subject:"Re\: \[Jmol\-users\] Best way to access getproperty with JSmol"

Re: [Jmol-users] Best way to access getproperty with JSmol

2016-10-23 Thread Kubasik, Matthew A.

Bob,

Thanks to you and the team, for your ongoing development of JSmol!

I think Mark’s initial approach was consistent with an orientation in the 
bioinformatics world of “grab-everything-and-sort-later.”  It makes sense to do 
that…sometimes!

Best,

Matt




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Re: [Jmol-users] Best way to access getproperty with JSmol

2016-10-23 Thread Robert Hanson

Matt's suggestion is excellent. Definitely the preferred method. Half way
through my reply I switched from

jmolApplet0._applet.viewer.ms.getAuxiliaryInfo(6)

to

jmolApplet0._applet.viewer.ms.am[6].auxiliaryInfo

Both work, but Matt's suggestion is better. Thank  you, Matt!





On Sat, Oct 22, 2016 at 9:41 PM, Kubasik, Matthew A.  wrote:

> Mark,
>
> One other thing.  You wrote that "when you load the model it prints all
> the vibrational energies out”.
>
> But here’s the thing…I think that, technically, the “names” of the models
> containing vibrations are printed, i.e., what you would get from
> x = getproperty("modelinfo.models.name”)
>
> yes


> The file reader seems to be set up to name the models containing
> vibrational modes according to the energy of the vibration.
>
>
To get vibrational energies in cm^-1, use getproperty(“modelinfo.models.
> modelproperties.Frequency”)
>
> To get only the value of the energy, use getproperty(“modelinfo.models.
> modelproperties.FreqValue”)
>
> The Gaussian file reader seems to be coded to print model numbers with the
> model name/frequency value, while the GAMESS reader seems not to.  These
> seem to be arbitrary decisions of the authors of the file reading code.
>
> That is true. I've tried to standardize it to some extent, but these
readers -- some of our oldest code -- were written by different people (or
by me at different times), and particularly in the model name business and
what is reported upon loading, there are some differences.

Bob

On Sat, Oct 22, 2016 at 9:41 PM, Kubasik, Matthew A.  wrote:

> Mark,
>
> One other thing.  You wrote that "when you load the model it prints all
> the vibrational energies out”.
>
> But here’s the thing…I think that, technically, the “names” of the models
> containing vibrations are printed, i.e., what you would get from
> x = getproperty("modelinfo.models.name”)
>
> The file reader seems to be set up to name the models containing
> vibrational modes according to the energy of the vibration.
>
> To get vibrational energies in cm^-1, use getproperty(“modelinfo.models.
> modelproperties.Frequency”)
>
> To get only the value of the energy, use getproperty(“modelinfo.models.
> modelproperties.FreqValue”)
>
> The Gaussian file reader seems to be coded to print model numbers with the
> model name/frequency value, while the GAMESS reader seems not to.  These
> seem to be arbitrary decisions of the authors of the file reading code.
>
> Matt Kubasik
>
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
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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engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
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Re: [Jmol-users] Best way to access getproperty with JSmol

2016-10-22 Thread Kubasik, Matthew A.

Mark,

One other thing.  You wrote that "when you load the model it prints all the 
vibrational energies out”. 

But here’s the thing…I think that, technically, the “names” of the models 
containing vibrations are printed, i.e., what you would get from 
x = getproperty("modelinfo.models.name”)

The file reader seems to be set up to name the models containing vibrational 
modes according to the energy of the vibration.

To get vibrational energies in cm^-1, use 
getproperty(“modelinfo.models.modelproperties.Frequency”)

To get only the value of the energy, use 
getproperty(“modelinfo.models.modelproperties.FreqValue”)

The Gaussian file reader seems to be coded to print model numbers with the 
model name/frequency value, while the GAMESS reader seems not to.  These seem 
to be arbitrary decisions of the authors of the file reading code.  

Matt Kubasik




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Re: [Jmol-users] Best way to access getproperty with JSmol

2016-10-22 Thread Mark Perri

Dear Bob and Matt,

Thanks for the advice.  I couldn't get 
jmolApplet0._applet.viewer.getAuxiliaryInfo(6).get("moData") to work (I also 
tried .ms and .ms.am and various frames with MO Data) -- I got errors about 
a.get() not being a function and other things.

