Does the SMARTS string match the molecules in the first place? i.e. what is the output of obabel -ismi myFile.txt -s [CH2X3]-[C]=[OH0] -osmi
Chris can comment more, but I think it is likely that you are pushing the bondaries of what's possible via the reaction transformation code (we don't quite call it SMIRKS). You may have to write some Python or other code to do this kind of thing. - Noel On 27 March 2012 00:53, Samuele Sommariva <samuele.sommar...@gmail.com> wrote: > Hi everybody. > I work with high temperature kinetic scheme, hence I have radicals going > around. > I am using one of the latest developer version (updated at the beginning of > the month) on win7 home 64 bit. > > I need to assign a unique name to resonant radicals. In this example a > primary radical with a carbonyl group in alpha position should be > transformed into a vinoxy radical > > > From what I have understood I can force the transformation of a tautomer > into another following these steps: > 1 – Update the plugindefines.txt > > #Add to plugindefines.txt > OpTransform > > mesomers # ID. Commandline option > > SmmMesomers.txt # DataFile > > First blush: trying to replace resonant radicals > > > > 2 – Define the SMIRK reaction(s) in SmmMesomers.txt > #radical alpha-carbonyl >> vinoxy > > TRANSFORM [CH2X3:1]-[C:2]=[OH0:3] >> [CH2X3:1]=[C:2]-[OH0:3] > > > > 3 – test with obabel -:myFile.txt -ismi -ocan --mesomers > > myFile.txt contains > > [CH2]C=O > > [CH2]C(=O)C > > CCC=O > > The results I expected are the same as the one founded on > http://www.daylight.com/daycgi_tutorials/react.cgi > > [CH2]C=O [O]C=C > > [CH2]C(=O)C CC(=C)[O] > > CCC=O (doesn’t match) > > The results I obtained are NO transformation at all. What am I missing??? > Thank you for your help. > > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
