Re: [Jmol-users] extracting chain ID's into an array?

[Thomas S. <tho...@gm...>]

My sincere thanks to you Rolf!  I apologize for taking so long to respond,
but I had some unexpected travel to do over the weekend.  I was "not seeing"
the concept of "x=script("show chains");" -- it is not intuitively obvious
(to me) that that will create an array rather than just a string (although
it is rather flexible and handy that it does).

Thanks again!
-Tom

PS -- I've been busily working at implementing your suggestion and it does
appear to be working as expected, but I have currently gotten hung up with
something in this portion of my script causing the Jmol graphics to freeze
and stop responding.  It's quite odd: the console still works.


On Fri, Aug 1, 2008 at 3:37 AM, Rolf Huehne <rh...@fl...> wrote:

> Thomas Stout wrote:
> > Hi All --
> >
> > Well, I've stumbled over this long enough & I need to ask for help!  I
> have
> > a case where I want to step through the chains of a selection (many PDB
> > files have more than one identical protein-ligand complex per
> > crystallographic asymmetric unit and use the identical atom names and
> > residue numbering, thereby only differing in chain ID).  I would like to
> use
> > the "*show chains*" command introduced in 11.5.51, since that returns
> > exactly what I need, but I admit to not fully understanding how to grab
> this
> > output into my scripting environment.  I'd love to have an array that I
> > could loop through (eg "chains[0]", chains[1]", etc).   I could jump back
> > and forth between javascript and JmolScript and accomplish the task with
> > something like:
> >
> > function getChainArray() {
> >     var chainString = script("show chains");   //pass result of script
> into
> > variable as string
> >     var chains = chainString.split("\n");          //split string on
> > linefeeds, or \r\n if Windows linefeeds
> > }
> >
> > function UseTheSelection(){
> >              var chains = getChainArray();
> >              for (var j=0;j<chains.length;j++){
> >                  jmolScriptWait("select {selected} and chains[j]};");
> >                  jmolScriptWait("do other stuff");
> > }
> >
> >
> > but, I really don't want to have to throw it back and forth.  I'm
> guessing
> > there *must* be a simple way -- within JmolScript -- to get an array of
> > chain IDs from the current selection, but I've not come up with it yet.
> >
>
> You could use for example:
>
> x=script("show chains");
> for (i=1; i<=x.size; i=i+1);
>  # do some stuff using x[i]
> end for;
>
> Unfortunately you get more lines than chains. For example with '1deh',
> containing 2 protein chains (A,B) plus an empty chain identifier " " for
> the  water molecules you will get an array with 7 elements. so you still
> might have to check if it is a valid chain identifier.
>
> Currently I am using the following solution to identify valid protein
> chain identifiers:
>
> chain_id_list = array(" ","A","B","C","D","E","F","G","H","I","J","K",
> "L","M","N","O","P","Q","R","S","T","U","V","W","X","Y","Z","a","b","c",
> "d","e","f","g","h","i","j","k","l","m","n","o","p","q","r","s","t","u",
> "v","w","x","y","z","0","1","2","3","4","5","6","7","8","9");
>
> for (i=1; i<=chain_id_list.size; i=i+1);
>  selection_expression = "protein AND *:" + chain_id_list[i];
>  selected_atom_count  = {@selection_expression}.size;
>  if (selected_atom_count > 0);
>    # do whatever you want
>  end if;
> end for;
>
> Regards,
> Rolf
>
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