Dear Jyoti,
I really doubt that that SMILES string is an exact copy/paste from what was
generated by babel since it is invalid. If it really is so, you should report
it as a bug and send the sdf input with the report.
Kind regards,
Fredrik
> 29 nov. 2015 kl. 09:02 skrev Jyotiprakash Rath <rathjy...@gmail.com>:
>
> Dear Fedrik,
>
> I do not know much about the smiles, this particular smiles is being
> generated by babel from SDF input, therefore i think it should have worked
> with the babel command. May I know how can I short out the issue.
>
> Regards
> Jyoti
>
> On Sat, Nov 28, 2015 at 7:10 PM, Fredrik Wallner <fred...@wallner.nu
> <mailto:fred...@wallner.nu>> wrote:
> Hi,
>
> The error says Cannot read the SMILES string and if you look at the string it
> contains one more right parenthesis than left which is why you get the error.
>
> Kind regards,
> Fredrik
>
> Skickat från min iPhone
>
> > 26 nov. 2015 kl. 12:18 skrev rathjyoti <rathjy...@gmail.com
> > <mailto:rathjy...@gmail.com>>:
> >
> > Dear friends,
> > I am facing a similar problem.With open babel tutorial I could
> > able to generate a fast-search index (znd_unique) for 30 thousand molecule.
> > I have tried searching matches > 0.5 tanimoto similarity with one molecule
> > and the fast search index it worked well. The command line argument for the
> > same as follows -
> >
> > babel znd_unique.fs similar0.5_CID5310786.sdf
> > -s"O=[P@@](O)(O[C@@H]1[C@H](O)[C@H](O)[C@@H](O)[C@@H](O1)C)O[P@](=O)(O)OC[C@H]1O[C@H](C[C@@H]1O)n1c(=O)[nH]c(=O)c(C)c1"
> > -at0.5
> > 55 molecules converted
> > 1152 audit log messages
> >
> > But, when I tried with another molecule
> > SCCCn1c2c([nH]c1=O)cccc2)c1nc2n(c3c(c2nn1)cccc3)CC it did not work. The
> > command line argument and error message for the same is -
> >
> > babel znd_unique.fs similar0.5_CID5310786.sdf
> > -s"SCCCn1c2c([nH]c1=O)cccc2)c1nc2n(c3c(c2nn1)cccc3)CC" -at0.5
> > ==============================
> > *** Open Babel Error in ObtainTarget
> > Cannot read the SMILES string
> > 0 molecules converted
> > 1 errors 3 audit log messages
> >
> > Please help me out.
> >
> > Jyoti Prakash Rath
> >
> >
> >
> >
> >
> > --
> > View this message in context:
> > http://forums.openbabel.org/Examples-of-Openbabel-fast-substructure-searching-tp4657120p4659069.html
> >
> > <http://forums.openbabel.org/Examples-of-Openbabel-fast-substructure-searching-tp4657120p4659069.html>
> > Sent from the General discussion mailing list archive at Nabble.com.
> >
> > ------------------------------------------------------------------------------
> > _______________________________________________
> > OpenBabel-discuss mailing list
> > OpenBabel-discuss@lists.sourceforge.net
> > <mailto:OpenBabel-discuss@lists.sourceforge.net>
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> > <https://lists.sourceforge.net/lists/listinfo/openbabel-discuss>
>
>
>
> --
> Mr. Jyoti Prakash Rath
>
> Assistant Professor
>
> Medical Biotechnology & Bioinformatics
>
> Medical Bio-nanotechnology Department
>
> Chettinad University, Chennai
>
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