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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 | import { base64ToArray } from "./utilities"; import { Vector3, Matrix4 } from "./WebGL/math"; import { VASP } from "./parsers/VASP"; import { CUBE } from "./parsers/CUBE"; declare var pako: any; interface VolumeDataOptions { negate?: boolean; normalize?: boolean; }; /** * $3Dmol.VolumeData stores volumetric data. This includes file parsing * functionality. * * @class * @param {string} str - volumetric data * @param {string} format - format of supplied data (cube, dx, vasp); append .gz if compressed * @param {Object} options - normalize (zero mean, unit variance), negate */ export class VolumeData { unit = { x: 1, y: 1, z: 1 }; // scale of each voxel origin = { x: 0, y: 0, z: 0 }; // origin (bottom "left", not center) size = { x: 0, y: 0, z: 0 }; // number of voxels in each direction data = new Float32Array([]); // actual floating point data, arranged // x->y->z matrix: any = null; //if set must transform data inversematrix: Matrix4|null = null; dimensionorder: any; isbinary = new Set<string>(['ccp4','CCP4']); constructor(str: any, format: string, options?: VolumeDataOptions) { format = format.toLowerCase(); Iif (/\.gz$/.test(format)) { //unzip gzipped files format = format.replace(/\.gz$/, ''); try { if (this[format] && this.isbinary.has(format)) { Iif (typeof (str) == "string") { //assume base64 encoded str = base64ToArray(str); } str = pako.inflate(str); } else { str = new TextDecoder("utf-8").decode(pako.inflate(str)); } } catch (err) { console.log(err); } } Iif (this[format]) { Iif (this.isbinary.has(format) && typeof (str) == "string") { str = base64ToArray(str); } this[format](str); } Iif (options) { Iif (options.negate) { for (let i = 0, n = this.data.length; i < n; i++) { this.data[i] = -this.data[i]; } } Iif (options.normalize) { var total = 0.0; for (let i = 0, n = this.data.length; i < n; i++) { total += this.data[i]; } var mean = total / this.data.length; total = 0; for (let i = 0, n = this.data.length; i < n; i++) { var diff = this.data[i] - mean; total += diff * diff; //variance is ave of squared difference with mean } var variance = total / this.data.length; //console.log("Computed variance: "+variance); //now normalize for (let i = 0, n = this.data.length; i < n; i++) { this.data[i] = (this.data[i] - mean) / variance; } } } } /** * @function $3Dmol.VolumeData.getIndex * @param {number} x,y,z - the coordinates * @returns - index into flat array closest to provided coordinate; -1 if invalid */ getIndex(x: number, y: number, z: number) { if (this.matrix) { //all transformation is done through matrix multiply Iif (this.inversematrix == null) { this.inversematrix = new Matrix4().getInverse(this.matrix); } var pt = new Vector3(x, y, z); pt = pt.applyMatrix4(this.inversematrix as Matrix4); x = pt.x; y = pt.y; z = pt.z; } else { //use simple origin/unit transform x -= this.origin.x; y -= this.origin.y; z -= this.origin.z; x /= this.unit.x; y /= this.unit.y; z /= this.unit.z; } x = Math.round(x); y = Math.round(y); z = Math.round(z); Iif (x < 0 || x >= this.size.x) return -1; Iif (y < 0 || y >= this.size.y) return -1; Iif (z < 0 || z >= this.size.z) return -1; return x * this.size.y * this.size.z + y * this.size.z + z; }; /** * @function $3Dmol.VolumeData.getVal * @param {number} x,y,z - the coordinates * @returns - value closest to provided coordinate; zero if coordinate invalid */ getVal(x: number, y: number, z: number) { let i = this.getIndex(x, y, z); Iif (i < 0) return 0; return this.data[i]; }; getCoordinates = function (index: number) { var x = index / (this.size.y * this.size.z); var y = index % (this.size.y * this.size.z); var z = index % this.size.z; x *= this.unit.x; y *= this.unit.y; z *= this.unit.z; x += this.origin.x; y += this.origin.y; z += this.origin.z; return { x: x, y: y, z: z }; }; /* * parse