mirror of
https://github.com/schrodinger/pymol-open-source.git
synced 2026-06-04 20:04:21 +08:00
e514db1056
- fix "File > Open" from drive root on Windows - std::array replacement for pre-C++11 - define NOMINMAX, fmax -> std::max - correct setting-level handling in presets - unset: restore default for string/float3/color, warn for int/bool/float - fix "Display > Sequence" needs redisplay - migrate seq_view_label_color=white from old PSE - remove machine generated code from web/pymolhttpd.py - fix segfault in read_pdbx_struct_assembly
1139 lines
43 KiB
JavaScript
1139 lines
43 KiB
JavaScript
// This file contains source code for the PyMOL computer program
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// Copyright (c) Schrodinger, LLC.
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var pymol_fn_counter = 0;
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function PyMOL(host, port, bufferMode, prefix) {
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this.Path = "/apply?_json="; // URL path to pass json args to pymol
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// now using _underscore_names for internal attributes & methods
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this._cmd_buffer = [];
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// do we throw up visible alerts when exceptions occur?
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this._alerts = true;
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this._host = host;
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this._port = port;
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this._parseBufferMode = function (bufferMode) {
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if ((bufferMode != undefined) && (bufferMode == 'on')) {
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return 'on';
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} else {
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return 'off';
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}
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}
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this._bufferMode = this._parseBufferMode(bufferMode);
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if(prefix == undefined) {
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this._prefix = 'pymol'; // default remote object name
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} else {
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this._prefix = prefix;
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}
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try {
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xmlhttp = new XMLHttpRequest();
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} catch(e) {
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xmlhttp = new ActiveXObject("Microsoft.XMLHTTP");
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}
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this.setBufferMode = function(bufferMode) {
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this._bufferMode = this._parseBufferMode(bufferMode);
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if (this._bufferMode == 'off') {
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this.flush();
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}
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}
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this.flush = function(callback) {
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if (this._cmd_buffer.length > 0) {
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var result = this._json('[' + this._cmd_buffer.join(',') + ']', callback);
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this._cmd_buffer.length = 0;
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return result;
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}
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}
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this.getBufferJSON = function() {
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return ('[' + this._cmd_buffer.join(',') + ']');
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}
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this.getBufferURL = function() {
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return (this.Path + '[' + this._cmd_buffer.join(',') + ']');
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}
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this._send_ajax = function(pypath, callback) {
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if (host == null) {
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myurl = pypath;
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} else {
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myurl = "http://" + host + ":" + port + pypath;
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}
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if(myurl.length>2000) { /* some broswers can't handle long URLs */
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var part = myurl.split("?",2);
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short_url = part[0];
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long_param = part[1];
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if (callback) {
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xmlhttp.open("POST", short_url, true);
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xmlhttp.onreadystatechange = callback;
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} else {
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xmlhttp.open("POST", short_url, false);
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}
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xmlhttp.setRequestHeader("Content-type", "application/x-www-form-urlencoded");
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xmlhttp.setRequestHeader("Content-length", long_param.length);
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xmlhttp.setRequestHeader('Accept', 'text/json');
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xmlhttp.send(long_param);
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} else {
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if (callback) {
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xmlhttp.open("GET", myurl, true);
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xmlhttp.onreadystatechange = callback;
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} else {
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xmlhttp.open("GET", myurl, false);
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}
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xmlhttp.setRequestHeader('Accept', 'text/json');
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xmlhttp.send(null);
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}
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if (callback) {
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} else {
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if (xmlhttp.status == 500) {
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alert("PyMOL Exception:\n" + eval('(' + xmlhttp.responseText + ')').join("\n"));
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return null;
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}
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return eval('(' + xmlhttp.responseText + ')');
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}
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return false;
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}
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this._send_cross_script = function(pypath, callback) {
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if (host == null) {
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myurl = pypath;
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} else {
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myurl = "http://" + host + ":" + port + pypath;
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}
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if (callback == undefined) {
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//myurl += "&_callback=alert"
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myurl += "&_callback=void"
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} else {
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// IE does not have callback.name, so we invent a unique one
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// and store it in the "global" namespace, window. In this way,
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// the javascript callback from our cross-domain script hack
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// contains a javascript function name known to this page/window.
