OK! Great. Looks like you may have a supremely useful utility there, Daniel.
Bob
On Tue, Apr 12, 2011 at 6:41 AM, Daniel Carbajo <daniel.carb...@gmail.com>wrote:
> So I already solved everything! the final function looks like this:
> function crossMeasure(atomListN, atomListM){
> var lf = _lastframe
> var sp = lf.split(".")
> var n = sp[1]
> if (n>1){
>
> set measurementUnits angstroms
> set measurements 3
> font measure 16 serif bold
> for (var i = 2; i <= n; i++) {
> script inline @{"measure @{{" + atomListN + ".ca/1.1}} @{{" +
> atomListM + ".ca/" + i + ".1}}"}
> var modelfile=getProperty("modelInfo.models.file")[i]
> var spfile = modelfile.split("/")
> var modelname = spfile[spfile.length]
> var spname = modelname.split("-")
> var modelnum = spname[2]
> var j = i-1
> prompt "DISTANCE " + j + " --> " +
> getProperty("measurementinfo[" + j + "].strMeasurement") + "\n\nAtom 1: " +
> getProperty("measurementinfo[" + j + "].atoms[1].info") + " Coordinates: " +
> getProperty("measurementinfo[" + j + "].atoms[1].coord") + " --> NATIVE
> STRUCTURE\n" + "Atom 2: " + getProperty("measurementinfo[" + j +
> "].atoms[2].info") + " Coordinates: " + getProperty("measurementinfo[" + j +
> "].atoms[2].coord") + " --> MODEL " + modelnum
> }
> }
> }
>
> Thanks for everything!
> Cheers,
> Daniel
>
>
> 2011/4/11 Daniel Carbajo <daniel.carb...@gmail.com>
>
>> Oh thanks a lot! But returning to the thread question (ie, how to echo,
>> alert or prompt the distance results)...
>> This is the best I came up with but it does not work, and I cannot figure
>> out why:
>>
>> var atomListN='4:A'
>> var atomListM='7:A'
>> set measurementUnits angstroms
>> set measurements 3
>> font measure 16 serif bold
>> var n = atomListM.length
>> for (var i = 2; i <= n; i++) {
>> script inline @{"measure @{{" + atomListN + ".ca/1.1}} @{{" + atomListM +
>> ".ca/" + i + ".1}}"}
>> var j = i-1
>> prompt "DISTANCE: " + getProperty("measurementinfo[j].atoms[1].info") + "
>> AND " + getProperty("measurementinfo[j].atoms[2].info") + " = " +
>> getProperty("measurementinfo[j].strMeasurement")
>> }
>>
>>
>> measurementinfo[1] or whatever number works, but introducing the j does
>> not... I tried with double and single quotes, without quotes and everything,
>> I even tried to define j like @{i-1}
>> So which is the problem here?
>>
>> I also have problem with atoms[i].model as I told you... It is always 1
>> Thanks again!
>> Daniel
>>
>>
>>
>>
>>
>>
>>
>>
>> 2011/4/11 Robert Hanson <hans...@stolaf.edu>
>>
>>> first, I would use double quotes in PHP, not single. Makes life a lot
>>> easier:
>>>
>>> $content .= "<td><script>
>>> jmolCheckbox(\"myfunction('$residue')\", .......... ";
>>>
>>>
>>>
>>> On Mon, Apr 11, 2011 at 4:52 AM, Daniel Carbajo <
>>> daniel.carb...@gmail.com> wrote:
>>>
>>>> Apart from the atoms[i].model problem, I always find trouble when
>>>> passing the variables from php to a function...
>>>> If I pass '104:A' like this:
>>>> $content .= '<td><script>
>>>> jmolCheckbox("myfunction(\' '.$residue.' \')", ..........