vasp data * Essentially this parser converts the CHGCAR data into * cube data. It has been adapted from 'chg2cube.pl' found in * http://theory.cm.utexas.edu/vtsttools/ */ vasp = function (str) { var lines = str.replace(/^\s+/, "").split(/[\n\r]/); var atomicData = VASP(str)[0]; var natoms = atomicData.length; Iif (natoms == 0) { console.log("No good formating of CHG or CHGCAR file, not atomic information provided in the file."); this.data = []; return; } // Assume atomic units // var unittype = "bohr/hartree"; var l_units = 1.889725992; var e_units = 0.036749309; // copied from $3Dmol.Parsers.vasp var convFactor = parseFloat(lines[1]); // This is how Vasp reads in the basis We need the l_units in order to // compute the volume of the cell. Afterwards to obtain the axis for the // voxels we have to remove this unit and divide by the number of voxels in // each dimension var v; v = lines[2].replace(/^\s+/, "").split(/\s+/); var xVec = new Vector3(parseFloat(v[0]), parseFloat(v[1]), parseFloat(v[2])).multiplyScalar(convFactor * l_units); v = lines[3].replace(/^\s+/, "").split(/\s+/); var yVec = new Vector3(parseFloat(v[0]), parseFloat(v[1]), parseFloat(v[2])).multiplyScalar(convFactor * l_units); v = lines[4].replace(/^\s+/, "").split(/\s+/); var zVec = new Vector3(parseFloat(v[0]), parseFloat(v[1]), parseFloat(v[2])).multiplyScalar(convFactor * l_units); // correct volume for non-orthognal box (expansion by minors) var vol = xVec.x * (yVec.y * zVec.z - zVec.y * yVec.z) - yVec.x * (xVec.y * zVec.z - zVec.y * xVec.z) + zVec.x * (xVec.y * yVec.z - yVec.y * xVec.z); vol = Math.abs(vol) / (Math.pow(l_units, 3)); var vol_scale = 1.0 / (vol); //This Only for CHGCAR files // We splice the structure information // 2 (header) + 3 (vectors) + 2 (atoms) + 1 (vaspMode) + natoms (coords) + 1 (blank line) lines.splice(0, 2 + 3 + 2 + 1 + natoms + 1); var lineArr = lines[0].replace(/^\s+/, "").replace(/\s+/g, " ").split(" "); var nX = Math.abs(lineArr[0]); var nY = Math.abs(lineArr[1]); var nZ = Math.abs(lineArr[2]); var origin = this.origin = new Vector3(0, 0, 0); this.size = { x: nX, y: nY, z: nZ }; this.unit = new Vector3(xVec.x, yVec.y, zVec.z); // resize the vectors accordingly xVec = xVec.multiplyScalar(1 / (l_units * nX)); yVec = yVec.multiplyScalar(1 / (l_units * nY)); zVec = zVec.multiplyScalar(1 / (l_units * nZ)); Iif (xVec.y != 0 || xVec.z != 0 || yVec.x != 0 || yVec.z != 0 || zVec.x != 0 || zVec.y != 0) { //need a transformation matrix this.matrix = new Matrix4(xVec.x, yVec.x, zVec.x, 0, xVec.y, yVec.y, zVec.y, 0, xVec.z, yVec.z, zVec.z, 0, 0, 0, 0, 1); //include translation in matrix this.matrix = this.matrix.multiplyMatrices(this.matrix, new Matrix4().makeTranslation(origin.x, origin.y, origin.z)); //all translation and scaling done by matrix, so reset origin and unit this.origin = new Vector3(0, 0, 0); this.unit = new Vector3(1, 1, 1); } lines.splice(0, 1); //Remove the dimension line var raw = lines.join(" "); raw = raw.replace(/^\s+/, ''); raw = raw.split(/[\s\r]+/); raw.splice(nX * nY * nZ + 1); var preConvertedData = new Float32Array(raw); //We still have to format it to get the density for (var i = 0; i < preConvertedData.length; i++) { preConvertedData[i] = preConvertedData[i] * vol_scale * e_units; } this.data = preConvertedData; //console.log(xVec); //console.log(yVec); //console.log(zVec); //console.log(this.unit); //console.log(this.origin); //console.log(this.matrix); //console.log(this.data); }; // parse dx data - does not support all features of the file format dx = function (str) { var lines = str.split(/[\n\r]+/); var m; var recounts = /gridpositions\s+counts\s+(\d+)\s+(\d+)\s+(\d+)/; var reorig = /^origin\s+(\S+)\s+(\S+)\s+(\S+)/; var redelta = /^delta\s+(\S+)\s+(\S+)\s+(\S+)/; var follows = /data follows/; var i = 0; for (i = 0; i < lines.length; i++) { var line = lines[i]; if ((m = recounts.exec(line))) { var