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
------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit. See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
