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viewer.htm
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<html>
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
<title>Viewer - PrimaryDock</title>
<script src="https://code.jquery.com/jquery-3.6.0.min.js" integrity="sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4=" crossorigin="anonymous"></script>
<script src="https://unpkg.com/ngl@0.10.4/dist/ngl.js"></script>
<script>
var nglcitation
= "AS Rose, AR Bradley, Y Valasatava, JM Duarte, A Prlić and PW Rose.\n"
+ "Web-based molecular graphics for large complexes.\n"
+ "ACM Proceedings of the 21st International Conference on Web3D Technology (Web3D '16):\n"
+ "185-186, 2016. doi:10.1145/2945292.2945324\n"
+ "\n"
+ "AS Rose and PW Hildebrand.\n"
+ "NGL Viewer: a web application for molecular visualization.\n"
+ "Nucl Acids Res (1 July 2015) 43 (W1):\n"
+ "W576-W579 first published online April 29, 2015.\n"
+ "doi:10.1093/nar/gkv402";
const aa1let = "ARNDCEQGHOILKMFPOUSTWYVHHHHH";
const aa3let =
[
'ALA', 'ARG', 'ASN', 'ASP', 'CYS',
'GLU', 'GLN', 'GLY', 'HIS', 'HYP',
'ILE', 'LEU', 'LYS', 'MET', 'PHE',
'PRO', 'PYL', 'SEC', 'SER', 'THR',
'TRP', 'TYR', 'VAL',
'HIP', 'HID', 'HIE', 'HSD', 'HSE',
];
/******************************************************************************/
// http://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript
function getParameterByName(name, url)
{
if (!url)
{
url = window.location.href;
}
name = name.replace(/[\[\]]/g, "\\$&");
var regex = new RegExp("[?&]" + name + "(=([^&#]*)|&|#|$)"),
results = regex.exec(url);
if (!results) return null;
if (!results[2]) return '';
return decodeURIComponent(results[2].replace(/\+/g, " "));
}
/******************************************************************************/
const aa_aliphatic = 0,
aa_aromatic = 1,
aa_hydrophilic = 2,
aa_acidic = 3,
aa_basic = 4,
aa_sulfur = 5;
var opc_molecule = 1.0;
var opc_ligand = 1.0;
var opc_cartoon = 0.15;
var opc_sidechain = 0.333;
var opc_sidechain_active = 0.35;
var opc_metal = 1.0;
var mtl_bs = 0.0;
var mtl_licorice = 0.0;
var mtl_cartoon = 0.1;
var mtl_metal = 0.5;
var molid = getParameterByName('mol') ? getParameterByName('mol') : 'rand';
var protid = getParameterByName('prot') ? getParameterByName('prot') : false;
var website = "https://www.primaryodors.org";
var is_localhost = false;
var test = "http://127.0.0.1";
function loadFile(fileData, fileName = "")
{
$("#pleasewait").show();
window.setTimeout( function()
{
$("#pleasewait").hide();
}, 5381);
$("#affichage").hide();
initialize_arrays();
var fext = fileName.substr(fileName.lastIndexOf('.')+1);
orid = false; // 'OR1A1';
try
{
orid = fileName.match(/(OR[0-9]{1,2}[A-Z]{1,2}|TAAR|VN1R)[0-9]{1,2}/)[0];
}
catch (e)
{
;
}
$.ajax(
{
url: website + "/recepinfo.php",
data:
{
recep: orid,
},
fext: fext,
fileData: fileData,
success: function(poresult)
{
poresult = poresult.split("\n");
bw50r = new Array(99).fill(0);
var i;
for (i=0; i<poresult.length; i++)
{
var ln = poresult[i];
if (ln.substr(0, 6) == "METAL|")
{
var words = ln.split("|");
var j;
for (j=1; j<words.length; j++)
{
var m = words[j].match(/[0-9]{3}[:]/);
if (m && m.length)
mtlcoord.push(parseInt(m[0]));
}
}
if (ln.substr(0, 7) == "REGION|")
{
var words = ln.split("|");
if (words[1].substr(0, 3) == "TMR" || words[1].substr(0, 3) == "HXR")
{
var tmr = parseInt(words[1].substr(3));
tmstart[tmr] = parseInt(words[2]);
tmend[tmr] = parseInt(words[3]);
}
}
if (ln.substr(0, 3) == "BW|")
{
var words = ln.split("|");
var tmr = parseInt(words[1].split('.')[0]);
bw50r[tmr] = parseInt(words[2]);
}
if (ln.substr(0, 7) == "POCKET|")
{
if (!pocket[0] && !pocket[1] && !pocket[2]) // Only care about the first one for now.
