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] <mailto:[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 <http://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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chemagic.com
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