OK, if you have ever wanted to get atom information from a file, this is
for you. The following command would be given from a web page:
var info = "" + jmolGetPropertyAsJavaObject("evaluate",
'"" + {molecule=1} + "\n\n" + {molecule=1}.label("%a %x %y %z")'
)
The new thing here is the "evaluate" option. It says, "Return what you
get when you evaluate the expression:
"" + {molecule=1} + "\n\n" + {molecule=1}.label("%a %x %y %z")
Believe it or not, this single command delivers a fully valid XYZ file
for a subset of the model. The variable "info" would contain, perhaps:
3
O 0.00000000 0.00000000 -0.11460000
H -0.75400000 0.00000000 0.45840000
H 0.75400000 0.00000000 0.45840000
Here's how it works:
"" + {molecule=1} + "\n\n" + {molecule=1}.label("%a %x %y %z")
is going to be evaluated:
"" means "turn anything after this into a string"
+ {molecule=1} means "the number of atoms in molecule 1"
+ "\n\n" means "then two line feeds (a blank line)"
and then
+ {molecule=1}.label("%a %x %y %z")
adds for each atom in the first molecule a label consisting of an atom
name, x, y, and z coordinate. That's the XYZ format.
I think I'll stop here and wait for reaction to all of this. I know it's
been a flurry of activity. But I think you can see that already it is
quite powerful. You can check it out for yourself at:
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm
I look forward to see what people do with this.
Bob
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