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