Greetings,
I've no doubt that there is a simple explanation for each of these items;
however, I haven't been able to search any out.
>From the following script:
zap; load SYNC "file:///C:/Compchem/s-pentane/spentane.xyz"
rotdeg = 120
var steps=360/rotdeg
measure {C5}{C3}{C1}{H6}
targang = 0.00
conang = getproperty("measurementinfo[1].value")
for (var i=0;i<@steps;i++) {
targang = targang + rotdeg
newrot = targang - conang
rotate branch {C3} {C1} @newrot @newrot // this command will fail if the
last 2 params have different sign
conang = getproperty("measurementinfo[1].value")
print @targang.add("\t").add(conang)
print "before ".add(@targang).add("\t").add(conang)
script inline ("minimize constraint {C5}{C3}{C1}{H6} @targang")
//minimize (similar, but more verbose results when run)
conang = getproperty("measurementinfo[1].value")
print conang
minimize energy
results = getproperty("modelinfo.model.energy",{*})
}
I get this output:
59.9 °
NaN120.000015 -> targang, conang
before 120.0 120.000015 ->"before ", targang, conang
120.000015
Initial MMFF E = 35.017 kJ criterion = 0.004187 max steps = 0
NaN-119.99998
before 240.0 -119.99998
-119.99998
Initial MMFF E = 40.516 kJ criterion = 0.004187 max steps = 0
NaN-0.0
before 360.0 -0.0
-0.0
Initial MMFF E = 20.605 kJ criterion = 0.004187 max steps = 0
My confusions are:
Why is targang NaN? I initialized it as 0.00, can perform math operations on
it and the rotate command recognizes it as a value. When I want to print it,
it apparently is NaN and so needs the start the print sequence with a string
approach.
What is the systematic approach to using @ and var? The @ symbol didn't return
anything in a documentation search (too fundamental?). I have seen mentions
where "you won't need to use @". I'm afraid my method is strictly T&E, "if at
first, nature...". My experience with var is similar. Jmol docs say that it
is used to localize an instance of a variable. My empirical observation is
more consistent with "if initializing with a math operation, var is needed". I
believe in C (C#, at least), it is used to allow the compiler to assign type.
Again, by T&E, I use one when Jmol gives me red marks, because my script is so
short.
I know that I can get a read-in energy with
getproperty("modelinfo.model.energy",{*}). Is it possible to do the same from
the Jmol MMFF calculation? Or can I pipe the output from "minimize energy" and
parse it?
Thanks for any help,
George
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