protonation and structure normalization

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protonation and structure normalization

david.lagorce
Dear All,

After analysis of some compounds whose protonation is carried out by
openbabel command line, it would seem that the results are different
from those obtained with the AddHydrogens() method embedded in the pybel
library, with the correctforpH option.
Does pybel use also the /data/phmodel.txt file? If not, which file is
employed in order to check the involved SMARTS pattern…??

In a same way, I want to know of it possible to use pybel (maybe by the
ConvertDativeBonds method ??) to standardize a whole file for some
specials groups, e.g. nitro, carboxylic acids...
It is documented that it is possible to convert [N+]([O-])=O to N(=O)=O,
but it doesn't work for the other representations of the nitro groups,
like [N](-OH)=O.
To this end, which file (containing the SMARTS patterns) is employed in
the pybel method?

Does anybody know a alternative way to perform a structure normalization
using pybel ??

Thanks,

Regards

David

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Re: protonation and structure normalization

Geoffrey Hutchison
> openbabel command line, it would seem that the results are different
> from those obtained with the AddHydrogens() method embedded in the pybel
> library, with the correctforpH option.

Well yes, if you're comparing AddHydrogens() with and without correctForPH, then the results are different. But I can assure you that Pybel calls the same calls as the command-line when you supply the same options.

> Does pybel use also the /data/phmodel.txt file?

Yes.

> It is documented that it is possible to convert [N+]([O-])=O to N(=O)=O,
> but it doesn't work for the other representations of the nitro groups,
> like [N](-OH)=O.

I have never seen a nitro group represented with an explicit H. Can you give us a real example? Or a list of the "other representations of nitro groups" that you expect?

> To this end, which file (containing the SMARTS patterns) is employed in
> the pybel method?

CorrectDativeBonds does not use SMARTS patterns. Instead, it looks for atom pairs with neighboring "+" and "-" formal charges and it increases the bond order to remove the formal charges.

Hope that helps,
-Geoff
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Re: protonation and structure normalization

david.lagorce
> openbabel command line, it would seem that the results are different
> from those obtained with the AddHydrogens() method embedded in the pybel
> library, with the correctforpH option.

>Well yes, if you're comparing AddHydrogens() with and without correctForPH, then the results are >different. But I can assure you that Pybel calls the same calls as the command-line when you supply >the same options.

> Does pybel use also the /data/phmodel.txt file?

> Yes.



ok, thanks a lot





> It is documented that it is possible to convert [N+]([O-])=O to N(=O)=O,
> but it doesn't work for the other representations of the nitro groups,
> like [N](-OH)=O.

>I have never seen a nitro group represented with an explicit H. Can you give us a real example? Or a >list of the "other representations of nitro groups" that you expect?



I am also agree with you, a nitro with an explicit H, by definition is not a cleary possible, but you can sometimes find it in some databases....Thus, how to correclty re-write it....with babel? In the same way, a nitro group as N(=O)=O loaded in pybel is converted internaly in background to  N(OH)OH....
N(=O)=O is possible, so pybel will found 2 H-Bond Donors (lipinski definition) but in fact there is no one...







> To this end, which file (containing the SMARTS patterns) is employed in
> the pybel method?

>CorrectDativeBonds does not use SMARTS patterns. Instead, it looks for atom pairs with neighboring "+" and "-" formal charges and it increases the bond order to remove the formal charges.

>Hope that helps,
>-Geoff

Thanks a lot for your help...

David