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if (callback.name == undefined) {
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callback.name = '_fn' + pymol_fn_counter++;
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window[ callback.name ] = callback;
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}
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myurl += "&_callback=" + callback.name;
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}
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var head = document.getElementsByTagName("head")[0];
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var script = document.createElement("script");
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script.src = myurl;
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head.appendChild(script);
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return true;
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}
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this._send = function(pypath, callback) {
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if ( (host == null) ||
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((host == document.domain) && (port == document.location.port)) ) {
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return this._send_ajax(pypath, callback);
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} else {
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return this._send_cross_script(pypath, callback);
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}
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}
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this._handle_response = function(status, text) {
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response = JSON.parse(text);
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if(status == 200) { // normal result
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return response;
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} else { // some kind of error condition
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if(this._alerts) {
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alert(response.join("\n"));
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}
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return;
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}
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}
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this._result = function(e) {
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if ((host == document.domain) || (host == null)) {
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if (typeof e == "object") {
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// asynchronous ajax was used
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if (xmlhttp.readyState == 4) {
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return this._handle_response(xmlhttp.status, xmlhttp.responseText);
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return;
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}
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}
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// "synchronous" (no-callback) ajax was used
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if(xmlhttp.responseText) {
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return this._handle_response(xmlhttp.status, xmlhttp.responseText);
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} else {
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return;
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}
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}
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// e was provided by cross-script callback, so just return it
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return e;
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}
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// for private use
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this._json = function(jcmd,callback) {
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return this._send(this.Path+jcmd,callback);
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}
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// for public use; args switched to match style of pymol.cmd calls
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this.sendJSON = function(anyargs) {
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if (typeof arguments[0] == 'function') {
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//this.sendJSON = function(callback, jcmd) {
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callback = arguments[0];
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jcmd = arguments[1];
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} else {
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//this.sendJSON = function(jcmd) {
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callback = null;
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jcmd = arguments[0];
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}
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return this._send(this.Path+jcmd,callback);
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}
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this._apply = function(name, args, kwds, callback) {
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// note: javascript's 'this' can refer to either pymol or cmd
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if (name.substring(0,1) == '.') { // .cmd.method -> pymol.cmd.method
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name = this._prefix + name;
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}
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var mypath = this.Path;
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var myargs = '["' + name + '"';
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if (args != null) {
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myargs = myargs + "," + JSON.stringify(args);
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if(kwds != null) {
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myargs = myargs + "," + JSON.stringify(kwds);
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}
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} else if(kwds != null) {
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myargs = myargs + ",[]," + JSON.stringify(kwds)
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}
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myargs = myargs + "]";
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// document.getElementById('debug').innerHTML = mypath;
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if (this._bufferMode == 'on') {
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this._cmd_buffer.push(myargs);
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if ( callback ) {
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this.flush(callback);
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} else {
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return;
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}
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} else {
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return this._send(mypath+myargs,callback);
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}
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}
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this.apply_cmd = function(name, args, kwds, callback) {
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this._apply(".cmd." + name, args, kwds, callback);
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}
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this.cmd = { // cmd is a public attribute of PyMOL instances
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_dispatch: function(anyargs) {
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// name is always first argument
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var name = ".cmd." + arguments[0];
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// callback function is optional second argument
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var callback = undefined;
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var argstart = 1;
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if (typeof arguments[1] == 'function') {