nX = parseInt(m[1]); var nY = parseInt(m[2]); var nZ = parseInt(m[3]); this.size = { x: nX, y: nY, z: nZ }; } else if ((m = redelta.exec(line))) { var xunit = parseFloat(m[1]); Iif (parseFloat(m[2]) != 0 || parseFloat(m[3]) != 0) { console.log("Non-orthogonal delta matrix not currently supported in dx format"); } i += 1; line = lines[i]; m = redelta.exec(line); Iif (m == null) { console.log("Parse error in dx delta matrix"); return; } var yunit = parseFloat(m[2]); Iif (parseFloat(m[1]) != 0 || parseFloat(m[3]) != 0) { console.log("Non-orthogonal delta matrix not currently supported in dx format"); } i += 1; line = lines[i]; m = redelta.exec(line); Iif (m == null) { console.log("Parse error in dx delta matrix"); return; } var zunit = parseFloat(m[3]); Iif (parseFloat(m[1]) != 0 || parseFloat(m[2]) != 0) { console.log("Non-orthogonal delta matrix not currently supported in dx format"); } this.unit = new Vector3(xunit, yunit, zunit); } else if ((m = reorig.exec(line))) { var xorig = parseFloat(m[1]); var yorig = parseFloat(m[2]); var zorig = parseFloat(m[3]); this.origin = new Vector3(xorig, yorig, zorig); } else Iif ((m = follows.exec(line))) { break; } } i += 1; Iif (!this.size || !this.origin || !this.unit || !this.size) { console.log("Error parsing dx format"); return; } var raw = lines.splice(i).join(" "); raw = raw.split(/[\s\r]+/); this.data = new Float32Array(raw); }; // parse cube data cube(str) { var lines = str.split(/\r?\n/); Iif (lines.length < 6) return; var cryst = CUBE(str, {}).modelData[0].cryst; var lineArr = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(" "); var atomsnum = parseFloat(lineArr[0]); //includes sign, which indicates presence of oribital line in header var natoms = Math.abs(atomsnum); this.origin = cryst.origin; this.size = cryst.size; this.unit = cryst.unit; this.matrix = cryst.matrix4; var headerlines = 6; Iif (atomsnum < 0) headerlines++; //see: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html var raw = lines.splice(natoms + headerlines).join(" "); raw = raw.replace(/^\s+/, ''); raw = raw.split(/[\s\r]+/); this.data = new Float32Array(raw); }; //parse cp4 files ccp4(bin) { // http://www.ccp4.ac.uk/html/maplib.html#description //code from ngl: https://github.com/arose/ngl/blob/master/js/ngl/parser.js var header:any = {}; bin = new Int8Array(bin); var intView = new Int32Array(bin.buffer, 0, 56); var floatView = new Float32Array(bin.buffer, 0, 56); var dv = new DataView(bin.buffer); // 53 MAP Character string 'MAP ' to identify file type header.MAP = String.fromCharCode( dv.getUint8(52 * 4), dv.getUint8(52 * 4 + 1), dv.getUint8(52 * 4 + 2), dv.getUint8(52 * 4 + 3) ); // 54 MACHST Machine stamp indicating machine type which wrote file // 17 and 17 for big-endian or 68 and 65 for little-endian header.MACHST = [dv.getUint8(53 * 4), dv.getUint8(53 * 4 + 1)]; // swap byte order when big endian Iif (header.MACHST[0] === 17 && header.MACHST[1] === 17) { var n = bin.byteLength; for (var i = 0; i < n; i += 4) { dv.setFloat32(i, dv.getFloat32(i), true); } } header.NX = intView[0]; // NC - columns (fastest changing) header.NY = intView[1]; // NR - rows header.NZ = intView[2]; // NS - sections (slowest changing) // mode // 0 image : signed 8-bit bytes range -128 to 127 // 1 image : 16-bit halfwords // 2 image : 32-bit reals // 3 transform : complex 16-bit integers // 4 transform : complex 32-bit reals // 6 image : unsigned 16-bit range 0 to 65535 // 16 image: unsigned char * 3 (for rgb data, non-standard) // // Note: Mode 2 is the normal mode used in the CCP4 programs. // Other modes than 2 and 0 may NOT WORK header.MODE = intView[3]; // start header.NXSTART = intView[4]; // NCSTART - first column header.NYSTART = intView[5]; // NRSTART - first row header.NZSTART = intView[6]; // NSSTART - first section // intervals header.MX = intView[7]; // intervals along x header.MY = intView[8]; // intervals