Thank you Chris, though I must say that canonical smiles definitely re-orders the atom to create an algorithm-unique ordering(except for a couple of buggy cases with tautomers and aromatic systems), though I believe that in some "regular" SMILES, the ordering is often the same as input SDF.
Geoffrey, thank you for your answer. Yes, I would really like that re-ordering of the SDF atoms - I believe an option like that already exists for non-canonical smiles: to output the atom coordinates in the order they appear in canonical form. So, I was wondering, does the following command already do the trick, and if so, what's the point of .can output? babel -isdf yournoncanonicalsdf.sdf -osmi yoursmilesfile.smi -xcx The -xc part should output canonical smiles, and -xx gives me the X-coordinate of the atoms in the order they appear in the canonical SMILES string. Is this usage safe/correct? Is the canonicalization algorithm in -osmi -xc the same as in -ocan ? Because if that's the case, no extra work needs to be done. Thank you all so much for your attention and help. Leonid Chepelev On Sat, Feb 20, 2010 at 9:14 PM, Geoffrey Hutchison <ge...@geoffhutchison.net> wrote: >> appearance) index of the SDF file atoms and the (order of appearance) >> index of the atoms in the newly created SMILES string. > > This would no longer be a canonical SMILES -- it would be a "regular" SMILES, > where there may be several SMILES strings with different ordering. > > There are ways to create a canonical SMILES and then re-order the SDF > appropriately. If you're curious, I can write up code which would do that. (I > don't think it's an option for SDF output yet.) > > Hope that helps, > -Geoff ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