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callback = arguments[1];
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argstart = 2;
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}
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return this._outer._apply(name,Array.prototype.slice.apply(arguments).slice(argstart),null,callback);
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},
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// BEGIN MACHINE-GENERATED CODE
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// python webapi.py
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load: function() {
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return this._dispatch.apply(this,
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["load"].concat(Array.prototype.slice.apply(arguments)));
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},
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load_traj: function() {
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return this._dispatch.apply(this,
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["load_traj"].concat(Array.prototype.slice.apply(arguments)));
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},
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load_png: function() {
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return this._dispatch.apply(this,
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["load_png"].concat(Array.prototype.slice.apply(arguments)));
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},
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fragment: function() {
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return this._dispatch.apply(this,
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["fragment"].concat(Array.prototype.slice.apply(arguments)));
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},
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fetch: function() {
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return this._dispatch.apply(this,
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["fetch"].concat(Array.prototype.slice.apply(arguments)));
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},
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read_mmodstr: function() {
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return this._dispatch.apply(this,
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["read_mmodstr"].concat(Array.prototype.slice.apply(arguments)));
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},
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read_molstr: function() {
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return this._dispatch.apply(this,
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["read_molstr"].concat(Array.prototype.slice.apply(arguments)));
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},
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read_sdfstr: function() {
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return this._dispatch.apply(this,
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["read_sdfstr"].concat(Array.prototype.slice.apply(arguments)));
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},
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read_pdbstr: function() {
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return this._dispatch.apply(this,
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["read_pdbstr"].concat(Array.prototype.slice.apply(arguments)));
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},
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read_xplorstr: function() {
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return this._dispatch.apply(this,
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["read_xplorstr"].concat(Array.prototype.slice.apply(arguments)));
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},
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get_pdbstr: function() {
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return this._dispatch.apply(this,
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["get_pdbstr"].concat(Array.prototype.slice.apply(arguments)));
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},
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get_fastastr: function() {
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return this._dispatch.apply(this,
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["get_fastastr"].concat(Array.prototype.slice.apply(arguments)));
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},
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copy: function() {
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return this._dispatch.apply(this,
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["copy"].concat(Array.prototype.slice.apply(arguments)));
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},
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create: function() {
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return this._dispatch.apply(this,
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["create"].concat(Array.prototype.slice.apply(arguments)));
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},
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extract: function() {
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return this._dispatch.apply(this,
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["extract"].concat(Array.prototype.slice.apply(arguments)));
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},
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split_states: function() {
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return this._dispatch.apply(this,
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["split_states"].concat(Array.prototype.slice.apply(arguments)));
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},
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symexp: function() {
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return this._dispatch.apply(this,
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["symexp"].concat(Array.prototype.slice.apply(arguments)));
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},
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ramp_new: function() {
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return this._dispatch.apply(this,
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["ramp_new"].concat(Array.prototype.slice.apply(arguments)));
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},
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set_name: function() {
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return this._dispatch.apply(this,
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["set_name"].concat(Array.prototype.slice.apply(arguments)));
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},
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map_new: function() {
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return this._dispatch.apply(this,
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["map_new"].concat(Array.prototype.slice.apply(arguments)));
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},
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map_set: function() {
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return this._dispatch.apply(this,
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["map_set"].concat(Array.prototype.slice.apply(arguments)));
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},
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map_set_border: function() {
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return this._dispatch.apply(this,
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["map_set_border"].concat(Array.prototype.slice.apply(arguments)));
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},
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map_double: function() {
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return this._dispatch.apply(this,
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["map_double"].concat(Array.prototype.slice.apply(arguments)));
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},
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map_halve: function() {
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return this._dispatch.apply(this,
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["map_halve"].concat(Array.prototype.slice.apply(arguments)));
