Sorry, the second example command is missing the ".Cl": obabel -:"CNC[C@@H](c1ccc(c(c1)O)O)O.Cl" -d --gen3d -osdf
On Thu, Dec 5, 2013 at 12:10 PM, Martin Guetlein <martin.guetl...@gmail.com> wrote: > Hi, > > apparently the --gen3D option takes ages and does not work for > mixtures in most cases. > Does anyone know the reason and/or a workaround? > > An Example: > obabel -:"CNC[C@@H](c1ccc(c(c1)O)O)O" -d --gen3d -osdf > works fine and takes about 8 seconds on my machine. > > obabel -:"CNC[C@@H](c1ccc(c(c1)O)O)O" -d --gen3d -osdf > takes about 5 minutes, and produces an erroneous 3d-structure (see > below, one bond length is >3). > > Kind regards, > Martin > > > > OpenBabel12051311593D > > 14 13 0 0 1 0 0 0 0 0999 V2000 > 3.9989 -1.9308 1.8375 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.0251 0.6398 1.7787 N 0 0 0 0 0 0 0 0 0 0 0 0 > 2.9371 1.0089 0.6399 C 0 0 0 0 0 0 0 0 0 0 0 0 > 4.5034 1.0523 0.7544 C 0 0 1 0 0 0 0 0 0 0 0 0 > 5.0234 1.3564 -0.6361 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.2317 2.6820 -1.0552 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.5467 2.9543 -2.3874 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.6293 1.9100 -3.3219 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.4306 0.5812 -2.9034 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.1478 0.3112 -1.5637 C 0 0 0 0 0 0 0 0 0 0 0 0 > 5.4605 -0.4418 -3.7834 O 0 0 0 0 0 0 0 0 0 0 0 0 > 5.8749 2.1790 -4.6204 O 0 0 0 0 0 0 0 0 0 0 0 0 > 4.9499 2.0285 1.6597 O 0 0 0 0 0 0 0 0 0 0 0 0 > -0.0991 1.9461 3.0701 Cl 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 1 0 0 0 0 > 2 3 1 0 0 0 0 > 4 3 1 6 0 0 0 > 4 5 1 0 0 0 0 > 4 13 1 0 0 0 0 > 5 6 2 0 0 0 0 > 5 10 1 0 0 0 0 > 6 7 1 0 0 0 0 > 7 8 2 0 0 0 0 > 8 9 1 0 0 0 0 > 8 12 1 0 0 0 0 > 9 10 2 0 0 0 0 > 9 11 1 0 0 0 0 > M END > $$$$ > > -- > Dipl-Inf. Martin Gütlein > Phone: > +49 (0)761 203 8442 (office) > +49 (0)177 623 9499 (mobile) > Email: > guetl...@informatik.uni-freiburg.de -- Dipl-Inf. Martin Gütlein Phone: +49 (0)761 203 8442 (office) +49 (0)177 623 9499 (mobile) Email: guetl...@informatik.uni-freiburg.de ------------------------------------------------------------------------------ Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
