> >   7  8  1  0  0  0  0
> >   7  9  2  0  0  0  0
> > M  END
> > 
> >
> > and the output ends up being:
> >
> >  RDKit  2D
> >
> >   9  9  0  0  0  0  0  0  0  0999 V2000
> >-1.30611.16970. O   0  0  0  0  0  0  0  0  0  0  0  0
> >-0.59160.75720. N   0  0  0  0  0  0  0  0  0  0  0  0
> > 0.12291.16970. O   0  0  0  0  0  0  0  0  0  0  0  0
> >-0.5916   -0.06780. C   0  0  0  0  0  0  0  0  0  0  0  0
> >-1.3060   -0.48030. C   0  0  0  0  0  0  0  0  0  0  0  0
> > 0.1229   -0.48030. C   0  0  0  0  0  0  0  0  0  0  0  0
> >-1.3060   -1.30540. C   0  0  0  0  0  0  0  0  0  0  0  0
> > 0.1229   -1.30540. C   0  0  0  0  0  0  0  0  0  0  0  0
> >-0.5916   -1.71790. C   0  0  0  0  0  0  0  0  0  0  0  0
> >   1  2  2  0
> >   2  3  2  0
> >   4  2  1  0
> >   4  5  2  0
> >   6  4  1  0
> >   5  7  1  0
> >   8  6  2  0
> >   7  9  2  0
> >   9  8  1  0
> > M  CHG  2   1  -1   2   1
> > M  END
> >
> > It seems the that NO bond is successfully converted to a double bond, but
> > the charges have not been changed, even though the reaction smarts
> indicates
> > that they N and O should be changed to neutral. Are there any glaring
> issues
> > with using reactions to do transformations like this?
> >
> > Thanks!
> >
> > -Chris
> >
> > 
> --
> > 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
> >
>
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Re: [Rdkit-discuss] Reaction changing bonds but not charges

2017-10-09 Thread Chris Earnshaw

Hi

I don't think the reaction SMARTS does specify a change in the
charges. The N and O have to be charged in order to match the reactant
pattern but they won't be altered by the transformation. If you
specify that the product atoms are explicitly neutral I think you'll
get the result you want -
[#8-:2]-[#7+:1]=[O:3]>>[O+0:2]=[N+0:1]=[O:3]

Chris Earnshaw

On 9 October 2017 at 15:57, Chris Murphy  wrote:
> Hi,
>
> I am using rdChemReactions to perform substructure transformations as
> defined by configurable reaction smarts. When I create the reaction and run
> a mol through it that I expect to be transformed by the indicated reaction
> smarts, I see that the bonds have been changed according to the smarts, but
> the charges are not changed.
>
> I am using the following smarts to define the transformation:
> [#8-:2]-[#7+:1]=[O:3]>>[O:2]=[N:1]=[O:3]
>
> The input molecule is as follows:
>
>   Mrv16c5 10061718252D
>
>   9  9  0  0  0  0999 V2000
>-0.5916   -0.06780. C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.3060   -0.48030. C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.3060   -1.30540. C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.5916   -1.71790. C   0  0  0  0  0  0  0  0  0  0  0  0
> 0.1229   -1.30540. C   0  0  0  0  0  0  0  0  0  0  0  0
> 0.1229   -0.48030. C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.59160.75720. N   0  3  0  0  0  0  0  0  0  0  0  0
>-1.30611.16970. O   0  5  0  0  0  0  0  0  0  0  0  0
> 0.12291.16970. O   0  0  0  0  0  0  0  0  0  0  0  0
>   1  2  2  0  0  0  0
>   2  3  1  0  0  0  0
>   3  4  2  0  0  0  0
>   4  5  1  0  0  0  0
>   5  6  2  0  0  0  0
>   6  1  1  0  0  0  0
>   1  7  1  0  0  0  0
>   7  8  1  0  0  0  0
>   7  9  2  0  0  0  0
> M  END
> 
>
> and the output ends up being:
>
>  RDKit  2D
>
>   9  9  0  0  0  0  0  0  0  0999 V2000
>-1.30611.16970. O   0  0  0  0  0  0  0  0  0  0  0  0
>-0.59160.75720. N   0  0  0  0  0  0  0  0  0  0  0  0
> 0.12291.16970. O   0  0  0  0  0  0  0  0  0  0  0  0
>-0.5916   -0.06780. C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.3060   -0.48030. C   0  0  0  0  0  0  0  0  0  0  0  0
> 0.1229   -0.48030. C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.3060   -1.30540. C   0  0  0  0  0  0  0  0  0  0  0  0
> 0.1229   -1.30540. C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.5916   -1.71790. C   0  0  0  0  0  0  0  0  0  0  0  0
>   1  2  2  0
>   2  3  2  0
>   4  2  1  0
>   4  5  2  0
>   6  4  1  0
>   5  7  1  0
>   8  6  2  0
>   7  9  2  0
>   9  8  1  0
> M  CHG  2   1  -1   2   1
> M  END
>
> It seems the that NO bond is successfully converted to a double bond, but
> the charges have not been changed, even though the reaction smarts indicates
> that they N and O should be changed to neutral. Are there any glaring issues
> with using reactions to do transformations like this?
>
> Thanks!
>
> -Chris
>
> --
> 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
>

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[Rdkit-discuss] Reaction changing bonds but not charges

2017-10-09 Thread Chris Murphy

Hi,

I am using rdChemReactions to perform substructure transformations as
defined by configurable reaction smarts. When I create the reaction and run
a mol through it that I expect to be transformed by the indicated reaction
smarts, I see that the bonds have been changed according to the smarts, but
the charges are not changed.

I am using the following smarts to define the transformation:
[#8-:2]-[#7+:1]=[O:3]>>[O:2]=[N:1]=[O:3]

The input molecule is as follows:

  Mrv16c5 10061718252D

  9  9  0  0  0  0999 V2000
   -0.5916   -0.06780. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3060   -0.48030. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3060   -1.30540. C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5916   -1.71790. C   0  0  0  0  0  0  0  0  0  0  0  0
0.1229   -1.30540. C   0  0  0  0  0  0  0  0  0  0  0  0
0.1229   -0.48030. C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.59160.75720. N   0  3  0  0  0  0  0  0  0  0  0  0
   -1.30611.16970. O   0  5  0  0  0  0  0  0  0  0  0  0
0.12291.16970. O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  1  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END


and the output ends up being:

 RDKit  2D

  9  9  0  0  0  0  0  0  0  0999 V2000
   -1.30611.16970. O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.59160.75720. N   0  0  0  0  0  0  0  0  0  0  0  0
0.12291.16970. O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5916   -0.06780. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3060   -0.48030. C   0  0  0  0  0  0  0  0  0  0  0  0
0.1229   -0.48030. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3060   -1.30540. C   0  0  0  0  0  0  0  0  0  0  0  0
0.1229   -1.30540. C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5916   -1.71790. C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  2  0
  4  2  1  0
  4  5  2  0
  6  4  1  0
  5  7  1  0
  8  6  2  0
  7  9  2  0
  9  8  1  0
M  CHG  2   1  -1   2   1
M  END

It seems the that NO bond is successfully converted to a double bond, but
the charges have not been changed, even though the reaction smarts
indicates that they N and O should be changed to neutral. Are there any
glaring issues with using reactions to do transformations like this?

Thanks!

-Chris
--
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engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [Rdkit-discuss] Reaction changing bonds but not charges

Re: [Rdkit-discuss] Reaction changing bonds but not charges

[Rdkit-discuss] Reaction changing bonds but not charges

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