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},
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map_trim: function() {
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return this._dispatch.apply(this,
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["map_trim"].concat(Array.prototype.slice.apply(arguments)));
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},
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isodot: function() {
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return this._dispatch.apply(this,
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["isodot"].concat(Array.prototype.slice.apply(arguments)));
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},
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isolevel: function() {
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return this._dispatch.apply(this,
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["isolevel"].concat(Array.prototype.slice.apply(arguments)));
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},
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isomesh: function() {
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return this._dispatch.apply(this,
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["isomesh"].concat(Array.prototype.slice.apply(arguments)));
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},
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isosurface: function() {
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return this._dispatch.apply(this,
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["isosurface"].concat(Array.prototype.slice.apply(arguments)));
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},
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slice_new: function() {
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return this._dispatch.apply(this,
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["slice_new"].concat(Array.prototype.slice.apply(arguments)));
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},
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gradient: function() {
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return this._dispatch.apply(this,
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["gradient"].concat(Array.prototype.slice.apply(arguments)));
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},
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ungroup: function() {
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return this._dispatch.apply(this,
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["ungroup"].concat(Array.prototype.slice.apply(arguments)));
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},
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group: function() {
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return this._dispatch.apply(this,
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["group"].concat(Array.prototype.slice.apply(arguments)));
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},
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pseudoatom: function() {
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return this._dispatch.apply(this,
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["pseudoatom"].concat(Array.prototype.slice.apply(arguments)));
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},
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fab: function() {
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return this._dispatch.apply(this,
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["fab"].concat(Array.prototype.slice.apply(arguments)));
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},
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enable: function() {
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return this._dispatch.apply(this,
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["enable"].concat(Array.prototype.slice.apply(arguments)));
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},
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disable: function() {
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return this._dispatch.apply(this,
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["disable"].concat(Array.prototype.slice.apply(arguments)));
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},
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delete_: function() {
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return this._dispatch.apply(this,
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["delete_"].concat(Array.prototype.slice.apply(arguments)));
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},
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reinitialize: function() {
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return this._dispatch.apply(this,
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["reinitialize"].concat(Array.prototype.slice.apply(arguments)));
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},
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deselect: function() {
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return this._dispatch.apply(this,
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["deselect"].concat(Array.prototype.slice.apply(arguments)));
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},
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select: function() {
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return this._dispatch.apply(this,
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["select"].concat(Array.prototype.slice.apply(arguments)));
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},
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indicate: function() {
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return this._dispatch.apply(this,
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["indicate"].concat(Array.prototype.slice.apply(arguments)));
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},
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select_list: function() {
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return this._dispatch.apply(this,
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["select_list"].concat(Array.prototype.slice.apply(arguments)));
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},
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pop: function() {
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return this._dispatch.apply(this,
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["pop"].concat(Array.prototype.slice.apply(arguments)));
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},
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angle: function() {
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return this._dispatch.apply(this,
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["angle"].concat(Array.prototype.slice.apply(arguments)));
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},
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dihedral: function() {
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return this._dispatch.apply(this,
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["dihedral"].concat(Array.prototype.slice.apply(arguments)));
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},
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dist: function() {
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return this._dispatch.apply(this,
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["dist"].concat(Array.prototype.slice.apply(arguments)));
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},
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distance: function() {
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return this._dispatch.apply(this,
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["distance"].concat(Array.prototype.slice.apply(arguments)));
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},
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get_angle: function() {
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return this._dispatch.apply(this,
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["get_angle"].concat(Array.prototype.slice.apply(arguments)));
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},
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get_dihedral: function() {
