On Mon, Aug 23, 2010 at 4:43 PM, Chris Morley <c.mor...@gaseq.co.uk> wrote: > I'm trying to get wedge and hash bonds displayed in SVGFormat, > starting with a 0D molecule. (Note the new SMILES input.)
We currently have no code to generate hash/wedge flags for a structure. This isn't difficult for most cases though. I'm doing some stereochemistry at the moment and could add this to my todo list. (I haven't looked at the mcdl code in detail but there is some code for this IIRC) Stereo bonds (i.e. hash, wedge) between stereocenters should be avoided at all cost. Next, stereo bonds in rings should be avoided (not always possible). This leaves candidate bonds for each center that could be used. From here on, coordinates should be used to generate the "best" looking diagram. The IUPAC recommendations are a good guide: http://old.iupac.org/publications/pac/2006/pdf/7810x1897.pdf (2006 version) I'm also implementing these recommendations to do the reverse (2d hashes/wedges -> stereo objects) Tim > This doesn't: > obabel -:b...@h](F)I --gen2D -O out.svg > > This does: > obabel -:b...@h](F)I -omol --gen2D -xw | obabel -imol -O out.svg > > This doesn't: > obabel -:b...@h](F)I -omol --gen2D | obabel -imol -O out.svg > > So presumably calling TetStereoTo0D() does the job and it really > should be called in --gen2D. There is a lack of documentation "(HASSLE > NOEL ABOUT THIS!!)" and I don't understand where the parameter > std::map<OBBond*, OBStereo::Ref> &from should come from. > > Can anybody help? > > I also guess we could talk about why it is necessary for > > obabel -:b...@h](F)I -omol | obabel -imol -osmi > > to drop the stereo information. > > Chris > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by > > Make an app they can't live without > Enter the BlackBerry Developer Challenge > http://p.sf.net/sfu/RIM-dev2dev > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
