Press n or j to go to the next uncovered block, b, p or k for the previous block.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 | 18x 18x 18x 18x 18x | //auto-initialization import { createViewer } from "./GLViewer"; import { SurfaceType } from "./ProteinSurface4"; import { specStringToObject } from "./utilities"; import { CC } from "./WebGL"; export var autoinit = false; export var processing_autoinit = false; declare var $; /** * Contains a dictionary of embedded viewers created from HTML elements * with a the viewer_3Dmoljs css class indexed by their id (or numerically * if they do not have an id). */ export var viewers: any = {}; //Create embedded viewer from HTML attributes if true //viewer and callback are used by the testing harness export function autoload(viewer?,callback?){ var i, dataname, type; Iif ($(".viewer_3Dmoljs")[0] !== undefined) autoinit = true; Iif (autoinit) { processing_autoinit = true; viewer =(viewer!= undefined) ? viewer :null; var nviewers = 0; $(".viewer_3Dmoljs").each( function() { var viewerdiv = $(this); var datauri = []; var datatypes = []; var uri = ''; var showUI = false; Iif(viewerdiv.css('position') == 'static') { //slight hack - canvas needs this element to be positioned viewerdiv.css('position','relative'); } Iif(viewerdiv.data('ui')) showUI = true; type = null; if (viewerdiv.data("pdb")) { datauri.push("https://files.rcsb.org/view/" + viewerdiv.data("pdb") + ".pdb"); datatypes.push("pdb"); } else if(viewerdiv.data("cid")) { //this doesn't actually work since pubchem does have CORS enabled datatypes.push("sdf"); datauri.push("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" + viewerdiv.data("cid") + "/SDF?record_type=3d"); } else Iif (viewerdiv.data("href") || viewerdiv.data("url")){ uri = viewerdiv.data("href"); datauri.push(uri); type = uri.substr(uri.lastIndexOf('.')+1); datatypes.push(type); var molName = uri.substring(uri.lastIndexOf('/') + 1, uri.lastIndexOf('.')); Iif(molName == '/') molName = uri.substring(uri.lastIndexOf('/') + 1); viewerdiv.data(datatypes[datatypes.length -1 ], molName); } var divdata=viewerdiv.data(); for(i in divdata){ if((i.substring(0,3) ==="pdb" && (i !== "pdb"))){ datauri.push("https://files.rcsb.org/view/" +divdata[i]+".pdb"); datatypes.push('pdb'); }else if(i.substring(0,4) ==="href" && (i!=="href")){ uri = divdata[i]; datauri.push(uri); datatypes.push(uri.substr(uri.lastIndexOf('.')+1)); }else Iif(i.substring(0,3)==="cid" && (i!=="cid")){ datauri.push("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" + divdata[i] + "/SDF?record_type=3d"); datatypes.push('sdf'); } } var options = {}; Iif(viewerdiv.data("options")) options = specStringToObject(viewerdiv.data("options")); //note that data tags must be lowercase var bgcolor = CC.color(viewerdiv.data("backgroundcolor")); var bgalpha = viewerdiv.data("backgroundalpha"); bgalpha = bgalpha == undefined ? 1.0 : parseFloat(bgalpha); var style = {line:{}}; Iif(viewerdiv.data("style")) style = specStringToObject(viewerdiv.data("style")); var select = {}; Iif(viewerdiv.data("select")) select = specStringToObject(viewerdiv.data("select")); var selectstylelist = []; var surfaces = []; var labels = []; var zoomto = {}; var spin = null; var d = viewerdiv.data(); //let users specify individual but matching select/style/surface tags, eg. //data-select1 data-style1 var stylere = /style(.+)/; var surfre = /surface(.*)/; var reslabre = /labelres(.