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return this._dispatch.apply(this,
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["get_dihedral"].concat(Array.prototype.slice.apply(arguments)));
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},
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get_distance: function() {
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return this._dispatch.apply(this,
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["get_distance"].concat(Array.prototype.slice.apply(arguments)));
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},
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get_area: function() {
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return this._dispatch.apply(this,
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["get_area"].concat(Array.prototype.slice.apply(arguments)));
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},
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color: function() {
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return this._dispatch.apply(this,
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["color"].concat(Array.prototype.slice.apply(arguments)));
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},
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bg_color: function() {
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return this._dispatch.apply(this,
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["bg_color"].concat(Array.prototype.slice.apply(arguments)));
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},
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rebuild: function() {
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return this._dispatch.apply(this,
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["rebuild"].concat(Array.prototype.slice.apply(arguments)));
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},
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refresh: function() {
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return this._dispatch.apply(this,
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["refresh"].concat(Array.prototype.slice.apply(arguments)));
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},
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recolor: function() {
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return this._dispatch.apply(this,
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["recolor"].concat(Array.prototype.slice.apply(arguments)));
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},
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set_color: function() {
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return this._dispatch.apply(this,
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["set_color"].concat(Array.prototype.slice.apply(arguments)));
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},
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set_object_color: function() {
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return this._dispatch.apply(this,
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["set_object_color"].concat(Array.prototype.slice.apply(arguments)));
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},
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show: function() {
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return this._dispatch.apply(this,
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["show"].concat(Array.prototype.slice.apply(arguments)));
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},
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show_as: function() {
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return this._dispatch.apply(this,
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["show_as"].concat(Array.prototype.slice.apply(arguments)));
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},
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hide: function() {
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return this._dispatch.apply(this,
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["hide"].concat(Array.prototype.slice.apply(arguments)));
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},
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cartoon: function() {
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return this._dispatch.apply(this,
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["cartoon"].concat(Array.prototype.slice.apply(arguments)));
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},
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spectrum: function() {
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return this._dispatch.apply(this,
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["spectrum"].concat(Array.prototype.slice.apply(arguments)));
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},
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center: function() {
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return this._dispatch.apply(this,
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["center"].concat(Array.prototype.slice.apply(arguments)));
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},
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zoom: function() {
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return this._dispatch.apply(this,
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["zoom"].concat(Array.prototype.slice.apply(arguments)));
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},
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reset: function() {
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return this._dispatch.apply(this,
|
|
["reset"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
clip: function() {
|
|
return this._dispatch.apply(this,
|
|
["clip"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
orient: function() {
|
|
return this._dispatch.apply(this,
|
|
["orient"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
origin: function() {
|
|
return this._dispatch.apply(this,
|
|
["origin"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
set_view: function() {
|
|
return this._dispatch.apply(this,
|
|
["set_view"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_view: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_view"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
move: function() {
|
|
return this._dispatch.apply(this,
|
|
["move"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
turn: function() {
|
|
return this._dispatch.apply(this,
|
|
["turn"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
rock: function() {
|
|
return this._dispatch.apply(this,
|
|
["rock"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
stereo: function() {
|
|
return this._dispatch.apply(this,
|
|
["stereo"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get: function() {
|
|
return this._dispatch.apply(this,
|
|
["get"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
set: function() {
|
|
return this._dispatch.apply(this,
|
|
["set"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
set_bond: function() {
|
|
return this._dispatch.apply(this,
|
|
["set_bond"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
unset: function() {
|
|
return this._dispatch.apply(this,
|
|
["unset"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
unset_bond: function() {
|
|
return this._dispatch.apply(this,
|
|
["unset_bond"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_setting_boolean: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_setting_boolean"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_setting_int: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_setting_int"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_setting_float: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_setting_float"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_setting_tuple: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_setting_tuple"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_setting_text: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_setting_text"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
window: function() {
|
|
return this._dispatch.apply(this,
|
|
["window"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
viewport: function() {
|
|
return this._dispatch.apply(this,
|
|
["viewport"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
full_screen: function() {