{
var words = ln.split("|");
var j;
for (j=1; j<words.length; j++)
{
var kv = words[j].split('=');
if (kv.length > 1)
{
if (kv[0] == 'center_x') pocket[0] = parseFloat(kv[1]);
if (kv[0] == 'center_y') pocket[1] = parseFloat(kv[1]);
if (kv[0] == 'center_z') pocket[2] = parseFloat(kv[1]);
$('#pktbtn').show();
}
}
}
}
}
var fext = this.fext;
switch (fext)
{
case 'sdf':
case 'pdb':
$("#vstats").hide();
stage.removeAllComponents();
visicomp = [];
window.result = fileData;
cen_ligand = false;
initialize_arrays();
bw50r = new Array(99).fill(0);
if (fext == 'pdb')
{
disable_spacefill();
hydrogens = false;
$("#nohyd").click();
var i;
var lines = fileData.split("\n");
var lres = 0;
cavities = [];
var tmpstr = "";
var ligtmp = "";
var h2otmp = "";
var strandid = "A";
var last_strandid = "";
var strand_has_tms = false;
for (i=0; i<lines.length; i++)
{
var ln = lines[i];
if ((ln.substr(0, 6) == "HETATM" || ln.substr(17,3) == "LIG"))
{
if (ln.substr(17,3) != "HOH" && ln.substr(17,3)) ligtmp += ln + "\n";
else h2otmp += ln + "\n";
}
if (ln.substr(0, 3) == 'TER') strand_has_tms = false;
if (ln.substr(0, 6) == 'REMARK')
{
var pieces = ln.split(" ");
if (pieces[2] == 'HELIX' && (pieces[3].substr(0,3) == 'TMR' || pieces[3].substr(0,3) == 'HXR'))
{
var tmrno = parseInt(pieces[3].substr(-1));
tmstart[tmrno] = parseInt(pieces[4]);
tmend[tmrno] = parseInt(pieces[5]);
strand_has_tms = true;
// tmstrand = []; // Force reassignment later on.
}
else if (pieces[3] == "LIGAND_BINDING")
{
var resno = parseInt(pieces[4]);
ligbs.push(resno);
}
else if (pieces[3] == "BW")
{
var tmr = parseInt(pieces[4]);
var resno = parseInt(pieces[5]);
bw50r[tmr] = resno;
}
else if (pieces[3] == "MCOORD")
{
var resno = parseInt(pieces[4]);
mcres.push(resno);
}
else if (pieces[1] == "503") process_lsrb_ln(ln, 1, 0);
else if (pieces[1] == "821" && typeof pieces[3] != "undefined")
{
process_cavity_ln(ln);
}
}
else
{
var resno = parseInt(ln.substr(22,4));
strandid = ln.substr(21,1).trim();
if (!strandid) strandid = "A";
var aa1let = aa_1let_from_3let(ln.substr(17,3).trim());
if (/* !tmstrand.length && */ strand_has_tms && tmstart[6] && (tmstrand.indexOf(strandid) < 0) ) tmstrand.push(strandid);
if (lres != resno)
{
if (ln.length > 20 || ln.trim() == "TER")
{
if (aa1let != '?' || ln.trim() == "TER")
{
var stringBlob6 = new Blob( [tmpstr], { type: 'text/plain'} );
stage.loadFile( stringBlob6, { ext: 'pdb' } ).then( function( comp6 )
{
resmdl.push(comp6);
restoggled.push(0);
});
// console.log(tmpstr);
// console.log(aa1let + resno + " of strand " + strandid);
if (isNaN(resno)) resno = 0;
lres = resno;
mdlresno.push(resno);
resstrandid.push(strandid);
tmpstr = "";
sequence.push(aa1let);
}
}
}
}
if (ln.length < 20) continue;
tmpstr += ln + "\n";
last_strandid = strandid;
}
finish_cavity_lines();
/*if (tmpstr)
{
var stringBlob6a = new Blob( [tmpstr], { type: 'text/plain'} );
stage.loadFile( stringBlob6a, { ext: 'pdb' } ).then( function( comp6a )
{
resmdl.push(comp6a);
restoggled.push(0);
});
if (isNaN(resno)) resno = 0;
mdlresno.push(resno);
