Since I didn't do the integration with OpenBabel, I'll have to check with the programmers ----perhaps they assumed they had to invoke SMILES. Possible they didn't understand the programming needed for simply reading in and translating files---- OR more likely, perhaps I suggested it would be nice to show benzene rings, for example, with aromatic bonds so they decided to invoke SMILES because it would identify aromatic bonds. In the latter case, added aromatic bond capability would have been likely over 3 years ago, so I don't recall the details.
The examples I showed only surfaced recently during my testing more unusual or theoretical reactions. Don On Aug 29, 2018, at 8:06 PM, Geoffrey Hutchison <geoff.hutchi...@gmail.com> wrote: >> 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