|
|
return this._dispatch.apply(this,
|
|
["full_screen"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
quit: function() {
|
|
return this._dispatch.apply(this,
|
|
["quit"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
draw: function() {
|
|
return this._dispatch.apply(this,
|
|
["draw"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
ray: function() {
|
|
return this._dispatch.apply(this,
|
|
["ray"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
align: function() {
|
|
return this._dispatch.apply(this,
|
|
["align"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
super_: function() {
|
|
return this._dispatch.apply(this,
|
|
["super_"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
fit: function() {
|
|
return this._dispatch.apply(this,
|
|
["fit"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
rms: function() {
|
|
return this._dispatch.apply(this,
|
|
["rms"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
rms_cur: function() {
|
|
return this._dispatch.apply(this,
|
|
["rms_cur"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
intra_fit: function() {
|
|
return this._dispatch.apply(this,
|
|
["intra_fit"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
intra_rms: function() {
|
|
return this._dispatch.apply(this,
|
|
["intra_rms"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
intra_rms_cur: function() {
|
|
return this._dispatch.apply(this,
|
|
["intra_rms_cur"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
pair_fit: function() {
|
|
return this._dispatch.apply(this,
|
|
["pair_fit"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
space: function() {
|
|
return this._dispatch.apply(this,
|
|
["space"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
order: function() {
|
|
return this._dispatch.apply(this,
|
|
["order"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
edit_mode: function() {
|
|
return this._dispatch.apply(this,
|
|
["edit_mode"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
button: function() {
|
|
return this._dispatch.apply(this,
|
|
["button"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
config_mouse: function() {
|
|
return this._dispatch.apply(this,
|
|
["config_mouse"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
mouse: function() {
|
|
return this._dispatch.apply(this,
|
|
["mouse"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
mask: function() {
|
|
return this._dispatch.apply(this,
|
|
["mask"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
unmask: function() {
|
|
return this._dispatch.apply(this,
|
|
["unmask"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
count_atoms: function() {
|
|
return this._dispatch.apply(this,
|
|
["count_atoms"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_chains: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_chains"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_color_index: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_color_index"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_color_indices: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_color_indices"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_object_color_index: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_object_color_index"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_object_list: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_object_list"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_color_tuple: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_color_tuple"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_atom_coords: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_atom_coords"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_extent: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_extent"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_names: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_names"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_names_of_type: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_names_of_type"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_legal_name: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_legal_name"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_unused_name: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_unused_name"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_object_matrix: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_object_matrix"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_phipsi: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_phipsi"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_position: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_position"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_raw_alignment: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_raw_alignment"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_renderer: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_renderer"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_symmetry: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_symmetry"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_title: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_title"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_type: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_type"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_version: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_version"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
id_atom: function() {
|
|
return this._dispatch.apply(this,
|
|
["id_atom"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
identify: function() {
|
|
return this._dispatch.apply(this,
|
|
["identify"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
index: function() {
|
|
return this._dispatch.apply(this,
|
|
["index"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
phi_psi: function() {
|
|
return this._dispatch.apply(this,
|
|
["phi_psi"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
matrix_copy: function() {
|
|
return this._dispatch.apply(this,
|
|
["matrix_copy"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
matrix_reset: function() {
|
|
return this._dispatch.apply(this,
|
|
["matrix_reset"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
rotate: function() {
|
|
return this._dispatch.apply(this,
|
|
["rotate"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
translate: function() {
|
|
return this._dispatch.apply(this,
|
|
["translate"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
set_object_ttt: function() {
|
|
return this._dispatch.apply(this,
|
|
["set_object_ttt"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
set_dihedral: function() {
|
|
return this._dispatch.apply(this,
|
|
["set_dihedral"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
transform_object: function() {
|
|
return this._dispatch.apply(this,
|
|
["transform_object"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
transform_selection: function() {
|
|
return this._dispatch.apply(this,
|
|
["transform_selection"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
translate_atom: function() {
|
|
return this._dispatch.apply(this,
|
|
["translate_atom"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
update: function() {
|
|
return this._dispatch.apply(this,
|
|
["update"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
attach: function() {
|
|
return this._dispatch.apply(this,
|
|
["attach"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
bond: function() {
|
|
return this._dispatch.apply(this,
|
|
["bond"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
unbond: function() {
|
|
return this._dispatch.apply(this,
|
|
["unbond"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
cycle_valence: function() {
|
|
return this._dispatch.apply(this,
|
|
["cycle_valence"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
drag: function() {
|
|
return this._dispatch.apply(this,
|
|
["drag"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
dss: function() {
|
|
return this._dispatch.apply(this,
|
|
["dss"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
edit: function() {
|
|
return this._dispatch.apply(this,
|
|
["edit"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
unpick: function() {
|
|
return this._dispatch.apply(this,
|
|
["unpick"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
fix_chemistry: function() {
|
|
return this._dispatch.apply(this,
|
|
["fix_chemistry"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