resstrandid.push(last_strandid);
sequence.push(aa1let);
}*/
if (ligtmp.length)
{
var stringBlob6b = new Blob( [ ligtmp ], { type: 'text/plain'} );
stage.loadFile( stringBlob6b, { ext: 'pdb', name: "ligand" } ).then( function( comp6b )
{
var rparam =
{
opacity: opc_ligand,
multipleBond: true,
colorScheme: PODefSchemeLigand,
metalness: mtl_bs,
};
model.push(comp6b);
mrep.push("ball+stick");
mrparams.push(rparam);
is_ligand.push(1);
curr_ligand = comp6b;
ligand_params = rparam;
if (curr_ligand) $('#ligbtn, #prsv').show();
var lpn = comp6b.name.split("|");
mpos.push(parseInt(lpn[0]));
mnod.push(parseInt(lpn[1]));
$('#clip').trigger("input");
curr_ligand.addRepresentation( "licorice", rparam );
} );
ligtmp = "";
}
if (h2otmp.length)
{
var stringBlob6b = new Blob( [ h2otmp ], { type: 'text/plain'} );
stage.loadFile( stringBlob6b, { ext: 'pdb', name: "ligand" } ).then( function( comp6b )
{
var rparam =
{
opacity: opc_ligand,
multipleBond: true,
colorScheme: PODefSchemeLigand,
metalness: mtl_bs,
};
model.push(comp6b);
mrep.push("ball+stick");
mrparams.push(rparam);
is_ligand.push(0);
if (curr_ligand) $('#ligbtn, #prsv').show();
var lpn = comp6b.name.split("|");
mpos.push(parseInt(lpn[0]));
mnod.push(parseInt(lpn[1]));
$('#clip').trigger("input");
comp6b.addRepresentation( "licorice", rparam );
} );
h2otmp = "";
}
}
if (fext == 'sdf')
{
$('#posey').show();
$('#posey')[0].innerText = fileData.split("\n")[0];
enable_spacefill();
}
var fileStrands = fileData.split("\nTER");
fileStrands.forEach(function(strandData)
{
if (fext != "sdf" && (strandData.trim().length < 20 || strandData.indexOf("\nATOM ") < 0)) return;
var strandid = strandData.substr(strandData.indexOf("\nATOM "), 100).trim().substr(21,1).trim();
if (!strandid) strandid = "A";
var stringBlob = new Blob( [ strandData ], { type: 'text/plain'} );
stage.loadFile( stringBlob, { ext: fext, name: strandid } ).then( ( comp ) =>
{
if (fext == 'sdf')
{
var rp =
{
opacity: opc_molecule,
colorScheme: PODefSchemeHilite,
multipleBond: true,
metalness: mtl_bs,
};
comp.addRepresentation( "ball+stick", rp);
gmodel.push(comp);
gmvisible.push(true);
mdlligands.push(comp);
gmrep.push("ball+stick");
gmrparams.push(rp);
comp.autoView();
}
if (fext == 'pdb')
{
var rp =
{
opacity: opc_cartoon,
colorScheme: (tmstrand.indexOf(comp.name) >= 0) ? PODefRgnScheme : POAAScheme,
// colorScale: 'rainbow',
metalness: mtl_cartoon,
};
comp.addRepresentation( "cartoon", rp);
gmodel.push(comp);
gmvisible.push(true);
mdlstrands.push(comp);
gmrep.push("cartoon");
gmrparams.push(rp);
var i;
var subset = [], shiny = [];
var result = window.result.split("\n");
for (i=0; i<result.length; i++)
{
var ln = result[i];
var resno = parseInt(ln.substr(22,4));
var aname = ln.substr(12,4).trim();
if (mtlcoord.indexOf(resno) >= 0
&& aname != "N"
&& aname != "HN"
&& aname != "H"
&& aname != "CA"
&& aname != "HA"
&& aname != "HA1"
&& aname != "HA2"
// Due to a bug in NGL, the C and O atoms are required if including CA in
// licorice, ball+stick, or line mode. Hyperball avoids this but is slower to render.
