On 7 May 2010 15:42, Geoffrey Hutchison <ge...@geoffhutchison.net> wrote: > > On May 7, 2010, at 8:01 AM, Tim Vandermeersch wrote: > >>>> However, I can't see any reason not to treat 2D structures like 0D >>>> ones. It works very well. > > As long as the stereochemistry is preserved, I don't think it matters much.
When read in, 2D structures (like 0D and 3D) have their stereo perceived. These stereo objects are used by the builder. >> No, sounds good. The reason why flat structures stay flat is an >> optimization issue. If all forces are in a plane, there is no driving >> force to make an atom move perpendicular to that plane. > > Perhaps we should add a step which slightly tweaks the dihedral angles before > running MM? I don't know - we could just issue a warning and suggest conversion to 3D first. There is one advantage in optimising in the plane - that's 2D layout. > Cheers, > -Geoff ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
