> 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.
If all you want is the XYZ coordinates, then you can certainly use that method. There is no difference between using "-xc" to indicate that you want canonical SMILES and using the so-called "can" format. There's just more than one way to do it. 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
