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// pdbshow.js to be included in an html doc to toggle on and
// off various representations fo proteins and ligands.
//
// These functions tied to onClick (or other) events.
// Toggle state is maintained by global variables here,
// such as load_state, cartoon_state, etc.
// These are implemented as a Hash object, defined in hash.js
// which must be included in the html file that includes this pdbshow.js
//
var load_state = new Hash;
var zoom = ""; // let first molecule zoom
function get_protein(a) {
// load protein, unless already loaded
if (load_state[a] == undefined) {
load = "load?filename=$PYMOL_PATH/modules/web/examples/data/" + a + ".pdb.gz" + zoom;
cmd(load);
zoom = "&zoom=0"; // subsequent loads shold not zoom
cmd("orient?selection=bymol organic and elem n&animate=2");
cmd("hide?representation=everything&selection=" + a);
load_state[a] = true;
cartoon_state[a] = false;
surface_state[a] = false;
nonbonded_state[a] = false;
ribbon_state[a] = false;
ligand_state[a] = false;
active_site_state[a] = false;
}
}
var cartoon_state = new Hash;
function toggle_cartoon(a) {
// toggle cartoon display
get_protein(a);
var arg = "representation=cartoon&selection=" + a;
if (cartoon_state[a] == true) {
cmd("hide?" + arg);
cartoon_state[a] = false;
} else {
cmd("show?" + arg);
cartoon_state[a] = true;
}
}
var surface_state = new Hash;
function toggle_surface(a) {
// toggle surface display
get_protein(a);
var arg = "representation=surface&selection=polymer and (" + a + " within 5 of bymol (" + a + " and organic and elem n))";
if (surface_state[a] == true) {
cmd("hide?" + arg);
surface_state[a] = false;
} else {
cmd("show?" + arg);
cmd("set?name=two_sided_lighting");
cmd("set?name=transparency&value=0.3");
surface_state[a] = true;
}
}
var ribbon_state = new Hash;
function toggle_ribbon(a) {
// toggle polymer ribbon display
get_protein(a);
var arg = "representation=ribbon&selection=" + a + " and polymer";
if (ribbon_state[a] == true) {
cmd("hide?" + arg);
ribbon_state[a] = false;
} else {
cmd("show?" + arg);
ribbon_state[a] = true;
}
}
var nonbonded_state = new Hash;
function toggle_nonbonded(a) {
// toggle solvent/water display
get_protein(a);
var arg = "representation=nonbonded&selection=(" + a + " and solvent) within 5 of bymol (" + a + " and organic and elem n)";
if (nonbonded_state[a] == true) {
cmd("hide?" + arg);
nonbonded_state[a] = false;
} else {
cmd("show?" + arg);
nonbonded_state[a] = true;
}
}
var ligand_state = new Hash;
function toggle_ligand(a) {
// toggle organic/ligand display
get_protein(a);
var arg = "representation=sticks&selection=bymol (" + a + " and organic and elem n)";
if (ligand_state[a] == true) {
cmd("hide?" + arg);
ligand_state[a] = false;
} else {
cmd("show?" + arg);
ligand_state[a] = true;
}
}
var active_site_state = new Hash;
function toggle_active_site(a) {
// toggle active site/polymer near organic display
get_protein(a);
var arg = "representation=lines&selection=byres polymer and (" + a + " within 5 of bymol (" + a + " and organic and elem n))";
if (active_site_state[a] == true) {
cmd("hide?" + arg);
active_site_state[a] = false;
} else {
cmd("show?" + arg);
active_site_state[a] = true;
}
}
var hb_state = new Hash;
function toggle_hb(a) {
// toggle hydrogen bond display
get_protein(a);
var arg = "name=" + a + "_hb";
var arg2 = arg + "&selection1=" + a + " and polymer" + "&selection2=" + a + " and organic" + "&cutoff=3.2&mode=2";
if (hb_state[a] == true) {
cmd("delete?" + arg);
hb_state[a] = false;
} else {
cmd("dist?" + arg2);
hb_state[a] = true;
}
}
function reinitialize() {
// reinitialize PyMOL and my state variables
// if ( confirm("Really reinitialize") ) {
cmd("reinitialize");
var keys = load_state.keys();
for (k in keys) {
a = keys[k];
load_state[a] = undefined;
cartoon_state[a] = 0;
surface_state[a] = 0;
nonbonded_state[a] = 0;
ribbon_state[a] = 0;
ligand_state[a] = 0;
active_site_state[a] = 0;
}
document.forms[0].reset();
zoom = "";
// }
}
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