> Thanks for comments. When I print out files from Avogadro that we use for > input to our program, the atoms are in a given sequence. After going through > OpenBabel, the atom numbering and sequence is totally different from the > files that were read as evidenced by the numbering that appears in our > displays and the input files for the MO program.
I'm sorry, that's not possible unless you're modifying the molecule somehow in "going through Open Babel." What exactly are you doing? > Intuitively I would think SMILES might have to resequence atoms to get the > most efficient description. Aha. What does SMILES have to do with what you want to do? Why don't you back up and tell us what you're trying to do with Open Babel in your program? Yes, SMILES may re-order atoms and remove hydrogens. But why does SMILES have anything to do with "reading in a file and displaying some orbitals?" > that ignoring the "Isaromatic" bonds should leave the 1, 2, 3 type bond > information intact that our program will still be able to use. Do I > understand that correctly? Yes. > The reason we have included PDB files (which work fine from Avogadro) is that > the Spartan ab initio program can generate such 3d files and their PDB files > work ok. Oddly, the MOL files generated by Spartan don't work. We are > trying to allow file types from other programs besides Avogadro that can > generate 3d structure files. IIRC, Spartan produces decidedly non-standard files. Please feel free to open a bug report and upload some "MOL" files from Spartan. Best regards, -Geoff ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
