Obfit woes (basic chemistry question?)

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Obfit woes (basic chemistry question?)

JP

Hi there - my lack of chemistry knowledge is catching up with me

Can anyone explain why the following obfit does not output any RMSDs values (using babel 2.3.0).  I mean obfit does not spit out any rmsd values because one of the molecules do not match the smarts pattern - so my question should probably be why does it not match the smarts pattern (and how do I fix it) ?

I generated the smarts pattern as a smiles using babel on the input mol file (ligand.babel.mol)... so that side of things *should* work

obfit 'Cc1nc(N)c(C[n+]2csc(CCO)c2C)cn1' ligand.babel.mol frog2_conformers.sdf

I tried removing the charge - knowing more often than not that is the problem.  As well as I have tried setting the atomic numbers [#7] instead of n/N and [#6] instead of c/C knowing things might get broken with the aromaticity of rings...
To no avail...

I have attached the files I am using for your inspection...

Cheers - and happy new 2011 (late, but better than never)
JP



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ligand.babel.mol (4K) Download Attachment
frog2_conformers.sdf (242K) Download Attachment
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Re: Obfit woes (basic chemistry question?)

Noel O'Boyle
Administrator
You need to narrow it down to a single molecule that should, but
doesn't, match the SMARTS. The easiest way to do this is using "obabel
-s" or "obabel -v" (see the docs).

- Noel

On 19 January 2011 16:01, JP <[hidden email]> wrote:

>
> Hi there - my lack of chemistry knowledge is catching up with me
> Can anyone explain why the following obfit does not output any RMSDs values
> (using babel 2.3.0).  I mean obfit does not spit out any rmsd values because
> one of the molecules do not match the smarts pattern - so my question should
> probably be why does it not match the smarts pattern (and how do I fix it) ?
> I generated the smarts pattern as a smiles using babel on the input mol file
> (ligand.babel.mol)... so that side of things *should* work
>>
>> obfit 'Cc1nc(N)c(C[n+]2csc(CCO)c2C)cn1' ligand.babel.mol
>> frog2_conformers.sdf
>
> I tried removing the charge - knowing more often than not that is the
> problem.  As well as I have tried setting the atomic numbers [#7] instead of
> n/N and [#6] instead of c/C knowing things might get broken with the
> aromaticity of rings...
> To no avail...
> I have attached the files I am using for your inspection...
> Cheers - and happy new 2011 (late, but better than never)
> JP
>
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>

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Download using promo code Free_Logger_4_Dev2Dev. Offer expires
February 28th, so secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsight-sfd2d
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