sounds like a nightmare to align the two atoms in 3D. Any other ideas?
On Mon, Jun 14, 2010 at 10:29 AM, Otis Rothenberger
<[email protected]>wrote:
> Bob,
>
> In my mind, I see this at a two atom at a time operation - like drag to
> bond. The difference would be that the"drag bond really forms a spiro
> connection. Two "spiro" connects = a fusion.
>
> Otis
>
>
> On 6/14/2010 10:20 AM, Robert Hanson wrote:
>
> 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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> lucky parental unit. See the prize list and enter to win:
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>
>
> _______________________________________________
> Jmol-users mailing
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>
>
> --
> Otis Rothenbergerchemagic.com
>
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
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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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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
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