// && aname != "C"
// && aname != "O"
) subset.push(ln);
if (ln.substr(17,3) == "MTL") shiny.push(ln);
}
var stringBlob2 = new Blob( [ shiny.join("\n") ], { type: 'text/plain'} );
stage.loadFile( stringBlob2, { ext: 'pdb' } ).then( function( comp2 )
{
var rp =
{
opacity: opc_metal,
colorScheme: PODefScheme,
metalness: mtl_metal,
};
comp2.addRepresentation( "spacefill", rp);
gmodel.push(comp2);
gmvisible.push(true);
mdlligands.push(comp2);
gmrep.push("spacefill");
gmrparams.push(rp);
});
stage.autoView();
if (!hydrogens) $("#nohyd").click();
}
} );
mdlstrandid.push(strandid);
});
if (fext != 'sdf') $("#affichage").show();
break;
case 'txt':
case 'dock':
dock_result_txt = [];
stage.removeAllComponents();
visicomp = [];
var lines = fileData.split("\n");
cen_ligand = true;
disable_spacefill();
hydrogens = false;
$("#nohyd").click();
var i;
var mod = "m";
for (i=0; i<100; i++)
{
if (lines[i].substr(0, 10) == "PDB file: ")
{
if (lines[i].indexOf(".metal.") < 0) mod = "";
break;
}
}
var lln = lines.length;
var lpose = -1, lnode = -1, llpose = -1, llnode = -1;
var reading_benerg = false;
cavities = [];
for (i=0; i<lln; i++)
{
if (lines[i].substr(0,10) == "REMARK 503") process_lsrb_ln(lines[i], llpose, llnode);
else if (lines[i].substr(0,10) == "REMARK 821") process_cavity_ln(lines[i]);
else if (lines[i].substr(0, 6) == "Pose: ")
{
llpose = lpose = parseInt(lines[i].substr(6));
if (typeof dock_result_txt[lpose] == "undefined") dock_result_txt[lpose] = [];
}
else if (lines[i].substr(0, 6) == "Node: ")
{
llnode = lnode = parseInt(lines[i].substr(6));
dock_result_txt[lpose][lnode] = "";
$("#vstats").show();
}
else if (lines[i] == "Original PDB:")
{
lpose = lnode = -1;
orid = false;
var pdbdat = "";
for (i++; i<lln; i++) pdbdat += lines[i] + "\n";
apply_pdb(pdbdat);
}
else if (lines[i].substr(0, 7) == "ATOM " || lines[i].substr(0, 7) == "HETATM " || lines[i] == "# PDB Data" || lines[i] == "PDBDAT:")
{
lpose = lnode = -1;
if (llpose >= 0 && llnode >= 0)
{
if (lines[i].substr(0, 7) == "ATOM " || lines[i].substr(0, 7) == "HETATM ")
{
var resno = parseInt(lines[i].substr(20,6));
var aname = lines[i].substr(11, 6).trim();
var x = parseFloat(lines[i].substr(30, 8));
var y = parseFloat(lines[i].substr(38, 8));
var z = parseFloat(lines[i].substr(46, 8));
var esym = lines[i].substr(77, 2).replace(/[+-]/g, '');
if (lines[i].substr(0, 7) == "ATOM ")
