On Sun, Jul 8, 2012 at 6:54 PM, Kubasik, Matt <[email protected]>wrote:
> Thanks, Bob, I will use the syntax you recommend below. On my machine (OS
> X with Jmol 12.3.31) , no "" needed for the atom expression.
>
> It seems like
>
> x = getProperty("atominfo.x", {_N}[7])
> Show x
>
> yes -- right, that's it. My error there. I'm glad you've got that
mechanism now. Much better.
> Gives x as a the sole element of a vector, whereas the syntax I was trying
> to use (x=getproperty(atominfo[10].x) ) offers x as a number (when it
> offers a result in Jmol.jar).
>
> I suppose this result makes sense, since x = getProperty("atominfo",
> {_N}[7]) offers the full array of all atom properties. Excellent!
>
>
The idea here is to deliver as little extra as possible. If you were to use
{*} with atom properties with a protein and then filter it, that would be
really a lot of wasted flips. Jmol's scripting language is not compiled in
any optimized way, so thinks like this:
for (var i = 1; i < {protein}.length; i++)
is VERY inefficient and way worse than
for(var i = {protein}.length; i > 0; --i)
Maybe the next generation of Jmol guru's can clean that up, but that's just
the way it is for now.
Bob
> From: Robert Hanson <[email protected]<mailto:[email protected]>>
> Reply-To: <[email protected]<mailto:
> [email protected]>>
> Date: Sun, 8 Jul 2012 16:19:43 -0500
> To: <[email protected]<mailto:
> [email protected]>>
> Subject: Re: [Jmol-users] Jmol .jar vs JmolData.jar: help with getproperty
>
> OK, I know what it is. Good idea to use -onx; ignore the last comment. The
> default second parameter is "{visible}" for getProperty("atomInfo"). With
> JmolData, it is determining that nothing is visible. Which, of course, it
> isn't, but.... So I'll see what I can do about that. In the mean time, use
>
> x = getProperty("atomInfo", "{*}")
>
> or -- here's your opportunity to to that right!
>
> x = getProperty("atominfo", "{_N}[7]")
>
> There we go! Much more efficient!
>
>
>
> On Sun, Jul 8, 2012 at 4:03 PM, Robert Hanson <[email protected]<mailto:
> [email protected]>> wrote:
> I guess there's a difference there with those flags. JmolData doesn't need
> any flags because it automatically adds -onx, but there is something odd
> there. In any case, with JmolData, just do this:
>
> java -jar $JmolData $freqfile -s $script
>
>
>
>
> On Fri, Jul 6, 2012 at 2:07 PM, Kubasik, Matt <[email protected]
> <mailto:[email protected]>> wrote:
> Bob,
>
>
>
> However, I'm still having difficulty with JmolData.jar and Jmol.jar. In
> the following script, Jmol.jar prints values for getproperty, but
> JmolData.jar does not print values.
>
>
>
> bindex=({_N}[3].atomindex+1)
> print bindex
> bx=GetProperty("atomInfo["+bindex+"].x");
> print bx
>
> (No difference if using "show" or "print")
>
> For a direct comparison, the shell script I'm using invokes Jmol right
> after JmolData (Jmol 12.3.31):
>
> java -jar $JmolData -onx $freqfile -s $script
> java -jar $Jmol -onx $freqfile -s $script
>
>
>
>
> Any thoughts? Is it some kind of variable typing issue? Could it be
> something with my file, which contains 322 models, the last 321 of which
> contain vibrational mode info from a Gaussian calc?
>
> The syntax bx=GetProperty("atominfo.x",bindex), where bindex={(* and
> 1.322)[29]}, seems to work in JmolData.jar (and in Jmol.jar).
>
> Matt
>
> From: Robert Hanson <[email protected]<mailto:[email protected]><mailto:
> [email protected]<mailto:[email protected]>>>
> Reply-To: <[email protected]<mailto:
> [email protected]><mailto:[email protected]
> <mailto:[email protected]>>>
> Date: Fri, 6 Jul 2012 11:38:30 -0500
> To: <[email protected]<mailto:
> [email protected]><mailto:[email protected]
> <mailto:[email protected]>>>
> Subject: Re: [Jmol-users] Jmol .jar vs JmolData.jar: help with getproperty
>
> Oh, right. You can't do that. The string must contain a simple expression
> like atomInfo[3]:
>
> print getProperty("atomInfo[" + ({_N}[7].atomIndex + 1) + "].x")
>
> Sorry about the "+1" but that's because atomIndex is one of the very few
> 0-based properties.
