On 27/03/2012 00:53, Samuele Sommariva wrote: The OpenBabel class OBChemTsfm that does the work here is rather old and is known to have bugs, as you have found. Wrapping it as an op was intended to make it easier to debug, but unfortunately this didn't happen and OBChemTsfm is still not very useful. Openbabel could really do with a facility like this, so anybody interested in sorting out this code would be doing the community a service.
Incidentally, it's good for people to be reminded that Openbabel finds a use outside pharma (or would do without the bugs). Chris > 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