Matt's suggestion works well.  I was just extracting the MO energies, so I used 
getPropertyAsArray to only get an array of the energies, which was much much 
faster than what I was doing.  I then iterated through the frames to get the 
vibrational frequencies as well.  I thought there should be a faster way -- 
when you load the model it prints all the vibrational energies out, but I 
wasn't sure how to associate them with their particular frame so that I could 
animate them. But iterating frame by frame works out OK.

I have a feeling I could optimize it even more, but it's definitely improved 
now.

Thanks,
Mark




From: Kubasik, Matthew A. <mkuba...@fairfield.edu>
Sent: Saturday, October 22, 2016 8:51 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Best way to access getproperty with JSmol

Dear Mark and Bob,

Perhaps getting a large quantity of “auxiliarydata” is slowing things down?

Maybe, Mark, you could drill down a bit to get the specific auxiliary data that 
you want.  So, for example, maybe instead of

var x = Jmol.getPropertyAsArray(jmolApplet0,"auxiliaryInfo");

You could use

var x = Jmol.getPropertyAsArray(jmolApplet0, 
“auxiliaryinfo.models[1].modata.mos.coefficients”)  // where [1] is the model # 
with the mo data

I’m not sure exactly what properties of the mos that you want, and I am not 
familiar with GAMESS.  However, the above line might get you a 2D array 
containing mo coefficients.  So, for example, the coefficients of the first mo 
would be in (x[1])[1], the second set of coefficients would be in (x[1])[2], 
etc.

Also, the frequencies can be obtained from

x=Jmol.getPropertyAsArray(jmolApplet0, 
"modelinfo.models.modelproperties.frequency”)

That’s how I understand it, but I’m not 100% sure this will work.

Matt Kubasik

On Oct 22, 2016, at 8:30 AM, Robert Hanson 
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:

If you are interested in just getting one model's auxiliary info, you can use _M

$ load c:/temp/t.gamess
7 models
46 molecular orbitals in model 1.2
17 molecular orbitals in model 1.7

$ frame 1.7
$ print _M.keys
Energy
EnergyString
dipole
fileName
fileType
initialAtomCount
initialBondCount
moData
modelFileNumber
modelName
modelNumber
modelNumberDotted
modelProperties


>From JavaScript you would use:


info = Jmol.evaluateVar(jmolApplet0, "_M")

Should be relatively efficient.

Alternatively, if you want instantaneous direct access to that Java object you 
can use

info = 
jmolApplet0._applet.viewer.ms.am<http://applet.viewer.ms.am/>[0].auxiliaryInfo

But two caveats:

1) You are bypassing the interfaces and tapping in to officially "nonpublic" 
objects. Sometimes those underlying objects get name changes or are otherwise 
refactored.

2) You are working with a transpiled Java Object. In this case, 
java.util.Hashtable. You  have to use .get(key) to access its information:

jmolApplet0._applet.viewer.ms.getAuxiliaryInfo(6).__CLASS_NAME__
"java.util.Hashtable"

modata = jmolApplet0._applet.viewer.getAuxiliaryInfo(6).get("moData")
modata.__CLASS_NAME__
"java.util.Hashtable"

and deal with all of those values appropriately as well.








On Fri, Oct 21, 2016 at 7:54 PM, Mark Perri 
<per...@sonoma.edu<mailto:per...@sonoma.edu>> wrote:


Dear users list,


I'm trying to get MO energies and vibrational frequencies from a GAMESS output 
file that I read into JSmol.  Right now I use:

var x = Jmol.getPropertyAsArray(jmolApplet0,"auxiliaryInfo");


Then I iterate over every frame and look at x.models[i].moData.mos and 
x.models[i].modelProperties.Frequency


But for a large file the getPropertyAsArray takes > 10 seconds and freezes 
Firefox while it's loading.  Reading the manual it seems that I can use 
getProperty asynchronously, but I don't understand how to use it properly.


