Graph (cyclic kind, not pretty picture kind) rendering algorithm?

[Andrew Dalke]

s713221 at student.gu.edu.au wrote:
>I don't know of any, but I'd be interested if anyone else could direct
>us to one, I need exactly this for a chem editor I'm building at the
>moment.
>
>Joal Heagney/AncientHart

Having been involved in several of these discussions,
don't use that approach.  There is a lot of chemistry
involved in making a chemical layout algorithm look
correct.

Your best bet is to look at how JMDraw
  http://vanilla.ice.mpg.de/~stein/projects/SmilesViewer/
or JChemPaint
  http://jchempaint.sourceforge.net/
do their layout.  The latter is LGPL'ed.  There isn't
much other publically available source code to look
at for development of new layout algorithms.

Even they won't be exactly what a chemist wants, because
chemists disagree with what they expect.  Eg, many
companies have guidelines on how different families
of compounds should be laid out, so the only real
solution involves a lot of substructure matching against
a set of templates.  Or you hire someone to draw
every molecule, which is done!

                    Andrew
                    dalke at acm.org