Re: [Jmol-developers] jmol assistance needed

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Well, if you want to get information back from Jmol, the easiest way is
using jmolEvaluate:

<script type="text/javascript">
var x = jmolEvaluate('script("for(var i = 0; i < 10;i++){print i}")')
</script>

note the careful use of single and double quotes. You can avoid some of that
complexity by first defining the script:

var script = 'script("for(var i = 0; i < 10;i++){print i}")'
var x = jmolEvaluate(script)

so for my script it would be:

var script =  'script(" for (var i = 0; i < site_list.length; i++) {script
inline @{\'select atomIndex = _atomhovered and \' + site_list[i]};if
({selected}) {print site_list[i] }}")'
var x = jmolEvaluate(script)

(I think)

Or you could first get all the information with

var info = jmolEvaluate('getProperty("stateInfo")')

and then work from there.

Bob

On Fri, Dec 25, 2009 at 1:08 PM, Aya <ae...@ii...> wrote:

> Hello,
> I'm not understanding a fundamental part, and I think this is why I am
> having such troubles.
>
>
> > Decoding that, I see:
> >
> > if ({atomIndex=_atomHovered}&{site1}) {
> >   hover "default1"; select site1; halos 25%;color halos red; select all;
> > } else if ({atomIndex=_atomHovered}&!{site1}) {
> >   hover %U; select site1; halos off
> > }
>
> So this is a clip of what I have in the head of my page:
>
> <script language="javascript">
> function customhover(){
>
>       if(myListL.options[1].selected == true){ jmolScript(
>                         'if ({atomIndex=_atomHovered}&{site1}); ' +
>                                 'hover "default1"; select site1; halos
> 25%;color halos red; select all;' +
>                         'else if ({atomIndex=_atomHovered}&!{site1}); ' +
>                                 'hover %U; select site1; halos off;' +
>                         'end if; ',"LeftApplet")
>         }
> }
> </script>
>
>
> And here in the end of the body:
>
> <script type="text/javascript">
>         jmolApplet([410,480],'load jmol/models/practice.pdb;set
> hoverCallback "customhover"; define site1 atomno=1; define site2
> atomno=2;','LeftApplet')
>  </script>
>
>
> How do I run the script as you have suggested?
> As for the last part ...hm.  I know "@" allows you to define a variable and
> I see you've made an array of sites...
> Thank you!
> Aya
>
>
>
>
>
>
>
>
>
> On Fri, Dec 25, 2009 at 3:54 PM, Robert Hanson <ha...@st...> wrote:
> >
> >
> > On Fri, Dec 25, 2009 at 4:56 AM, Aya <ae...@ii...> wrote:
> >>
> >> Hello,
> >> I am making a webpage in which the molecule has some 10 sites (defined
> >> as site1, site2 ... upon loading the applet ), and the user can select
> >> which site(s) he wants to view (the halos get turned on and an
> >> isosurface gets generated).  When the mouse hovers over a site that
> >> has been selected, I want a specific hover message to appear.
> >> Additionally, some atoms may belong to more than one site.  In this
> >> case, the hover message must append additional information.
> >>
> >> Here is one attempt at this.  This code is within my custom hover
> >> function called by the set hovercallback:
> >>              if(myListL.options[1].selected == true){jmolScript(
> >>                        'if ({atomIndex=_atomHovered}&{site1}); ' +
> >>                                'hover "default1"; select site1; halos
> >> 25%;color halos red; select all;' +
> >>                        'else if ({atomIndex=_atomHovered}&!{site1}); ' +
> >>                                'hover %U; select site1; halos off;' +
> >>                        'end if; ',"Leftapplet")}
> >>
> >
> > Decoding that, I see:
> >
> > if ({atomIndex=_atomHovered}&{site1}) {
> >   hover "default1"; select site1; halos 25%;color halos red; select all;
> > } else if ({atomIndex=_atomHovered}&!{site1}) {
> >   hover %U; select site1; halos off
> > }
> >
> >
> >> This says that if the first site is selected and the first site is
