Re: [Jmol-users] Use of variable in a call to getProperty

[Kubasik, Matthew A.]

How about here?
http://wiki.jmol.org/index.php/Scripting/GetProperty


On Jul 8, 2016, at 11:46 AM, Angel Herráez 
mailto:angel.herr...@uah.es>> wrote:

Sure!
The question is... where to locate it?

Goes to the to-do list. Suggestions or actual page edition are welcome



On 8 Jul 2016 at 9:59, Robert Hanson wrote:

Might be a nice addition to the Wiki.


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Re: [Jmol-users] Use of variable in a call to getProperty

[Angel Herráez]

Sure!
The question is... where to locate it?

Goes to the to-do list. Suggestions or actual page edition are welcome



On 8 Jul 2016 at 9:59, Robert Hanson wrote:

Might be a nice addition to the Wiki.


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Re: [Jmol-users] Use of variable in a call to getProperty

[Robert Hanson]

Might be a nice addition to the Wiki.

On Fri, Jul 8, 2016 at 9:16 AM, Latévi Max LAWSON DAKU 
wrote:

> Dear Bob,
>
> Thanks a lot for your answer.
>
> Your solution is also the one given by Matt and it works :)
>
>
> I'm attaching a README file, which I wrote to keep track of what I did.
> It's far from being perfect. But I hope it may be helpful to someone.
>
> Thanks again, Bob, Matt and Angel!
>
>
> Best,
> Max
>
>
>
>
>
> On 08. 07. 16 07:09, Robert Hanson wrote:
>
>> My message came out somewhat garbled, I think.  Trying again:
>>
>> i = 7
>> print getproperty('modelInfo.models['+i+'].modelProperties.FreqValue')
>>
>>
>>
>>
>>
>>
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>>
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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
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Re: [Jmol-users] Use of variable in a call to getProperty

[Latévi Max LAWSON DAKU]

Dear Bob,

Thanks a lot for your answer.

Your solution is also the one given by Matt and it works :)


I'm attaching a README file, which I wrote to keep track of what I did.
It's far from being perfect. But I hope it may be helpful to someone.

Thanks again, Bob, Matt and Angel!


Best,
Max




On 08. 07. 16 07:09, Robert Hanson wrote:

My message came out somewhat garbled, I think.  Trying again:

i = 7
print getproperty('modelInfo.models['+i+'].modelProperties.FreqValue')





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# 
# Animating vibrations with Jmol (600x435) & Imagemagick
# 

# Jmol
# 


# Load the results file and adjust a few settings 
# (no need here to change the orientation)
# --

load "vib_analysis.molden"

color background black;
restrict not selected;select not selected;wireframe 0.04


# Number of vibrational modes
# --

number_of_vib_modes = 177


# Index of the frame/model associated with the first normal mode 
# --

starting_frame_index = 7


# Move to the frame/model associated with the first normal mode
# and make the necessary for displaying useful information and
# animating the vibrations
# --

i_frame = @{starting_frame_index}
frame @{i_frame}
i_vib = 1
vectors on; vectors 0.04
vectors scale 3.5; color vectors yellow
vibration on; vibration scale 2

set echo bottom left; font echo 12; color echo white;
echo DOI: uu.uuu/..v

freq = getproperty('modelInfo.models['+i_frame+'].modelProperties.FreqValue')
set echo top left; font echo 16; color echo white;
echo @{format("%.1f",freq)} cm-1;

zoom 85


# Generate the JPG files for the animation of the first mode
# --

filename = "vib_" + format("%03i",i_vib) + "_"
filename += format("%04i",freq) + "_.jpg"
write vibration 4 @{filename}


# Redo, for the other vibrational modes
# --

while (i_vib < number_of_vib_modes)
{
  ++i_vib;
  ++i_frame;
  frame next;

  freq = getproperty('modelInfo.models['+i_frame+'].modelProperties.FreqValue');
  echo @{format("%.1f",freq)} cm-1;

  filename = "vib_" + format("%03i",i_vib) + "_"
  filename += format("%04i",freq) + "_.jpg"
  write vibration 4 @{filename}

  #delay 3;
}


# Imagemagick
# 

for i in $(seq 1 1 177); do x=$(printf "%03i\n" $i); PREFIX="vib_$x"; 
MP4=$(echo $(ls ${PREFIX}_*_0001.jpg) | sed -e 's/_0001.jpg/.mp4/'); echo 
${MP4}; convert ${PREFIX}_*.jpg ${MP4}; done

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Re: [Jmol-users] Use of variable in a call to getProperty

[Robert Hanson]

My message came out somewhat garbled, I think.  Trying again:

i = 7
print getproperty('modelInfo.models['+i+'].modelProperties.FreqValue')
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Re: [Jmol-users] Use of variable in a call to getProperty