flag: function() {
|
|
return this._dispatch.apply(this,
|
|
["flag"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
fuse: function() {
|
|
return this._dispatch.apply(this,
|
|
["fuse"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_editor_scheme: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_editor_scheme"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
h_add: function() {
|
|
return this._dispatch.apply(this,
|
|
["h_add"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
h_fill: function() {
|
|
return this._dispatch.apply(this,
|
|
["h_fill"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
h_fix: function() {
|
|
return this._dispatch.apply(this,
|
|
["h_fix"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
invert: function() {
|
|
return this._dispatch.apply(this,
|
|
["invert"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
torsion: function() {
|
|
return this._dispatch.apply(this,
|
|
["torsion"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
valence: function() {
|
|
return this._dispatch.apply(this,
|
|
["valence"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
clean: function() {
|
|
return this._dispatch.apply(this,
|
|
["clean"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
deprotect: function() {
|
|
return this._dispatch.apply(this,
|
|
["deprotect"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
protect: function() {
|
|
return this._dispatch.apply(this,
|
|
["protect"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
reference: function() {
|
|
return this._dispatch.apply(this,
|
|
["reference"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
remove: function() {
|
|
return this._dispatch.apply(this,
|
|
["remove"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
remove_picked: function() {
|
|
return this._dispatch.apply(this,
|
|
["remove_picked"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
rename: function() {
|
|
return this._dispatch.apply(this,
|
|
["rename"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
replace: function() {
|
|
return this._dispatch.apply(this,
|
|
["replace"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
sculpt_purge: function() {
|
|
return this._dispatch.apply(this,
|
|
["sculpt_purge"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
sculpt_deactivate: function() {
|
|
return this._dispatch.apply(this,
|
|
["sculpt_deactivate"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
sculpt_activate: function() {
|
|
return this._dispatch.apply(this,
|
|
["sculpt_activate"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
sculpt_iterate: function() {
|
|
return this._dispatch.apply(this,
|
|
["sculpt_iterate"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
set_geometry: function() {
|
|
return this._dispatch.apply(this,
|
|
["set_geometry"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
set_symmetry: function() {
|
|
return this._dispatch.apply(this,
|
|
["set_symmetry"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
set_title: function() {
|
|
return this._dispatch.apply(this,
|
|
["set_title"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
smooth: function() {
|
|
return this._dispatch.apply(this,
|
|
["smooth"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
sort: function() {
|
|
return this._dispatch.apply(this,
|
|
["sort"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
undo: function() {
|
|
return this._dispatch.apply(this,
|
|
["undo"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
push_undo: function() {
|
|
return this._dispatch.apply(this,
|
|
["push_undo"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
redo: function() {
|
|
return this._dispatch.apply(this,
|
|
["redo"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
wizard: function() {
|
|
return this._dispatch.apply(this,
|
|
["wizard"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
replace_wizard: function() {
|
|
return this._dispatch.apply(this,
|
|
["replace_wizard"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
count_frames: function() {
|
|
return this._dispatch.apply(this,
|
|
["count_frames"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
count_states: function() {
|
|
return this._dispatch.apply(this,
|
|
["count_states"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
mset: function() {
|
|
return this._dispatch.apply(this,
|
|
["mset"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
madd: function() {
|
|
return this._dispatch.apply(this,
|
|
["madd"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
mclear: function() {
|
|
return this._dispatch.apply(this,
|
|
["mclear"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
mmatrix: function() {
|
|
return this._dispatch.apply(this,
|
|
["mmatrix"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
mdump: function() {
|
|
return this._dispatch.apply(this,
|
|
["mdump"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
mview: function() {
|
|
return this._dispatch.apply(this,
|
|
["mview"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
forward: function() {
|
|
return this._dispatch.apply(this,
|
|
["forward"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
backward: function() {
|
|
return this._dispatch.apply(this,
|
|
["backward"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
rewind: function() {
|
|
return this._dispatch.apply(this,
|
|
["rewind"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
middle: function() {
|
|
return this._dispatch.apply(this,
|
|
["middle"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
ending: function() {
|
|
return this._dispatch.apply(this,
|
|
["ending"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
mplay: function() {
|
|
return this._dispatch.apply(this,
|
|
["mplay"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
mtoggle: function() {
|
|
return this._dispatch.apply(this,
|
|
["mtoggle"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
mstop: function() {
|
|
return this._dispatch.apply(this,
|
|
["mstop"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
frame: function() {
|
|
return this._dispatch.apply(this,
|
|
["frame"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_movie_playing: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_movie_playing"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_state: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_state"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_frame: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_frame"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
view: function() {
|
|
return this._dispatch.apply(this,
|
|
["view"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
get_scene_list: function() {
|
|
return this._dispatch.apply(this,
|
|
["get_scene_list"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
scene: function() {
|
|
return this._dispatch.apply(this,
|
|
["scene"].concat(Array.prototype.slice.apply(arguments)));
|
|
},
|
|
scene_order: function() {
|
|
return this._dispatch.apply(this,
|
|
["scene_order"].concat(Array.prototype.slice.apply(arguments)));
|
|
}
|
|
|
|
// END MACHINE-GENERATED CODE
|
|
|
|
}
|
|
|
|
this.getattr = {
|
|
dispatch: function(attrname) {
|
|
if (attrname) {
|
|
mypath = "/getattr/pymol." + attrname;
|
|
this._outer._send(mypath);
|
|
}
|
|
}
|
|
// viewing: function() {
|
|
// this._dispatch("viewing");
|
|
// }
|
|
}
|
|
|
|
// enable inner pseudo-inner-instance to find the outer instance
|
|
|
|
this.cmd._outer = this
|
|
this.getattr._outer = this
|
|
}
|
|
|
|
// utility functions not used above, but of use to some users, one hopes
|
|
function parse_file(f) {
|
|
var re = /[\\\/]/;
|
|
fields = f.split(re);
|
|
filename = fields[fields.length-1];
|
|
dot = filename.lastIndexOf('.');
|
|
if (dot > -1) {
|
|
name = filename.slice(0,dot);
|
|
ext = filename.slice(dot);
|
|
} else {
|
|
name = filename;
|
|
ext = "";
|
|
}
|
|
// Javascript 1.7+ only in Mozilla?
|
|
// return [name, ext];
|
|
return new Array(name, ext);
|
|
}
|
|
function validate_file(n,f) {
|
|
if (f.value) {
|
|
// Javascript 1.7+ only in Mozilla?
|
|
// [name, ext] = parse_file(f.value);
|
|
parsed = parse_file(f.value);
|
|
name = parsed[0];
|
|
ext = parsed[1];
|
|
if (name) {
|
|
n.value = name;
|
|
//add_checkbox(name, "objects");
|
|
return true;
|
|
} else {
|
|
alert('cannot extract name from file');
|
|
return false;
|
|
}
|
|
} else {
|
|
alert('no file selected');
|
|
return false;
|
|
}
|
|
}
|