smiles into xyz

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smiles into xyz

Dari
Hello !

I'm sorry if this question is stupid, but I don't have any knowledge about chemistry. (I'm just a little softewaredeveloper.. well not yet, but I'm working on it ;D )
My colleagues wants me to find out which program is the best for translating smile strings into xyz files. I googled and found openBabel. An other colleague said openBabel fails in doing this translation...

Has anyone experience in that? Is that right, or was it a fail made by him?

An other thing is: Can I use openBabel from the Shell/Terminal - Line? To put it into a script or something like that..?

Well, thanks for answering!
Dari


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Re: smiles into xyz

Noel O'Boyle
Administrator
It can do it:

  babel myfile.smi myfile.xyz --gen3d

However, it can have problems with rings, though. It relies on a ring
structure library - and if it can't find the ring, it's not going to
work very well.

See also comments at
http://blueobelisk.shapado.com/questions/3d-coordinates-best-options-cdk-rdkit-openbabel-anything-else

- Noel

On 10 August 2010 08:22, Dari <[hidden email]> wrote:

>
> Hello !
>
> I'm sorry if this question is stupid, but I don't have any knowledge about
> chemistry. (I'm just a little softewaredeveloper.. well not yet, but I'm
> working on it ;D )
> My colleagues wants me to find out which program is the best for translating
> smile strings into xyz files. I googled and found openBabel. An other
> colleague said openBabel fails in doing this translation...
>
> Has anyone experience in that? Is that right, or was it a fail made by him?
>
> An other thing is: Can I use openBabel from the Shell/Terminal - Line? To
> put it into a script or something like that..?
>
> Well, thanks for answering!
> Dari
>
>
>
> --
> View this message in context: http://open-babel.957263.n4.nabble.com/smiles-into-xyz-tp2319397p2319397.html
> Sent from the openbabel-discuss mailing list archive at Nabble.com.
>
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