>>>>
>>>> How can I, inside the function, especify 104:A.ca as a variable that I
>>>> can use in the function? I try this:
>>>>
>>>> function myfunction(res){
>>>> var atoms="{" + res + ".ca}"
>>>> var n = atoms.length
>>>> var fileNameArray = getProperty("modelInfo.models.file")
>>>> for (var i = 1; i <= n; i++) {
>>>> atoms[i].label = "***%M - " + atoms[i].model + " - lig bin res
>>>> %n_%c_%r temperature=%b"
>>>> }
>>>> }
>>>>
>>>> But this obviously does not work... so which should be the correct way
>>>> to define "atoms" (104:A.ca) out of "res" (104:A)? Thanks!
>>>> Daniel
>>>>
>>>>
>>>>
>>> If you really need to do that, you have to use script inline or select:
>>>
>>> var atoms = "" + res + ".ca"
>>> script inline "atoms = {" + atoms + "}"
>>> # now atoms is that set of atoms
>>>
>>> or select can take a string as a variable:
>>>
>>> select @{"" + res + ".ca"}
>>> var atoms = {selected}
>>>
>>>
>>>
>>>
>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> 2011/4/8 Daniel Carbajo <daniel.carb...@gmail.com>
>>>>
>>>>> I am close to it but a strange things happens; I apply this on console
>>>>> when I have 3 proteins loaded (the native structure plus two homology
>>>>> models):
>>>>> var natmod = "MOD"
>>>>> var desc = "SS"
>>>>> var atoms = {104:A.ca}
>>>>> var info = "lig bin res"
>>>>>
>>>>> var fileNameArray = getProperty("modelInfo.models.file")
>>>>> var n = atoms.length
>>>>> if (desc == "SS"){
>>>>> var sarray = ["H","B","E","G","I","T","S","U"]
>>>>> for (var i = 1; i <= n; i++) {
>>>>> atoms[i].label = "***%M - " + atoms[i].model + " - " +
>>>>> info + " %n_%c_%r " + desc + ":" + sarray[atoms[i].temperature]
>>>>>
>>>>> }
>>>>> }
>>>>> else{
>>>>> for (var i = 1; i <= n; i++) {
>>>>> atoms[i].label = "***%M - " + atoms[i].model + " - " +
>>>>> info + " %n_%c_%r " + desc + ":%b"
>>>>>
>>>>> }
>>>>> }
>>>>> font label 14 serif bold
>>>>> color label black
>>>>>
>>>>>
>>>>> So I get correclty 3 atoms labeled, but atoms[i].model turns out to be
>>>>> 1 in all three situations, I get the following labels:
>>>>>
>>>>> ***1.1 - 1 - lig bin res PHE_A_104 SS:H
>>>>> ***2.1 - 1 - lig bin res PHE_A_104 SS:H
>>>>> ***3.1 - 1 - lig bin res PHE_A_104 SS:H
>>>>>
>>>>> And so when I extract the file name I get always the same... (by the
>>>>> way: can I parse the file name removing everything before the last "/" and
>>>>> the ".pdb" at the end?). What am I doing wrong? I do not get it...
>>>>> Thanks!
>>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Xperia(TM) PLAY
>>>> It's a major breakthrough. An authentic gaming
>>>> smartphone on the nation's most reliable network.
>>>> And it wants your games.
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>>>> _______________________________________________
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>>>>
>>>>
>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Professor of Chemistry
>>> St. Olaf College
>>> 1520 St. Olaf Ave.
>>> Northfield, MN 55057
>>> http://www.stolaf.edu/people/hansonr
>>> phone: 507-786-3107
>>>
>>>
>>> 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
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Xperia(TM) PLAY
>>> It's a major breakthrough. An authentic gaming
>>> smartphone on the nation's most reliable network.
>>> And it wants your games.
>>> http://p.sf.net/sfu/verizon-sfdev
>>> _______________________________________________
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
------------------------------------------------------------------------------
Forrester Wave Report - Recovery time is now measured in hours and minutes
not days. Key insights are discussed in the 2010 Forrester Wave Report as
part of an in-depth evaluation of disaster recovery service providers.
Forrester found the best-in-class provider in terms of services and vision.
Read this report now! http://p.sf.net/sfu/ibm-webcastpromo
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