I set a message callback function to handle getProperty, but I'm not sure how 
to actually read in the moData.  It appears to be in arguments[1], but 
everything I try is undefined.  Here's an example of what I've tried.


Thanks,

Mark


var Info = {
width: 450,
height: 450,
debug: false,
color: "white",
addSelectionOptions: false,
serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php;,
use: "HTML5",
j2sPath: "/jsmol/j2s",
readyFunction: jmol_isReady,
script: script,
loadStructCallback: "onJSmolLoad",
messageCallback: "processFrames",
disableInitialConsole: true
}


function processFrames()
{

 for (i=0; i<argumen

Re: [Jmol-users] Best way to access getproperty with JSmol

2016-10-22 Thread Kubasik, Matthew A.

Dear Mark and Bob,

Perhaps getting a large quantity of “auxiliarydata” is slowing things down?

Maybe, Mark, you could drill down a bit to get the specific auxiliary data that 
you want.  So, for example, maybe instead of

var x = Jmol.getPropertyAsArray(jmolApplet0,"auxiliaryInfo");

You could use

var x = Jmol.getPropertyAsArray(jmolApplet0, 
“auxiliaryinfo.models[1].modata.mos.coefficients”)  // where [1] is the model # 
with the mo data

I’m not sure exactly what properties of the mos that you want, and I am not 
familiar with GAMESS.  However, the above line might get you a 2D array 
containing mo coefficients.  So, for example, the coefficients of the first mo 
would be in (x[1])[1], the second set of coefficients would be in (x[1])[2], 
etc.

Also, the frequencies can be obtained from

x=Jmol.getPropertyAsArray(jmolApplet0, 
"modelinfo.models.modelproperties.frequency”)

That’s how I understand it, but I’m not 100% sure this will work.

Matt Kubasik

On Oct 22, 2016, at 8:30 AM, Robert Hanson 
> wrote:

If you are interested in just getting one model's auxiliary info, you can use _M

$ load c:/temp/t.gamess
7 models
46 molecular orbitals in model 1.2
17 molecular orbitals in model 1.7

$ frame 1.7
$ print _M.keys
Energy
EnergyString
dipole
fileName
fileType
initialAtomCount
initialBondCount
moData
modelFileNumber
modelName
modelNumber
modelNumberDotted
modelProperties

From JavaScript you would use:

info = Jmol.evaluateVar(jmolApplet0, "_M")

Should be relatively efficient.

Alternatively, if you want instantaneous direct access to that Java object you 
can use

info = 
jmolApplet0._applet.viewer.ms.am[0].auxiliaryInfo

But two caveats:

1) You are bypassing the interfaces and tapping in to officially "nonpublic" 
objects. Sometimes those underlying objects get name changes or are otherwise 
refactored.

2) You are working with a transpiled Java Object. In this case, 
java.util.Hashtable. You  have to use .get(key) to access its information:

jmolApplet0._applet.viewer.ms.getAuxiliaryInfo(6).__CLASS_NAME__
"java.util.Hashtable"

modata = jmolApplet0._applet.viewer.getAuxiliaryInfo(6).get("moData")
modata.__CLASS_NAME__
"java.util.Hashtable"

and deal with all of those values appropriately as well.

On Fri, Oct 21, 2016 at 7:54 PM, Mark Perri 
> wrote:

Dear users list,

I'm trying to get MO energies and vibrational frequencies from a GAMESS output 
file that I read into JSmol.  Right now I use:

var x = Jmol.getPropertyAsArray(jmolApplet0,"auxiliaryInfo");

Then I iterate over every frame and look at x.models[i].moData.mos and 
x.models[i].modelProperties.Frequency

But for a large file the getPropertyAsArray takes > 10 seconds and freezes 
Firefox while it's loading.  Reading the manual it seems that I can use 
getProperty asynchronously, but I don't understand how to use it properly.

I set a message callback function to handle getProperty, but I'm not sure how 
to actually read in the moData.  It appears to be in arguments[1], but 
everything I try is undefined.  Here's an example of what I've tried.

