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

[Rolf H. <rh...@fl...>]

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