// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 

// Sept 2008 found that this OLD url didn't work. When used directly, it
// redirects, but FGiJ doesn't get the coordinates.
//OLD var url_pqs = "http%3A//pqs.ebi.ac.uk/pqs-doc/macmol/";
//NEW:
var url_pqs = "http%3A//www.ebi.ac.uk/msd-srv/pqs/macmol/";

var url_mse = "http%3A//molvis.sdsc.edu/pdb/"; // molvis.sdsc.edu = mse

// MUST BE LOCAL!
var url_pe = "../protexpl/pe.htm?id=";
var url_fjmol = "http://firstglance.jmol.org/fg.htm?mol=";
var url_pp = "http://proteopedia.org/wiki/index.php/";

// In the initial implementation, src will be blank because we can
// discern the 3 common sources from mol0:
//  pdb = 1abc
//  pqs = 1abc_1.mmol
//  mse = 1abc[...].pdb

function atlas_pdb(src, mol0, label, postlabel)
{
	var pdbname = "";
	var mol_pe = url_pe;
	var mol_fjmol = url_fjmol;
	var mol_pp = url_pp;
	if (typeof(label) == "undefined")
		label = "";

	if (typeof(postlabel) == "undefined")
		postlabel = "";

	if (src == "url") // arbitrary url, none of the standard 3
	{
		pdbname = label;
		if (pdbname.length == 0)
			pdbname = mol0.substring(lastIndexOf("/") + 1);

		mol_pe += mol0;
		mol_fjmol += mol0;
		mol_pp = "";
	}
	else if (mol0.length == 4)
	{
		pdbname = mol0.toUpperCase();
		mol_pe += mol0;
		mol_fjmol += mol0;
		mol_pp += mol0.toLowerCase();
	}
	// src "mse" is for .mmol alpha-carbon only files
	else if (mol0.indexOf(".pdb") != -1 || src == "mse")
	{
		pdbname = label;
		if (pdbname.length == 0)
			pdbname = mol0;
		mol_pe += url_mse + mol0;
		mol_fjmol += url_mse + mol0;
		mol_pp = "";
	}
	else if (mol0.indexOf(".mmol") != -1)
	{
		pdbname = "<b>" + mol0.substring(0, 4) + "</b>" + mol0.substring(4);
		mol_pe += url_pqs + mol0;
		mol_fjmol += url_pqs + mol0;
		mol_pp = "";
	}

	var lkm = pdbname + " [";
	if (mol_pp != "")
		lkm += "<a href='" + mol_pp + "' target='_blank'>Proteopedia</a> | ";
	lkm += "<a href='" + mol_fjmol + "' target='_blank'>FGJmol</a> | " 
		+ "<a href='" + mol_pe + "'>PE</a>]"
		+ postlabel;

//	alert(lkm);
	document.writeln(lkm);
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
function atlas_pe_only(src, mol, label, postlabel)
{
	var mol_pe = url_pe;
	if (src == ".") // local atlas PDB file
		mol_pe += mol;

	var lkm = "<a href='" + mol_pe + "'>" + label + "</a>" + postlabel;
//	alert(lkm);
	document.writeln(lkm);
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
function make_igloss_link(targ, label, postlabel)
{
	if (typeof(postlabel) == "undefined")
		postlabel = "";

	if (label == "NMR ensemble")
		postlabel = " (See <a href=\"#hint2\">Hint #2</a>)" + postlabel;

	var lig = "<a href=\"../protexpl/igloss.htm" + targ
		+ "\" target=\"_blank\"><font color=\"#00b000\"><b>"
		+ label + "</b></font></a>" + postlabel;

	return (lig);
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
function igloss_link(targ, label, postlabel)
{
	document.writeln(make_igloss_link(targ, label, postlabel));
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
function pqs_link(pdbcode, tail)
{
	if (typeof(tail) == "undefined")
		tail = "";

	pdbcode = pdbcode.toUpperCase();

	var pqslk = make_igloss_link("#pqs",
		"Probable Quaternary Structure (PQS)", "");

	pqslk += " [<a href=\"../protexpl/pqs.htm?id=" + pdbcode
		+ "\" target=\"_blank\">PQS explanation</a>; "
		+ "see <a href=\"#hint3\">Hint #3</a>]"
		+ tail;

	document.writeln(pqslk);
}
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -