[Jmol-users] Model Kit Ring Fusion

[Otis R. <osr...@ch...>]

Bob,

This isn't pretty, but it works - sort of. I need some advice on the 
aromatic fusion. I'd also like to know if this all suggests something 
more elegant to you.

First the fusion of two chair cyclohexanes. The atomIndexes represent 
adjacent carbons on each cyclohexane. The result is a trans fusion. It's 
not pretty to watch. It also takes some time:

select 
connected(atomIndex=20);{atomIndex=0}.atomX={atomIndex=20}.atomX;{atomIndex=0}.atomY= 
{atomIndex=20}.atomY;{atomIndex=0}.atomZ={atomIndex=20}.atomZ;delete 
atomIndex=20;connect (atomIndex=0)(selected);select 
connected(atomIndex=21);{atomIndex=1}.atomX={atomIndex=21}.atomX;{atomIndex=1}.atomY= 
{atomIndex=21}.atomY;{atomIndex=1}.atomZ={atomIndex=21}.atomZ;delete 
atomIndex=21;connect (atomIndex=1)(selected);set useMinimizationThread 
false;minimize;delete hydrogen;calculate hydrogens

Second the fusion of two benzenes - fusing aromatic doubles on both 
molecules:

select 
connected(atomIndex=12);{atomIndex=2}.atomX={atomIndex=12}.atomX;{atomIndex=2}.atomY= 
{atomIndex=12}.atomY;{atomIndex=2}.atomZ={atomIndex=12}.atomZ;delete 
atomIndex=12;connect (atomIndex=2)(selected);select 
connected(atomIndex=13);{atomIndex=3}.atomX={atomIndex=13}.atomX;{atomIndex=3}.atomY= 
{atomIndex=13}.atomY;{atomIndex=3}.atomZ={atomIndex=13}.atomZ;delete 
atomIndex=13;connect (atomIndex=3)(selected);set useMinimizationThread 
false;connect (atomIndex=2) (atomIndex=3) AROMATICDOUBLE;delete 
hydrogen;calculate hydrogens;reset aromatic;calculate aromatic;minimize 
steps 300;

The two aforementioned questions and one extra:

1) I had to cheat on the aromatic fusion. It's not a general case. It's 
rigged for double to double. Any thoughts on generalizing this.

2) I'm really hoping that the above catalyzes a more elegant approach in 
your mind - any thoughts?

3) I was kind of surprised that these scripts worked. I thought the 
deletions would screw up the atomIndexes. Then I recalled that you said 
something about the deleted atoms simply being marked deleted. Does this 
mean that all atoms retain their atomIndexes during editing?

Otis

-- 
Otis Rothenberger
chemagic.com