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Re: [Jmol-users] How to retrieve the label of an atom programmatically
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From: Robert H. <ha...@st...> - 2014-01-15 16:45:12
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You are almost there. drop the PRINT command part:
Jmol.evaluate(jmolApplet, "{atomNo=" + atomNo + "}.label");
or
Jmol.evaluate(jmolApplet, "@" + atomNo + ".label");
Note that you can use label() or label("..some format stuff here...")
Bob
On Wed, Jan 15, 2014 at 3:49 AM, Roberto Mosca <rob...@gm...> wrote:
> Thanks Robert,
>
> but how to you retrieve it then programmatically? The instruction
>
> Jmol.evaluate(jmolApplet, "print {atomNo=" + atomNo + "}.label");
>
> does not work.
>
> Let me know.
>
> Best,
> Roberto
>
>
> On Wed, Jan 15, 2014 at 6:58 AM, Robert Hanson <ha...@st...> wrote:
>
>> atom properties are numbers, not strings. You will have to set the atom
>> label instead of a property if you want a string.
>>
>>
>> On Tue, Jan 14, 2014 at 1:19 PM, Rolf Huehne <rh...@fl...>wrote:
>>
>>> On 01/14/2014 06:14 PM, Roberto Mosca wrote:
>>> > Dear Alexander and Rolf,
>>> >
>>> > thanks for your help! I tried the instruction
>>> >
>>> > Jmol.evaluate(jmolApplet, "print {atomNo=" + atomNo + "}.property_pp");
>>> >
>>> > in the following code:
>>> >
>>> > function pickResidue(jmolObj,msg,atomNo) {
>>> > var pp = Jmol.evaluate(jmolApplet, "print {atomNo=" + atomNo +
>>> > "}.property_pp");
>>> > }
>>> >
>>> >
>>> > after setting the property with the following script:
>>> >
>>> > set frank off
>>> > delete NOT :A
>>> > cartoon ONLY
>>> > color [xFADACB]
>>> > background hover [xFCD6E2]
>>> > color hover [xD60B51]
>>> > font hover 12 sanserif
>>> > hover %[label]
>>> > set hoverDelay 0.01
>>> > select 35; color [xbe1622]; spacefill 70%
>>> > set hoverLabel "P35";
>>> > data "property_pp"
>>> > Q13253_35
>>> > Q13253_35
>>> > Q13253_35
>>> > Q13253_35
>>> > Q13253_35
>>> > Q13253_35
>>> > Q13253_35
>>> > Q13253_35
>>> > Q13253_35
>>> > Q13253_35
>>> > end "property_pp"
>>> >
>>> > set PickCallback "pickResidue"
>>> >
>>> >
>>> > And the variable pp has the value "ERROR" after executing it. Any idea
>>> why
>>> > it is so? Or how to debug it?
>>> >
>>> One problem here will be that you didn't set the 'property_pp' to the
>>> correct atom. You would either need "select atomNo=35" or the shortcut
>>> "@35".
>>> And since you selected only a single atom the 'data' section would
>>> presumably only need a single "Q13253_35" line.
>>>
>>> But there seems to be a more general problem. I wasn't able to assign a
>>> string to a property in Jmol 14.0.1, just numbers.
>>>
>>> After applying the following commands (PDB entry 1OTZ loaded) the result
>>> is "PP:35.0":
>>> select atomno=35;
>>> data "property_pp"
>>> test 35
>>> end "property_pp"
>>> print "PP:" + {atomNo=35}.property_pp;
>>>
>>> If "test 35" is replaced with "test_35" the result is "PP:NaN".
>>>
>>> The result is the same if I try to set the property directly using this
>>> command:
>>>
>>> {atomNo=35}.property_pp = "test 35";
>>>
>>> But you should be able to overcome this limitation (or bug?) by storing
>>> the hoverlabel in your own global array, e.g.:
>>>
>>> ----- Jmol script ------
>>> my_labels = [];
>>> my_labels[35] = "test 35";
>>> ------------------------
>>>
>>> ----- Javascript -------
>>> Jmol.evaluate(jmolApplet, "print my_labels[" + atomNo + "]");
>>> ------------------------
>>>
>>> Regards,
>>> Rolf
>>> --
>>>
>>> Rolf Huehne
>>> Postdoc
>>>
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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
>>
>>
>>
>> ------------------------------------------------------------------------------
>> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
>> Learn Why More Businesses Are Choosing CenturyLink Cloud For
>> Critical Workloads, Development Environments & Everything In Between.
>> Get a Quote or Start a Free Trial Today.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
>> _______________________________________________
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>>
>>
>
>
> --
> La chiocciol@
> http://lachiocciola.tumblr.com/
>
>
> ------------------------------------------------------------------------------
> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> Learn Why More Businesses Are Choosing CenturyLink Cloud For
> Critical Workloads, Development Environments & Everything In Between.
> Get a Quote or Start a Free Trial Today.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> 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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