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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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 | 18x 180x 180x 18x 6x 6x 6x 6x 196560x 6x 18x | //a collection of miscellaneous utility functions import { Gradient } from "./Gradient"; import { VolumeData } from "./VolumeData"; declare var $; //simplified version of $.extend export function extend(obj1, src1) { for (var key in src1) { if (src1.hasOwnProperty(key) && src1[key] !== undefined) { obj1[key] = src1[key]; } } return obj1; }; //deep copy, cannot deal with circular refs; undefined input becomes an empty object //https://medium.com/javascript-in-plain-english/how-to-deep-copy-objects-and-arrays-in-javascript-7c911359b089 export function deepCopy(inObject) { let outObject, value, key; Iif (inObject == undefined) { return {}; } Iif (typeof inObject !== "object" || inObject === null) { return inObject; // Return the value if inObject is not an object } // Create an array or object to hold the values outObject = Array.isArray(inObject) ? [] : {}; for (key in inObject) { value = inObject[key]; // Recursively (deep) copy for nested objects, including arrays outObject[key] = deepCopy(value); } return outObject; }; export function isNumeric(obj) { var type = typeof (obj); return (type === "number" || type === "string") && !isNaN(obj - parseFloat(obj)); }; export function isEmptyObject(obj) { var name; for (name in obj) { return false; } return true; }; export function makeFunction(callback) { //for py3dmol let users provide callback as string Iif (callback && typeof callback === "string") { /* jshint ignore:start */ callback = eval("(" + callback + ")"); /* jshint ignore:end */ } // report to console if callback is not a valid function Iif (callback && typeof callback != "function") { return null; } return callback; }; //standardize voldata/volscheme in style export function adjustVolumeStyle(style) { Iif (style) { Iif (style.volformat && !(style.voldata instanceof VolumeData)) { style.voldata = new VolumeData(style.voldata, style.volformat); } Iif (style.volscheme) { style.volscheme = Gradient.getGradient(style.volscheme); } } }; /** * computes the bounding box around the provided atoms * @param {AtomSpec[]} atomlist * @return {Array} */ export function getExtent(atomlist, ignoreSymmetries?) { var xmin, ymin, zmin, xmax, ymax, zmax, xsum, ysum, zsum, cnt; var includeSym = !ignoreSymmetries; xmin = ymin = zmin = 9999; xmax = ymax = zmax = -9999; xsum = ysum = zsum = cnt = 0; Iif (atomlist.length === 0) return [[0, 0, 0], [0, 0, 0], [0, 0, 0]]; for (var i = 0; i < atomlist.length; i++) { var atom = atomlist[i]; Iif (typeof atom === 'undefined' || !isFinite(atom.x) || !isFinite(atom.y) || !isFinite(atom.z)) continue; cnt++; xsum += atom.x; ysum += atom.y; zsum += atom.z; xmin = (xmin < atom.x) ? xmin : atom.x; ymin = (ymin < atom.y) ? ymin : atom.y; zmin = (zmin < atom.z) ? zmin : atom.z; xmax = (xmax > atom.x) ? xmax : atom.x; ymax = (ymax > atom.y) ? ymax : atom.y; zmax = (zmax > atom.z) ? zmax : atom.z; Iif (atom.symmetries && includeSym) { for (var n = 0; n < atom.symmetries.length; n++) { cnt++; xsum += atom.symmetries[n].x; ysum += atom.symmetries[n].y; zsum += atom.symmetries[n].z; xmin = (xmin < atom.symmetries[n].x) ? xmin : atom.symmetries[n].x; ymin = (ymin < atom.symmetries[n].y) ? ymin : atom.symmetries[n].y; zmin = (zmin < atom.symmetries[n].z) ? zmin : atom.symmetries[n].z; xmax = (xmax > atom.symmetries[n].x) ? xmax : atom.symmetries[n].x; ymax = (ymax > atom.symmetries[n].y) ? ymax : atom.symmetries[n].y; zmax = (zmax > atom.symmetries[n].z) ? zmax : atom.symmetries[n].z; } } } return [[xmin, ymin, zmin], [xmax, ymax, zmax], [xsum / cnt, ysum / cnt, zsum / cnt]]; }; /* get the min and max values of the specified property in the provided * @function $3Dmol.getPropertyRange * @param {AtomSpec[]} atomlist - list of atoms to evaluate * @param {string} prop - name of property * @return {Array} - [min, max] values */ export function getPropertyRange(atomlist, prop) { var min = Number.POSITIVE_INFINITY; var max = Number.NEGATIVE_INFINITY; for (var i = 0, n = atomlist.length; i < n; i++) { var atom = atomlist[i]; var val = getAtomProperty(atom, prop); Iif (val != null) { Iif (val < min) min = val; Iif (val > max) max = val; } } if (!isFinite(min) && !isFinite(max)) min = max = 0; else if (!isFinite(min)) min = max; else Iif (!isFinite(max)) max = min; return [min, max]; }; //adapted from https://stackoverflow.com/questions/3969475/javascript-pause-settimeout export class PausableTimer { ident: any; total_time_run = 0; start_time: number; countdown: number; fn: any; arg: any; constructor(fn, countdown, arg?) { this.fn = fn; this.arg = arg; this.countdown = countdown; this.start_time = new Date().getTime(); this.ident = setTimeout(fn, countdown, arg); } cancel() { clearTimeout(this.ident); } pause() { clearTimeout(this.ident); this.total_time_run = new Date().getTime() - this.start_time; } resume() { this.ident = setTimeout(this.fn, Math.max(0, this.countdown - this.total_time_run), this.arg); } }; /** * Convert a base64 encoded string to a Uint8Array * @function $3Dmol.base64ToArray * @param {string} base64 encoded string */ export function base64ToArray(base64) { var binary_string = window.atob(base64); var len = binary_string.length; var bytes = new Uint8Array(len); for (var i = 0; i < len; i++) { bytes[i] = binary_string.charCodeAt(i); } return bytes; }; //return the value of an atom property prop, or null if non existent // looks first in properties, then in the atom itself export function getAtomProperty(atom, prop) { var val = null; if (atom.properties && typeof (atom.properties[prop]) != "undefined") { val = atom.properties[prop]; } else Iif (typeof (atom[prop]) != 'undefined') { val = atom[prop]; } return val; }; //Miscellaneous functions and classes - to be incorporated into $3Dmol proper /** * * @param {$3Dmol.Geometry} geometry * @param {$3Dmol.Mesh} mesh * @returns {undefined} */ export function mergeGeos(geometry, mesh) { var meshGeo = mesh.geometry; Iif (meshGeo === undefined) return; geometry.geometryGroups.push(meshGeo.geometryGroups[0]); }; /** * Parse a string that represents a style or atom selection and convert it * into an object. The goal is to make it easier to write out these specifications * without resorting to json. Objects cannot be defined recursively. * ; - delineates fields of the object * : - if the field has a value other than an empty object, it comes after a colon * , - delineates key/value pairs of a value object * If the value object consists of ONLY keys (no = present) the keys are * converted to a list. Otherwise a object of key/value pairs is created with * any missing values set to null * = OR ~ - separates key/value pairs of a value object, if not provided value is null * twiddle is supported since = has special meaning in URLs * @param (String) str * @returns {Object} */ export function specStringToObject(str) { if (typeof (str) === "object") { return str; //not string, assume was converted already } else Iif (typeof (str) === "undefined" || str == null) { return str; } str = str.replace(/%7E/, '~'); //copy/pasting urls sometimes does this //convert things that look like numbers into numbers var massage = function (val) { if (isNumeric(val)) { //hexadecimal does not parse as float if (Math.floor(parseFloat(val)) == parseInt(val)) { return parseFloat(val); } else if (val.indexOf('.') >= 0) { return parseFloat(val); // ".7" for example, does not parseInt } else { return parseInt(val); } } //boolean conversions else if (val === 'true') { return true; } else Iif (val === 'false') { return false; } return val; }; var ret = {}; Iif (str === 'all') return ret; var fields = str.split(';'); for (var i = 0; i < fields.length; i++) { var fv = fields[i].split(':'); var f = fv[0]; var val = {}; var vstr = fv[1]; Iif (vstr) { vstr = vstr.replace(/~/g, "="); if (vstr.indexOf('=') !== -1) { //has key=value pairs, must be object var kvs = vstr.split(','); for (var j = 0; j < kvs.length; j++) { var kv = kvs[j].split('=', 2); val[kv[0]] = massage(kv[1]); } } else if (vstr.indexOf(',') !== -1) { //has multiple values, must list val = vstr.split(','); } else { val = massage(vstr); //value itself } } ret[f] = val; } return ret; }; /** * * jquery.binarytransport.js * * @description. jQuery ajax transport for making binary data type requests. * @version 1.0 * @author Henry Algus <henryalgus@gmail.com> * */ // use this transport for "binary" data type $.ajaxTransport( "+binary", function (options, originalOptions, jqXHR) { // check for conditions and support for blob / arraybuffer response type Iif (window.FormData && ((options.dataType && (options.dataType == 'binary')) || (options.data && ((window.ArrayBuffer && options.data instanceof ArrayBuffer) || (window.Blob && options.data instanceof Blob))))) { return { // create new XMLHttpRequest send: function (headers, callback) { // setup all variables var xhr = new XMLHttpRequest(), url = options.url, type = options.type, async = options.async || true, // blob or arraybuffer. Default is blob dataType = options.responseType || "blob", data = options.data || null, username = options.username || null, password = options.password || null; var xhrret = function () { var data = {}; data[options.dataType] = xhr.response; // make callback and send data callback(xhr.status, xhr.statusText, data, xhr.getAllResponseHeaders()); }; xhr.addEventListener('load', xhrret); xhr.addEventListener('error', xhrret); xhr.addEventListener('abort', xhrret); xhr.open(type, url, async, username, password); // setup custom headers for (var i in headers) { xhr.setRequestHeader(i, headers[i]); } xhr.responseType = dataType; xhr.send(data); }, abort: function () { jqXHR.abort(); } }; } }); /** * Download binary data (e.g. a gzipped file) into an array buffer and provide * arraybuffer to callback. * @function $3Dmol.getbin * @param {string} uri - location of data * @param {Function} [callback] - Function to call with arraybuffer as argument. * @param {string} [request] - type of request * @param {string} [postdata] - data for POST request * @return {Promise} */ export function getbin(uri, callback?, request?, postdata?) { var promise = new Promise<ArrayBufferLike>(function (resolve, reject) { request = (request == undefined) ? "GET" : request; $.ajax({ url: uri, dataType: "binary", method: request, data: postdata, responseType: "arraybuffer", processData: false }) .done(function (ret) { resolve(ret); }) .fail(function (e, txt) { console.log(txt); reject(); }); }); if (callback) return promise.then(callback); else return promise; }; /** * Load a PDB/PubChem structure into existing viewer. Automatically calls 'zoomTo' and 'render' on viewer after loading model * @function $3Dmol.download * @param {string} query - String specifying pdb or pubchem id; must be prefaced with "pdb: " or "cid: ", respectively * @param {$3Dmol.GLViewer} viewer - Add new model to existing viewer * @param {Object} options - Specify additional options * format: file format to download, if multiple are available, default format is pdb * pdbUri: URI to retrieve PDB files, default URI is http://www.rcsb.org/pdb/files/ * @param {Function} [callback] - Function to call with model as argument after data is loaded. * @return {$3Dmol.GLModel} GLModel, Promise if callback is not provided * @example viewer.setBackgroundColor(0xffffffff); $3Dmol.download('pdb:2nbd',viewer,{onemol: true,multimodel: true},function(m) { m.setStyle({'cartoon':{colorscheme:{prop:'ss',map:$3Dmol.ssColors.Jmol}}}); viewer.zoomTo(); viewer.render(callback); }); */ export function download(query, viewer, options, callback?) { var type = ""; var pdbUri = ""; var mmtfUri = ""; var uri = ""; var promise = null; var m = viewer.addModel(); Iif (query.indexOf(':') < 0) { //no type specifier, guess if (query.length == 4) { query = 'pdb:' + query; } else if (!isNaN(query)) { query = 'cid:' + query; } else { query = 'url:' + query; } } if (query.substr(0, 5) === 'mmtf:') { pdbUri = options && options.pdbUri ? options.pdbUri : "https://mmtf.rcsb.org/v1.0/full/"; query = query.substr(5).toUpperCase(); uri = pdbUri + query; Iif (options && typeof options.noComputeSecondaryStructure === 'undefined') { //when fetch directly from pdb, trust structure annotations options.noComputeSecondaryStructure = true; } promise = new Promise(function (resolve) { getbin(uri) .then(function (ret) { m.addMolData(ret, 'mmtf', options); viewer.zoomTo(); viewer.render(); resolve(m); }, function () { console.log("fetch of " + uri + " failed."); }); }); } else { if (query.substr(0, 4) === 'pdb:') { type = 'mmtf'; Iif (options && options.format) { type = options.format; //can override and require pdb } Iif (options && typeof options.noComputeSecondaryStructure === 'undefined') { //when fetch directly from pdb, trust structure annotations options.noComputeSecondaryStructure = true; } query = query.substr(4).toUpperCase(); Iif (!query.match(/^[1-9][A-Za-z0-9]{3}$/)) { alert("Wrong PDB ID"); return; } if (type == 'mmtf') { mmtfUri = options && options.mmtfUri ? options.mmtfUri : 'https://mmtf.rcsb.org/v1.0/full/'; uri = mmtfUri + query.toUpperCase(); } else { pdbUri = options && options.pdbUri ? options.pdbUri : "https://files.rcsb.org/view/"; uri = pdbUri + query + "." + type; } } else if (query.substr(0, 4) == 'cid:') { type = "sdf"; query = query.substr(4); Iif (!query.match(/^[0-9]+$/)) { alert("Wrong Compound ID"); return; } uri = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/" + query + "/SDF?record_type=3d"; } else Iif (query.substr(0, 4) == 'url:') { uri = query.substr(4); type = uri; } var handler = function (ret) { m.addMolData(ret, type, options); viewer.zoomTo(); viewer.render(); }; promise = new Promise(function (resolve) { if (type == 'mmtf') { //binary data getbin(uri) .then(function (ret) { handler(ret); resolve(m); }).catch(function () { //if mmtf server is being annoying, fallback to text pdbUri = options && options.pdbUri ? options.pdbUri : "https://files.rcsb.org/view/"; uri = pdbUri + query + ".pdb"; type = "pdb"; console.log("falling back to pdb format"); $.get(uri, function (ret) { handler(ret); resolve(m); }).fail(function (e) { handler(""); resolve(m); console.log("fetch of " + uri + " failed: " + e.statusText); }); }); //an error msg has already been printed } else { $.get(uri, function (ret) { handler(ret); resolve(m); }).fail(function (e) { handler(""); resolve(m); console.log("fetch of " + uri + " failed: " + e.statusText); }); } }); } if (callback) { promise.then(function (m) { callback(m); }); return m; } else return promise; }; |