{
if (typeof resapos[llpose] == 'undefined') resapos[llpose] = [];
if (typeof resapos[llpose][llnode] == 'undefined') resapos[llpose][llnode] = [];
if (typeof resapos[llpose][llnode][resno] == 'undefined') resapos[llpose][llnode][resno] = {};
resapos[llpose][llnode][resno][aname] = [x, y, z, esym.trim()];
}
else if (lines[i].substr(0, 7) == "HETATM "
&& lines[i].substr(17,3) != "HOH" && lines[i].substr(17,3) != "H2O"
)
{
if (typeof ligapos[llpose] == 'undefined') ligapos[llpose] = [];
if (typeof ligapos[llpose][llnode] == 'undefined') ligapos[llpose][llnode] = {};
ligapos[llpose][llnode][aname] = [x, y, z, esym.trim()];
}
}
}
}
else if (lpose >= 0 && lnode >= 0)
{
dock_result_txt[lpose][lnode] += lines[i] + "\n";
}
}
for (i=0; i<lln; i++)
{
if (lines[i].trim() == "BENERG:")
{
reading_benerg = true;
}
else if (lines[i].substr(0, 6) == "Pose: ")
{
llpose = lpose = parseInt(lines[i].substr(6));
}
else if (lines[i].substr(0, 6) == "Node: ")
{
llnode = lnode = parseInt(lines[i].substr(6));
$("#vstats").show();
}
else if (lpose >= 0 && lnode >= 0)
{
if (reading_benerg)
{
var pieces = lines[i].split(':');
if (pieces.length < 2)
{
reading_benerg = false;
continue;
}
var resno = pieces[0];
if (!resno.match(/^[A-Za-z]{3}[0-9 ]{1,4}/))
{
reading_benerg = false;
continue;
}
resno = parseInt(resno.substr(3));
var energy = parseFloat(pieces[1]);
if (energy > -0.3) continue;
if (typeof resapos[lpose] == 'undefined') continue;
if (typeof resapos[lpose][lnode] == 'undefined') continue;
if (typeof resapos[lpose][lnode][resno] == 'undefined') continue;
if (typeof resapos[lpose][lnode][resno]['CA'] == 'undefined') continue;
var liga = nearest_lig_apos(lpose, lnode, resapos[lpose][lnode][resno]['CA']);
var resa = nearest_res_apos(lpose, lnode, resno, liga);
liga = nearest_lig_apos(lpose, lnode, resa);
resa = nearest_res_apos(lpose, lnode, resno, liga);
liga = nearest_lig_apos(lpose, lnode, resa);
var thing = [resa, liga, energy];
if (typeof visinter[lpose] == 'undefined') visinter[lpose] = [];
if (typeof visinter[lpose][lnode] == 'undefined') visinter[lpose][lnode] = [];
visinter[lpose][lnode].push(thing);
}
}
}
finish_cavity_lines();
if (orid)
{
$.ajax(
{
url: website + "/pdb.php",
data:
{
"p": orid,
"mod": mod,
},
success: function(poresult)
{
apply_pdb(poresult);
} // end orpdb success.
}); // end orpdb ajax.
} // end if orid.
