When we last spoke on irc we agreed to push forward on the plan to further
integrate cdk AtomTypes into this release of Jmol.
Afterward, I made a few changes to cdk to get the colors working properly
and to get the jmol_atomtypes.txt file read properly on the old JVMs (see
I then took a look at jmol.AtomType and jmol.BaseAtomType ... and frankly
I am getting nervous.
As far as I can tell, the proper cdk.Atom constructor does not exist. That
is, there is no Atom constructor which takes a "name" and a "root". It
looks like to me that this is needed to support the existing jmol file
(Interestingly, this does exist at the AtomType level, but not at the Atom
This, plus general difficulties I am having with the cdk code, lead me to
change my recommendation:
Previously I said that if you wanted to get rid of jmol.AtomType
and jmol.BaseAtomType then go ahead and do so.
Now, I strongly recommend that you hold off on this, that we
stabilize the Jmol code. We should release Jmol version 6 before
attempting such a radical change.
We'll talk next week when you get back.