>
>
>
>
> On Fri, Jul 6, 2012 at 10:58 AM, Kubasik, Matt <[email protected]
> <mailto:[email protected]><mailto:[email protected]<mailto:
> [email protected]>>> wrote:
> Thanks, Bob.
>
> My problem is in combining atom expression syntax and the brackets in the
> getproperty command.
>
> Of the two below, the first is empty, and the second returns the correct
> value. What is wrong with the first?
>
> nx=getproperty("atomInfo[{(_N)[7]}].x")
> print nx
>
> nx=getproperty("atomInfo.x",{(_N)[7]})
> print nx
>
> Matt
>
> From: Robert Hanson <[email protected]<mailto:[email protected]><mailto:
> [email protected]<mailto:[email protected]>><mailto:[email protected]
> <mailto:[email protected]><mailto:[email protected]<mailto:
> [email protected]>>>>
> Reply-To: <[email protected]<mailto:
> [email protected]><mailto:[email protected]
> <mailto:[email protected]>><mailto:
> [email protected]<mailto:[email protected]
> ><mailto:[email protected]<mailto:
> [email protected]>>>>
> Date: Fri, 6 Jul 2012 10:27:18 -0500
> To: <[email protected]<mailto:
> [email protected]><mailto:[email protected]
> <mailto:[email protected]>><mailto:
> [email protected]<mailto:[email protected]
> ><mailto:[email protected]<mailto:
> [email protected]>>>>
> Subject: Re: [Jmol-users] Jmol .jar vs JmolData.jar: help with getproperty
>
> Yes. The only thing JmolData does not have is a graphical interface.
>
>
> On Thu, Jul 5, 2012 at 11:01 AM, Kubasik, Matt <[email protected]
> <mailto:[email protected]><mailto:[email protected]<mailto:
> [email protected]>><mailto:[email protected]<mailto:
> [email protected]><mailto:[email protected]<mailto:
> [email protected]>>>> wrote:
> Dear list,
>
> I am seeking guidance on getproperty (and possibly correct atom
> expressions) within JmolData.jar. Will x=getproperty(“atominfo[nnn].xxx”}
> work in JmolData.jar?
>
> I would like to use JmolData.jar to process Gaussian output files
> containing vibrational vectors of atoms in different vibrational modes.
>
> The following sequence works fine in Jmol.jar (invoked via terminal’s
> command-line, e.g." java -jar $Jmol -on $freqfile -s $script"), but it
> prints an empty string in JmolData.jar:
>
> framenumber=258
> frame @framenumber
> c_index=16
> cvibvector=getproperty("atomInfo["+c_index+"].vibVector")
> show cvibvector
>
>
> try
>
> print
>
> instead of
>
> show
>
>
>
> Is it that “frame” does not work in JmolData.jar? Do I need a rigorous
> atom expression (for the 16th atom of the 258th frame) for JmolData.jar?
>
> As a work-around, the following syntax for getproperty places the
> vibvector for EVERY 16th atom of EVERY frame in an array in JmolData.jar:
>
> c_index=16
> allcvibes=getproperty("atominfo.vibVector",{atomno=c_index})
>
> Is there a better way to specify a particular atom of a particular
> frame/model in JmolData.jar?
>
> Matt Kubasik
> Department of Chemistry and Biochemistry
> Fairfield University
>
> PS Getproperty "modelinfo" seems to work equally well in either Jmol.jar
> or JmolData.jar. E.g., the following works the same in both:
>
> freq=getproperty("modelinfo.models["+framenum+"].modelProperties.Frequency");
>
>
> Details:
> Jmol Version: 12.3.31 2012-06-16 00:04
> java.vendor: Apple Inc.
> java.version: 1.6.0_31
> os.name<http://os.name><http://os.name><http://os.name>: Mac OS X
> Access: ALL
> memory: 11.3/85.0
>
>
>
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> >>>
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>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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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>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference Exclusive live event will cover all the
> ways today's security and threat landscape has changed and how IT managers
> can respond. Discussions will include endpoint security, mobile security
> and the latest in malware threats.
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> mailing list
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> [email protected]>>
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>
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> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
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>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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
>
>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference Exclusive live event will cover all the
> ways today's security and threat landscape has changed and how IT managers
> can respond. Discussions will include endpoint security, mobile security
> and the latest in malware threats.
> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________Jmol-users
> mailing list
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> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
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> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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