pybel ring numbering

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pybel ring numbering

giovannicianchetta
Hi,
I am having a strange problem with openbabel and pybel.
look at the code below, please:


>>> import pybel
>>> mol=pybel.readstring('smi','c1ccccc1CCc2ccccc2')
>>> print mol
c1ccccc1CCc1ccccc1

as you can notice the second ring has been renumbered as 1 so now I have two rings with the same index.
has anyone found this problem before?
is there a solution for this?

thanks

Giovanni
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Re: pybel ring numbering

Noel O'Boyle
Administrator
Have you read the OpenSMILES spec? It's at
http://opensmiles.org/spec/open-smiles-3-input.html#3.4: "It is
permissable to re-use ring-closure numbers. Once a particular number
has been encountered twice, that number is available again for
subsequent ring closures."

HTH,
   Noel

On 4 November 2011 21:12, giovannicianchetta
<[hidden email]> wrote:

> Hi,
> I am having a strange problem with openbabel and pybel.
> look at the code below, please:
>
>
>>>> import pybel
>>>> mol=pybel.readstring('smi','c1ccccc1CCc2ccccc2')
>>>> print mol
> c1ccccc1CCc1ccccc1
>
> as you can notice the second ring has been renumbered as 1 so now I have two
> rings with the same index.
> has anyone found this problem before?
> is there a solution for this?
>
> thanks
>
> Giovanni
>
> --
> View this message in context: http://forums.openbabel.org/pybel-ring-numbering-tp3991497p3991497.html
> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>
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