Feature Requests item #1664357, was opened at 2007-02-20 08:24
Message generated for change (Comment added) made by hansonr
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Category: Interface Improvements
Group: None
>Status: Closed
Priority: 9
Private: No
Submitted By: Bob Hanson (hansonr)
Assigned to: Bob Hanson (hansonr)
Summary: Jmol variable math
Initial Comment:
With the addition of multi-type variable manipulation in Jmol 11.1.14 we move
into a new stage with Jmol, in which much of what previously was only available
in the applet and only available using some pretty hefty JavaScript is now
trivially possible.
Basically we can now look at Jmol as a visualization database processor. Load a
model, and then start asking questions.
How many oxygens are there?
x = {oxygen}
What is the degree of unsaturation?
x = (2.0 * {carbon} + 2 + {nitrogen} - {hydrogen})/2
What is the distance from the center of molecule 1 to the center of molecule 2?
x = ({molecule=1}.xyz).distance({molecule=2}.xyz)
And we can do data extractions amazingly simply:
xyzData = "" + {selected} + "\n\n" + {selected}.label("%a %x %y %z")
pdbAtomData = {selected and not hetero}.label("ATOM %5i %-4a%1A%3n %1c%4R%1E
%8.3x%8.3y%8.3z%6.2q%6.2b %2e%2C")
pdbHeteroData = {selected and hetero}.label("HETATM%5i %-4a%1A%3n %1c%4R%1E
%8.3x%8.3y%8.3z%6.2q%6.2b %2e%2C")
pdbFile = pdbAtomData + pdbHeteroData
OK, so with this message I suggest we discuss additional possibilities. The
framework is there; the main questions are:
1) Do I have the functionality right?
2) What additional functionality would be useful?
I can suggest a few additions:
simple string commands:
x = "some string".find("xxx")
x = "some string"[1][10]
x = "some string".lines
x = "some string".lines[3]
x = "some string".lines[1][10]
x = "".load("some file name")
write {....} filename (application only)
Bob
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>Comment By: Bob Hanson (hansonr)
Date: 2007-06-17 07:59
Message:
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Originator: YES
all are part of 11.2
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Comment By: Bob Hanson (hansonr)
Date: 2007-02-20 12:42
Message:
Logged In: YES
user_id=1082841
Originator: YES
I went ahead and added
write VAR varName "fileName"
for example:
xyzData = "" + {selected} + "\n\n" + {selected}.label("%a %x %y %z")
write VAR xyzData "myfile.xyz"
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