Re: [Jmol-users] aromatic bonds

[Miguel H. <mi...@ho...>]

> Yes, I think your idea will work. All aromatic bonds have to have
> adjacent aromatic bonds. So if you find an adjacent aromatic bond, that
> should tell you the inside of the ring.

The code for rendering aromatic bonds in Jmol implemented and checked into
CVS.

It correctly detects the inside of the ring.

Note that this is only rendering the bonds as 'aromatic' if the file
contents indicate that it is an aromatic bond. The only file type that
supports this currently is .mol

The outstanding issues are:
 - the inside (dashed) lines are a bit too long. As with other bonds, they
run to the center of the atom. This means that they actually overlap by a
few pixels. Doesn't look very good. The inside/dashed line needs to be
shortened a bit.

 - The cylinder representation of a dashed line is ugly. I did it as a
series of spheres, but it needs to be a broken/dashed cylinder.

> The only problem you might run into is if you have two adjacent aromatic
> rings how can the bond common to the two rings be rendered? Then you
> might want to consider placing a dashed line on both sides of the bond.

In the situation where an aromatic bond participates in more than one ring:
 - the 'inside' will be determined based upon the first ring that is
encountered
 - there is (effectively) no way to control which ring it is associated with
 - it *will* be consistent, in that it will not change from one ring to
another while the molecular model is rotated.


Miguel