[Robert Hanson]

On Thu, Jul 7, 2016 at 9:38 AM, Latévi Max LAWSON DAKU 
wrote:

> Dear Jmol users/developers,
>
> I would like to be able to use a variable in a call to getProperty.
> So far, the following command works.
>
>  $ print getproperty('modelInfo.models[7].modelProperties.FreqValue')
>  129.529358
>
> But I rwould like to use a variable as follows
>
>  $ i=7
>  $ print getproperty('modelInfo.models[i].modelProperties.FreqValue')
>
>
i = 7
print getproperty('modelInfo.models['+i+'].modelProperties.FreqValue')
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Re: [Jmol-users] Use of variable in a call to getProperty

[Kubasik, Matthew A.]

Thanks, Angel.  I'm never sure about these things.  Sometimes in my scripts I 
get "TRUE" when I'm expecting a numerical result.  This makes me think I'm 
mixing types.  Maybe I'm just mis-using built in functions.  But that's for 
another thread!

From: Herráez Sánchez Ángel [angel.herr...@uah.es]
Sent: Thursday, July 07, 2016 11:50 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Use of variable in a call to getProperty


Yes, Matt

it will be corrrect and safe. Jmol scripting does not care about variable 
types, as far as I know


You are right this is a string issue and concatenation is the right approach.


<https://lists.sourceforge.net/lists/listinfo/jmol-users>


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Re: [Jmol-users] Use of variable in a call to getProperty

[Herráez Sánchez Ángel]

Yes, Matt

it will be corrrect and safe. Jmol scripting does not care about variable 
types, as far as I know


You are right this is a string issue and concatenation is the right approach.




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Re: [Jmol-users] Use of variable in a call to getProperty

[Kubasik, Matthew A.]

Hi, Max,

Yes, I think the stuff inside the parentheses is literally a string, so,if you 
want to vary the string, you need to reconstruct the string in your loop with 
the + signs.  Although it "works", I think the line sums two different types 
(string and integer), so, I am not certain the syntax is strictly correct.

Best,

Matt

From: Latévi Max LAWSON DAKU [max.law...@unige.ch]
Sent: Thursday, July 07, 2016 11:15 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Use of variable in a call to getProperty

On 07. 07. 16 17:04, Kubasik, Matthew A. wrote:
> Max,
>

Hi Matt,

Thanks for your suggestions.

> Two suggestions.
>
> First, something like:
>
> freqvalues = getproperty('modelInfo.models.modelProperties.FreqValue')
>
> will look for frequency values of all models and put them in the array 
> "freqvalues".
>
> Unfortunately, this array will have empty entries for models lacking 
> frequency values.
>
> Second, if you know the range of models that contain freq values (say, models 
> 300 to 370), you can use something like:
>
> for (var i=300; i<370;i+=1){
> print getproperty('modelInfo.models['+i+'].modelProperties.FreqValue')
> }

I tried this latter and it works !! :D

Thanks again!

Best,
Max


>
> Perhaps more skilled coders on the list could suggest improvements to these 
> clunky lines!
>
> Matt
>
>
>
>
> 
> From: Latévi Max LAWSON DAKU [max.law...@unige.ch]
> Sent: Thursday, July 07, 2016 10:38 AM
> To: jmol-users@lists.sourceforge.net
> Subject: [Jmol-users] Use of variable in a call to getProperty
>
> Dear Jmol users/developers,
>
> I would like to be able to use a variable in a call to getProperty.
> So far, the following command works.
>
>  $ print getproperty('modelInfo.models[7].modelProperties.FreqValue')
>  129.529358
>
> But I rwould like to use a variable as follows
>
>  $ i=7
>  $ print getproperty('modelInfo.models[i].modelProperties.FreqValue')
>
> But this doesn't work. I also tried to use @{i}, with no success as
> well. I'm not comfortable with dereferencing a variable in Jmol.
>
> The reason for trying to do so us that I'ld like to iterate through the
> frames and use the variable i hold the index of the frame.
>
>
> I thank you in advance for your help.
>
> Best regards,
> Max
>
> --
> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape
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Re: [Jmol-users] Use of variable in a call to getProperty

[Latévi Max LAWSON DAKU]

On 07. 07. 16 17:04, Kubasik, Matthew A. wrote:
> Max,
>

Hi Matt,

Thanks for your suggestions.