$('#posey').show();
var posey = $('#posey')[0];
var i, writing=false, p=0, n=0;
var protmp = "", ligtmp = "", h2otmp = "";
posey.innerHTML = "Pose: ";
model = [];
is_ligand = [];
mpos = [];
mnod = [];
for (i=0; i<lln; i++)
{
var ln = lines[i];
if (ln == "Original PDB:") break;
if (ln.substr(0,6) == "Pose: ")
{
p = parseInt(ln.substr(6));
ligtmp += "REMARK 225 " + ln + "\n";
}
else if (ln.substr(0,6) == "Node: ")
{
n = parseInt(ln.substr(6));
ligtmp += "REMARK 225 " + ln + "\n";
}
else if (ln.substr(0,4) == "ACM ")
{
var words = ln.split(" ");
if (words.length < 11) continue;
acvnode = parseInt(words[1]);
var matrixln =
{
name: words[2],
sr: parseInt(words[3]),
er: parseInt(words[4]),
nx: parseFloat(words[5]),
ny: parseFloat(words[6]),
nz: parseFloat(words[7]),
cx: parseFloat(words[8]),
cy: parseFloat(words[9]),
cz: parseFloat(words[10]),
};
if (!acvmatrix.length) acvmatrix.push(matrixln);
else
{
var j;
var found = false;
for (j=0; j<acvmatrix.length; j++)
{
if (acvmatrix[j].name == matrixln.name)
{
acvmatrix[j] = matrixln;
found = true;
break;
}
}
if (!found) acvmatrix.push(matrixln);
}
}
else if (ln.substr(0,4) == "ACR ")
{
var words = ln.split(" ");
if (words.length < 11) continue;
acvnode = parseInt(words[1]);
acvmatrix = [];
var rot8ln =
{
name: words[2],
sr: parseInt(words[3]),
er: parseInt(words[4]),
tx: parseFloat(words[5]), // transform xyz.
ty: parseFloat(words[6]),
tz: parseFloat(words[7]),
ox: parseFloat(words[8]), // origin xyz.
oy: parseFloat(words[9]),
oz: parseFloat(words[10]),
ax: parseFloat(words[11]), // axis xyz, relative to origin.
ay: parseFloat(words[12]),
az: parseFloat(words[13]),
angle: parseFloat(words[14]), // radians.
};
if (!acvrot8.length) acvrot8.push(rot8ln);
else
{
var j;
var found = false;
for (j=0; j<acvrot8.length; j++)
{
if (acvrot8[j].name == rot8ln.name)
{
acvrot8[j] = rot8ln;
found = true;
break;
}
}
if (!found) acvrot8.push(rot8ln);
}
}
else if (ln.trim() == "PDBDAT:")
{
if (p>0) writing = true;
}
else if (ln.trim() == "END")
{
if (!n)
{
var btnid = "posebtn"+p;
if (!$('#'+btnid).length)
{
var posea = document.createElement("a");
posea.className = "posebtn";
if (p==1) $(posea).addClass("hilite");
posea.innerText = p;
posea.id = btnid;
posea.setAttribute("onclick", "showPose("+p+");");
posey.appendChild(posea);
}
}
if (writing)
{
var stringBlob7a = new Blob( [ protmp ], { type: 'text/plain'} );
stage.loadFile( stringBlob7a, { ext: 'pdb', name: p+"|"+n } ).then( function( comp7a )
{
var rparam =
{
opacity: opc_sidechain_active,
colorScheme: PODefSchemeHilite,
metalness: mtl_licorice,
};
model.push(comp7a);
mrep.push("licorice");
mrparams.push(rparam);
is_ligand.push(0);
var lpn = comp7a.name.split("|");
mpos.push(parseInt(lpn[0]));
mnod.push(parseInt(lpn[1]));
$('#clip').trigger("input");
} );
var stringBlob7b = new Blob( [ ligtmp ], { type: 'text/plain'} );
stage.loadFile( stringBlob7b, { ext: 'pdb', name: p+"|"+n } ).then( function( comp7b )
{
var rparam =
{
opacity: opc_ligand,
multipleBond: true,
colorScheme: PODefSchemeLigand,
metalness: mtl_bs,
};
model.push(comp7b);
mrep.push("licorice");
mrparams.push(rparam);
is_ligand.push(1);
if (!curr_ligand)
