Bob,
I think my script is doing the equivalent of your fuse atoms at about
the same spot suggestion. Focusing on only half of the move, which would
be a spiro connection if two rings were involved, the script:
1) Selects all groups attached to the atom that will be deleted.
2) Moves the atom NOT being deleted to the exact coordinates of the atom
that will be deleted without breaking bonds to the moved atom.
3) Deletes the stationary atom leaving its groups in correct bonding
distance to the moved atom.
4) Selects the moved atom and the previously selected and now orphaned
groups.
5) Issues a connect for only the selected groups.
6) Lets delete hydrogen, calculate hydrogens, and minimize clean up the
mess.
All in all, it's a drag fuse if it's hooked to a drag operation. After I
clean up my execScript mess, I'll try to set up a demo.
Otis
On 6/14/2010 12:25 PM, Robert Hanson wrote:
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] <mailto:[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] <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
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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 <http://chemagic.com>
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<mailto:[email protected]>
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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
lucky parental unit. See the prize list and enter to win:
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_______________________________________________
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[email protected]
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--
Otis Rothenberger
chemagic.com
------------------------------------------------------------------------------
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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
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