See also --align for whole molecule alignment. This assumes that the atom orderings are the same in the two molecules.
http://open-babel.readthedocs.org/en/latest/Command-line_tools/babel.html#aligning-molecules-or-substructures - Noel On 31 May 2013 00:18, Demetrio A. da Silva Filho <dasf....@gmail.com> wrote: > Hi Geoff, > > Thanks! I will give it another try. > Indeed, I can write an arbitrary number of decimals in the input file. But > will open babel write with the same number of decimals? If not, is there a > way to change it? > > Regards, > Demetrio Filho > > > On Thu, May 30, 2013 at 7:25 PM, Geoffrey Hutchison > <geoff.hutchi...@gmail.com> wrote: >> >> > molecules using open babel. The catch is: I wish I could loose accuracy >> > as >> > minimum as possible. I mean, I wish I could extract the two geometries >> > from >> > the fchk file keeping as many decimal digits as possible and then >> > generate >> > two new geometries with as many decimal digits as possible. How can I do >> > it? >> > Which format allow me to use the largest number of decimal digits? >> >> You can write out an arbitrary number of digits, e.g. with XYZ. If you >> want an existing format in Open Babel, I'd suggest DMol3, which I think uses >> 14 decimals (albeit in Bohr). >> >> > I have looked into the obfit code but I have another question. How the >> > two >> > molecules should enter? One after the other? Any separation? just cat >> > molecule1 molecule2 > moleculefit? >> >> No, obfit takes one molecule and fits it onto another, e.g. >> >> obfit molecule1.xyz molecule2.xyz >newfile.xyz >> >> http://openbabel.org/wiki/Obfit >> >> > Besides, I wish all atoms could be used in the alignment. Which SMILES >> > should I use? >> >> You'd pick a SMARTS that corresponds to the molecular SMILES. So, for >> example, if you wanted to superimpose two benzenes: >> >> c1ccccc1 >> >> Hope that helps, >> -Geoff > > > > > -- > Demétrio A. da Silva Filho > Instituto de Física - Universidade de Brasília > Multiuso II - Sala B1 11/4 > Fone: (61)3107.6089 > > ------------------------------------------------------------------------------ > Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET > Get 100% visibility into your production application - at no cost. > Code-level diagnostics for performance bottlenecks with <2% overhead > Download for free and get started troubleshooting in minutes. > http://p.sf.net/sfu/appdyn_d2d_ap1 > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with <2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