{
curr_ligand = comp7b;
ligand_params = rparam;
window.setTimeout(function()
{
showPose(1);
if (!hydrogens) $("#nohyd").click();
// curr_ligand.autoView();
}, 259);
}
var lpn = comp7b.name.split("|");
mpos.push(parseInt(lpn[0]));
mnod.push(parseInt(lpn[1]));
$('#clip').trigger("input");
} );
if (h2otmp.length)
{
var stringBlob7c = new Blob( [ h2otmp ], { type: 'text/plain'} );
stage.loadFile( stringBlob7c, { ext: 'pdb', name: p+"|"+n } ).then( function( comp7c )
{
var rparam =
{
opacity: opc_ligand,
multipleBond: true,
colorScheme: PODefSchemeLigand,
metalness: mtl_bs,
};
model.push(comp7c);
mrep.push("licorice");
mrparams.push(rparam);
is_ligand.push(0);
var lpn = comp7c.name.split("|");
mpos.push(parseInt(lpn[0]));
mnod.push(parseInt(lpn[1]));
$('#clip').trigger("input");
} );
}
}
writing = false;
protmp = ligtmp = h2otmp = "";
}
else if (writing)
{
if (ln.substr(0,6) == "HETATM" || ln.substr(17,3) == "LIG")
{
if (ln.substr(17,3) != "HOH" && ln.substr(17,3) != "H2O") ligtmp += ln + "\n";
else h2otmp += ln + "\n";
}
else protmp += ln + "\n";
}
}
window.setTimeout(function()
{
showPose(1);
// curr_ligand.autoView();
}, 259);
$("#affichage").show();
break;
default:
alert('Unknown file type ' + fext);
}
window.setTimeout(function()
{
$("#pleasewait").hide();
if (curr_ligand) curr_ligand.autoView();
$('#clip').trigger("input");
showPose(1);
}, 1536);
$("#clip").trigger("input");
}
});
}
function do_initial_load()
{
if (molid == "none") return;
var url = getParameterByName('url') ? getParameterByName('url') : website+'/sdf.php';
var literal_pdb = false;
var literal_fname = "";
if (literal_pdb)
{
loadFile(literal_pdb, literal_fname);
}
else if (protid)
{
load_remote_pdb(url);
}
else if (molid != "~")
{
load_remote_sdf(url);
}
}
if (!is_localhost) $.ajax(
{
url: test + "/instcheck.php",
cache: false,
success: function(result)
{
if (result == "b00d1cca")
{
website = test;
is_localhost = true;
do_initial_load();
}
},
error: function(result)
{
test = "http://127.0.0.1/primarydock";
if (!is_localhost) $.ajax(
{
url: test + "/instcheck.php",
cache: false,
success: function(result)
{
if (result == "b00d1cca")
{
website = test;
is_localhost = true;
do_initial_load();
}
},
error: function(result)
{
do_initial_load();
}
});
}
});
</script>
<style>
body
{
color: #69c;
width: 100%;
height: 100%;
overflow: hidden;
}
body.whtbk
{
color: #346;
background-color: #fed;
}
a
{ color: #2af;
text-decoration: none;
}
body.whtbk a
{
color: #259;
}
a:hover
{
text-decoration: underline;
}
#pleasewait
{
position: fixed;
top: 22%;
left: 40%;
right: 40%;
width: 20%;
text-align: center;
background-color: rgba(0,11,31,0.67);
color: #def;
padding: 15px;
border-radius: 25px;
box-shadow: 0px 0px 41px rgba(0,0,0,0.22), 5px 3px 5px rgba(0,0,0,0.41);
}
body.whtbk #pleasewait
{
background-color: rgba(224, 240, 255, 0.67);
}
#citefloat
{
position: fixed;
text-align: right;
right: 25px;
bottom: 15px;
font-family: Verdana, Arial, Sans-Serif;
font-size: 11px;
}
#citefloat, #citefloat a
{
color: #036;
}
#citefloat span
{
background-color: rgba(0,0,0,0.53);
color: rgba(0, 128, 255, 0);
font-size: 15px;
transition: color 2s, height 2s;