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 <jeanpaul.ebe...@inhibox.com> 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 > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > ------------------------------------------------------------------------------ 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 OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