*)/; var keys = []; for(dataname in d) { Iif(Object.prototype.hasOwnProperty.call(d,dataname)) { keys.push(dataname); } } keys.sort(); for(i = 0; i < keys.length; i++) { dataname = keys[i]; var m = stylere.exec(dataname); var selname, newsel, styleobj; Iif(m) { selname = "select"+m[1]; newsel = specStringToObject(d[selname]); styleobj = specStringToObject(d[dataname]); selectstylelist.push([newsel,styleobj]); } m = surfre.exec(dataname); Iif(m) { selname = "select"+m[1]; newsel = specStringToObject(d[selname]); styleobj = specStringToObject(d[dataname]); surfaces.push([newsel,styleobj]); } m = reslabre.exec(dataname); Iif(m) { selname = "select"+m[1]; newsel = specStringToObject(d[selname]); styleobj = specStringToObject(d[dataname]); labels.push([newsel,styleobj]); } Iif(dataname == "zoomto") { zoomto = specStringToObject(d[dataname]); } Iif(dataname == "spin") { spin = specStringToObject(d[dataname]); } } //apply all the selections/styles parsed out above to the passed viewer var applyStyles = function(glviewer) { glviewer.setStyle(select,style); Iif(showUI){ glviewer.ui.loadSelectionStyle(select, style); } for(i = 0; i < selectstylelist.length; i++) { let sel = selectstylelist[i][0] || {}; let sty = selectstylelist[i][1] || {"line":{}}; glviewer.setStyle(sel, sty); Iif(showUI){ glviewer.ui.loadSelectionStyle(sel, sty); } } for(i = 0; i < surfaces.length; i++) { let sel = surfaces[i][0] || {}; let sty = surfaces[i][1] || {}; let viewer = glviewer; if(showUI){ //seemingly unnecessary capturing of values due to jshint //not understanding let? let doload = function($3D, viewer, sel, sty) { viewer.addSurface($3D.SurfaceType.VDW, sty, sel, sel).then((surfid)=>{ viewer.ui.loadSurface("VDW", sel, sty, surfid); }); }; doload($3Dmol, viewer, sel, sty); } else { glviewer.addSurface(SurfaceType.VDW, sty, sel, sel); } } for(i = 0; i < labels.length; i++) { let sel = labels[i][0] || {}; let sty = labels[i][1] || {}; glviewer.addResLabels(sel, sty); } glviewer.render(); glviewer.zoomTo(zoomto); Iif(spin) { glviewer.spin(spin.axis,spin.speed); } }; var glviewer = viewer; try { var config = viewerdiv.data('config') || {}; Iif(config.backgroundColor === undefined) config.backgroundColor = bgcolor; Iif(config.backgroundAlpha === undefined) config.backgroundAlpha = bgalpha; config.ui = showUI; if(glviewer==null) { glviewer = viewers[this.id || nviewers++] = createViewer(viewerdiv, config); } else { glviewer.setBackgroundColor(bgcolor, bgalpha); glviewer.setConfig(config); Iif(showUI) glviewer.ui.initiateUI(); } } catch ( error ) { console.log(error); //for autoload, provide a useful error message viewerdiv.text("WebGL appears to be disabled."); } if (datauri.length!=0) { //load multiple data elements in serial i = 0; var process = function(moldata) { //add moldata to viewer and load next model uri = datauri[i]; //this is where the moldata came from var type = viewerdiv.data("type") || viewerdiv.data("datatype") || datatypes[i]; glviewer.addModel(moldata, type, options); Iif(showUI){ var modelName = viewerdiv.data(datatypes[i]); glviewer.ui.setModelTitle(modelName); } i += 1; if(i < datauri.length) { $.get(datauri[i], process, 'text'); } else { // or finalize if this is the last model applyStyles(glviewer); Iif(viewerdiv.data("callback")) { //evaluate javascript in the string, if it resolves to a function, //call it with the viewer /*jshint -W061 */ var runres = eval(viewerdiv.data("callback")); Iif(typeof(runres) == 'function') { runres(glviewer); } } processing_autoinit = false; Iif(callback) callback(glviewer); } }; $.get(datauri[0], process, 'text'); } else { Iif (viewerdiv.data("element")) { var moldata = $("#" + viewerdiv.data("element")).val() || ""; type = viewerdiv.data("type") || viewerdiv.data("datatype"); Iif (!type){ console.log("Warning: No type specified for embedded viewer with moldata from " + viewerdiv.data("element") + "\n assuming type 'pdb'"); type = 'pdb'; } glviewer.addModel(moldata, type, options); } applyStyles(glviewer); Iif(viewerdiv.data("callback")) { //evaluate javascript in the string, if it resolves to a function, //call it with the viewer /*jshint -W061 */ var runres = eval(viewerdiv.data("callback")); Iif(typeof(runres) == 'function') { runres(glviewer); } } processing_autoinit = false; Iif (callback) callback(glviewer); } }); }}; //if domcontent has already load Iif (document.readyState === "interactive") { $(document).ready(function() { autoload(); }); } else { document.addEventListener('DOMContentLoaded', function() { autoload(); }); } |