> Two suggestions.
>
> First, something like:
>
> freqvalues = getproperty('modelInfo.models.modelProperties.FreqValue')
>
> will look for frequency values of all models and put them in the array 
> "freqvalues".
>
> Unfortunately, this array will have empty entries for models lacking 
> frequency values.
>
> Second, if you know the range of models that contain freq values (say, models 
> 300 to 370), you can use something like:
>
> for (var i=300; i<370;i+=1){
> print getproperty('modelInfo.models['+i+'].modelProperties.FreqValue')
> }

I tried this latter and it works !! :D

Thanks again!

Best,
Max


>
> Perhaps more skilled coders on the list could suggest improvements to these 
> clunky lines!
>
> Matt
>
>
>
>
> 
> From: Latévi Max LAWSON DAKU [max.law...@unige.ch]
> Sent: Thursday, July 07, 2016 10:38 AM
> To: jmol-users@lists.sourceforge.net
> Subject: [Jmol-users] Use of variable in a call to getProperty
>
> Dear Jmol users/developers,
>
> I would like to be able to use a variable in a call to getProperty.
> So far, the following command works.
>
>  $ print getproperty('modelInfo.models[7].modelProperties.FreqValue')
>  129.529358
>
> But I rwould like to use a variable as follows
>
>  $ i=7
>  $ print getproperty('modelInfo.models[i].modelProperties.FreqValue')
>
> But this doesn't work. I also tried to use @{i}, with no success as
> well. I'm not comfortable with dereferencing a variable in Jmol.
>
> The reason for trying to do so us that I'ld like to iterate through the
> frames and use the variable i hold the index of the frame.
>
>
> I thank you in advance for your help.
>
> Best regards,
> Max
>
> --
> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
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Re: [Jmol-users] Use of variable in a call to getProperty

[Latévi Max LAWSON DAKU]

On 07. 07. 16 17:04, Herráez Sánchez Ángel wrote:
> Hi Max
>

Hi Herráez,

Thanks for your mail
>
> I also have trouble often using variables.
>
> @{i}  is unusual to me. The common syntax is either "i" or "@i "
>

:) I'm never sure when to use this; if using the bare name 'i' doesn't
work, i swicth to '@i'. I probably should take more time going through
the documentation :D

>
> Have you tried ...?
>
> print getproperty('modelInfo.models[@i].modelProperties.FreqValue')
>

I tried this :(

Best,
Max


> 
>
>
> --
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> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
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>
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Re: [Jmol-users] Use of variable in a call to getProperty

[Herráez Sánchez Ángel]

Hi Max


I also have trouble often using variables.

@{i}  is unusual to me. The common syntax is either "i" or "@i "


Have you tried ...?

print getproperty('modelInfo.models[@i].modelProperties.FreqValue')


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Re: [Jmol-users] Use of variable in a call to getProperty

[Kubasik, Matthew A.]

Max,

Two suggestions.

First, something like:

freqvalues = getproperty('modelInfo.models.modelProperties.FreqValue')

will look for frequency values of all models and put them in the array 
"freqvalues".  

Unfortunately, this array will have empty entries for models lacking frequency 
values. 

Second, if you know the range of models that contain freq values (say, models 
300 to 370), you can use something like:

for (var i=300; i<370;i+=1){
print getproperty('modelInfo.models['+i+'].modelProperties.FreqValue')
}

Perhaps more skilled coders on the list could suggest improvements to these 
clunky lines!

Matt





From: Latévi Max LAWSON DAKU [max.law...@unige.ch]
Sent: Thursday, July 07, 2016 10:38 AM
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] Use of variable in a call to getProperty

Dear Jmol users/developers,

I would like to be able to use a variable in a call to getProperty.
So far, the following command works.

 $ print getproperty('modelInfo.models[7].modelProperties.FreqValue')
 129.529358

But I rwould like to use a variable as follows

 $ i=7
 $ print getproperty('modelInfo.models[i].modelProperties.FreqValue')

But this doesn't work. I also tried to use @{i}, with no success as
well. I'm not comfortable with dereferencing a variable in Jmol.

The reason for trying to do so us that I'ld like to iterate through the
frames and use the variable i hold the index of the frame.


I thank you in advance for your help.

Best regards,
Max

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[Jmol-users] Use of variable in a call to getProperty

[Latévi Max LAWSON DAKU]

Dear Jmol users/developers,

I would like to be able to use a variable in a call to getProperty.
So far, the following command works.

 $ print getproperty('modelInfo.models[7].modelProperties.FreqValue')
 129.529358

But I rwould like to use a variable as follows

 $ i=7
 $ print getproperty('modelInfo.models[i].modelProperties.FreqValue')

But this doesn't work. I also tried to use @{i}, with no success as
well. I'm not comfortable with dereferencing a variable in Jmol.

The reason for trying to do so us that I'ld like to iterate through the
frames and use the variable i hold the index of the frame.


I thank you in advance for your help.

Best regards,
Max

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