Thanks,

Mark

var Info = {
width: 450,
height: 450,
debug: false,
color: "white",
addSelectionOptions: false,
serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php;,
use: "HTML5",
j2sPath: "/jsmol/j2s",
readyFunction: jmol_isReady,
script: script,
loadStructCallback: "onJSmolLoad",
messageCallback: "processFrames",
disableInitialConsole: true
}

function processFrames()
{

 for (i=0; i! http://sdm.link/slashdot
___
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
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

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! 
http://sdm.link/slashdot___

Re: [Jmol-users] Best way to access getproperty with JSmol

2016-10-22 Thread Robert Hanson

If you are interested in just getting one model's auxiliary info, you can
use _M

$ load c:/temp/t.gamess
7 models
46 molecular orbitals in model 1.2
17 molecular orbitals in model 1.7

$ frame 1.7
$ print _M.keys
Energy
EnergyString
dipole
fileName
fileType
initialAtomCount
initialBondCount
moData
modelFileNumber
modelName
modelNumber
modelNumberDotted
modelProperties


>From JavaScript you would use:


info = Jmol.evaluateVar(jmolApplet0, "_M")

Should be relatively efficient.

Alternatively, if you want *instantaneous direct access to that Java object*
you can use

info = jmolApplet0._applet.viewer.ms.am[0].auxiliaryInfo

But two caveats:

1) You are bypassing the interfaces and tapping in to officially
"nonpublic" objects. Sometimes those underlying objects get name changes or
are otherwise refactored.

2) You are working with a transpiled Java Object. In this case,
java.util.Hashtable. You  have to use .get(key) to access its information:

jmolApplet0._applet.viewer.ms.getAuxiliaryInfo(6).__CLASS_NAME__
"java.util.Hashtable"

modata = jmolApplet0._applet.viewer.getAuxiliaryInfo(6).get("moData")
modata.__CLASS_NAME__
"java.util.Hashtable"

and deal with all of those values appropriately as well.








On Fri, Oct 21, 2016 at 7:54 PM, Mark Perri  wrote:

> Dear users list,
>
>
> I'm trying to get MO energies and vibrational frequencies from a GAMESS
> output file that I read into JSmol.  Right now I use:
>
>
> var x = Jmol.getPropertyAsArray(jmolApplet0,"auxiliaryInfo");
>
>
> Then I iterate over every frame and look at x.models[i].moData.mos and
> x.models[i].modelProperties.Frequency
>
>
> But for a large file the getPropertyAsArray takes > 10 seconds and freezes
> Firefox while it's loading.  Reading the manual it seems that I can
> use getProperty asynchronously, but I don't understand how to use it
> properly.
>
>
> I set a message callback function to handle getProperty, but I'm not sure
> how to actually read in the moData.  It appears to be in arguments[1], but
> everything I try is undefined.  Here's an example of what I've tried.
>
>
> Thanks,
>
> Mark
>
>
> var Info = {
> width: 450,
> height: 450,
> debug: false,
> color: "white",
> addSelectionOptions: false,
> serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php;,
> use: "HTML5",
> j2sPath: "/jsmol/j2s",
> readyFunction: jmol_isReady,
> script: script,
> loadStructCallback: "onJSmolLoad",
> messageCallback: "processFrames",
> disableInitialConsole: true
> }
>
>
> function processFrames()
> {
>
>  for (i=0; i  {
> console.log(arguments[i])  // I see the model data here, but I
> can't figure out how to access it.
>
>  }
>  console.log ("I've tried a few things here");
> console.log(arguments[1].auxiliaryInfo.models[1]);
> console.log ("But nothing's worked");
> }
>
>
> Jmol.script(jmolApplet0,'getProperty auxiliaryInfo')
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
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
--
Check out the vibrant tech community on one of the world's most 
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
Jmol-users mailing list
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Re: [Jmol-users] Best way to access getproperty with JSmol

Re: [Jmol-users] Best way to access getproperty with JSmol

Re: [Jmol-users] Best way to access getproperty with JSmol

Re: [Jmol-users] Best way to access getproperty with JSmol

Re: [Jmol-users] Best way to access getproperty with JSmol

Re: [Jmol-users] Best way to access getproperty with JSmol

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