What's the exact user action you're after for this? Are we dragging a
cyclohexane and dropping it on another? Could we just look for atoms at
about the same spot and fuse them?
yes, all atoms retain their atom indexes when you are deleting individual
atoms. If you use
set debug
I think you can watch the atom indexes increasing as you delete and then add
new atoms.
On Mon, Jun 14, 2010 at 1:41 AM, Otis Rothenberger <[email protected]>wrote:
> 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
>
>
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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