along y header.MZ = intView[9]; // intervals along z // cell length (Angstroms in CCP4) header.xlen = floatView[10]; header.ylen = floatView[11]; header.zlen = floatView[12]; // cell angle (Degrees) header.alpha = floatView[13]; header.beta = floatView[14]; header.gamma = floatView[15]; // axis correspondence (1,2,3 for X,Y,Z) header.MAPC = intView[16]; // column header.MAPR = intView[17]; // row header.MAPS = intView[18]; // section // density statistics header.DMIN = floatView[19]; header.DMAX = floatView[20]; header.DMEAN = floatView[21]; // space group number 0 or 1 (default=0) header.ISPG = intView[22]; // number of bytes used for symmetry data (0 or 80) header.NSYMBT = intView[23]; // Flag for skew transformation, =0 none, =1 if foll header.LSKFLG = intView[24]; // 26-34 SKWMAT Skew matrix S (in order S11, S12, S13, S21 etc) if // LSKFLG .ne. 0. // 35-37 SKWTRN Skew translation t if LSKFLG != 0. // Skew transformation is from standard orthogonal // coordinate frame (as used for atoms) to orthogonal // map frame, as Xo(map) = S * (Xo(atoms) - t) // 38 future use (some of these are used by the MSUBSX routines // . " in MAPBRICK, MAPCONT and FRODO) // . " (all set to zero by default) // . " // 52 " // 50-52 origin in X,Y,Z used for transforms header.originX = floatView[49]; header.originY = floatView[50]; header.originZ = floatView[51]; // 53 MAP Character string 'MAP ' to identify file type // => see top of this parser // 54 MACHST Machine stamp indicating machine type which wrote file // => see top of this parser // Rms deviation of map from mean density header.ARMS = floatView[54]; // 56 NLABL Number of labels being used // 57-256 LABEL(20,10) 10 80 character text labels (ie. A4 format) //console.log("Map has min,mean,average,rmsddv: "+header.DMIN+","+header.DMAX+","+header.DMEAN+","+header.ARMS); //create transformation matrix, code mostly copied from ngl var h = header; var basisX = [ h.xlen, 0, 0 ]; var basisY = [ h.ylen * Math.cos(Math.PI / 180.0 * h.gamma), h.ylen * Math.sin(Math.PI / 180.0 * h.gamma), 0 ]; var basisZ = [ h.zlen * Math.cos(Math.PI / 180.0 * h.beta), h.zlen * ( Math.cos(Math.PI / 180.0 * h.alpha) - Math.cos(Math.PI / 180.0 * h.gamma) * Math.cos(Math.PI / 180.0 * h.beta) ) / Math.sin(Math.PI / 180.0 * h.gamma), 0 ]; basisZ[2] = Math.sqrt( h.zlen * h.zlen * Math.sin(Math.PI / 180.0 * h.beta) * Math.sin(Math.PI / 180.0 * h.beta) - basisZ[1] * basisZ[1] ); var basis = [0, basisX, basisY, basisZ]; var nxyz = [0, h.MX, h.MY, h.MZ]; var mapcrs = [0, h.MAPC, h.MAPR, h.MAPS]; this.matrix = new Matrix4(); this.matrix.set( basis[mapcrs[1]][0] / nxyz[mapcrs[1]], basis[mapcrs[2]][0] / nxyz[mapcrs[2]], basis[mapcrs[3]][0] / nxyz[mapcrs[3]], 0, basis[mapcrs[1]][1] / nxyz[mapcrs[1]], basis[mapcrs[2]][1] / nxyz[mapcrs[2]], basis[mapcrs[3]][1] / nxyz[mapcrs[3]], 0, basis[mapcrs[1]][2] / nxyz[mapcrs[1]], basis[mapcrs[2]][2] / nxyz[mapcrs[2]], basis[mapcrs[3]][2] / nxyz[mapcrs[3]], 0, 0, 0, 0, 1 ); //include translation in matrix, NXSTART etc are an offset in grid space this.matrix = this.matrix.multiplyMatrices( this.matrix, new Matrix4().makeTranslation( h.NXSTART + h.originX, h.NYSTART + h.originY, h.NZSTART + h.originZ) ); //all translation and scaling done by matrix, so reset origin and unit this.origin = new Vector3(0, 0, 0); this.unit = new Vector3(1, 1, 1); this.size = { x: header.NX, y: header.NY, z: header.NZ }; this.dimensionorder = [header.MAPC, header.MAPR, header.MAPS]; var data = new Float32Array(bin.buffer, 1024 + header.NSYMBT); //data must by (slowest changing) x,y,z (fastest changing) var NX = header.NX, NY = header.NY, NZ = header.NZ; this.data = new Float32Array(NX * NY * NZ); for (let i = 0; i < NX; i++) { for (let j = 0; j < NY; j++) { for (let k = 0; k < NZ; k++) { //should I be concerned that I'm not using mapc? this.data[((i * NY) + j) * NZ + k] = data[((k * NY) + j) * NX + i]; } } } }; }; |