> >> being hovered, there is the custom message, if it's anything But
> >> site1, then hover is normal.  This does not solve the problem! For
> >> several reasons.  What I need to do is include a some kind of
> >> jmolScript that will Return a boolean if the atom hovered is part of
> >> site1, site2.. (as in, a jmol  script that will evaluate
> >> ({atomIndex=_atomHovered}&{site1}) )  OR some kind of jmol script that
> >> will return the sites that the atom hovered belongs to  OR maybe a way
> >> to insert variables into the jmolScript that have been defined in the
> >> previous javascript. OR any other suggestion you may have!
> >>
> >
> >  for (var i = 0; i < site_list.length; i++) {script inline @{"select " +
> > site_list[i]};print {selected}}
> >
> > This gives all the atoms in each site. So if you could use:
> >
> >  for (var i = 0; i < site_list.length; i++) {
> >   script inline @{"select atomIndex = _atomhovered and " + site_list[i]}
> >   if ({selected}) {
> >     print site_list[i]
> >   }
> > }
> >
> >
> > That would at least get you the list.
> >
> > A slicker option would be to read the state once after file loading and
> then
> > parse it for the information you want:
> >
> >   @site_1 ({299:314 334:384 719:734 754:804 1139:1154 1174:1224 1559:1574
> > 1594:1644 1979:1994 2014:2064 2399:2414 2434:2484 2819:2834 2854:2904
> > 3239:3254 3274:3324 3659:3674 3694:3744 4079:4094 4114:4164 4499:4514
> > 4534:4584 4919:4934 4954:5004 5339:5354 5374:5424 5759:5774 5794:5844
> > 6179:6194 6214:6264});
> >   @site_ac1 ({19:34 439:454 859:874 1279:1294 1699:1714 2119:2134
> 2539:2554
> > 2959:2974 3379:3394 3799:3814 4219:4234 4639:4654 5059:5074 5479:5494
> > 5899:5914});
> >   @site_ac2 ({0:18 35:53 420:438 455:473 840:858 875:893 1260:1278
> 1295:1313
> > 1680:1698 1715:1733 2100:2118 2135:2153 2520:2538 2555:2573 2940:2958
> > 2975:2993 3360:3378 3395:3413 3780:3798 3815:3833 4200:4218 4235:4253
> > 4620:4638 4655:4673 5040:5058 5075:5093 5460:5478 5495:5513 5880:5898
> > 5915:5933});
> > ...
> >   site_ac1 = ["[IDS]2:A"];
> >   site_ac2 = ["[SGN]1:A", "[SGN]3:A"];
> >   site_ac3 = ["[IDS]2:A", "[IDS]4:A", "[SGN]5:A", "[IDS]6:A"];
> > ...
> >   site_list = ["site_BC9", "site_BC8", "site_BC7", "site_BC6",
> "site_BC5",
> > "site_BC4", "site_BC3", "site_BC2", "site_BC1", "site_AC9", "site_AC8",
> > "site_AC7", "site_AC6", "site_AC5", "site_AC4", "site_AC3", "site_AC2",
> > "site_CC6", "site_AC1", "site_CC5", "site_CC4", "site_CC3", "site_CC2",
> > "site_CC1"];
> >
> >
> > Bob
> >
> >
> >> Thank you kindly for your help!
> >> Aya
> >>
> >>
> >>
> ------------------------------------------------------------------------------
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> >> _______________________________________________
> >> Jmol-developers mailing list
> >> Jmo...@li...
> >> https://lists.sourceforge.net/lists/listinfo/jmol-developers
> >
> >
> >
> > --
> > 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
> >
> >
> ------------------------------------------------------------------------------
> > This SF.Net email is sponsored by the Verizon Developer Community
> > Take advantage of Verizon's best-in-class app development support
> > A streamlined, 14 day to market process makes app distribution fast and
> easy
> > Join now and get one step closer to millions of Verizon customers
> > http://p.sf.net/sfu/verizon-dev2dev
> > _______________________________________________
> > Jmol-developers mailing list
> > Jmo...@li...
> > https://lists.sourceforge.net/lists/listinfo/jmol-developers
> >
> >
>
>
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and
> easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> Jmol-developers mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>

-- 
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

Re: [Jmol-developers] jmol assistance needed

An interactive viewer for three-dimensional chemical structures.

Re: [Jmol-developers] jmol assistance needed