molstar
Version:
A comprehensive macromolecular library.
147 lines (146 loc) • 6.16 kB
JavaScript
;
/**
* Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Adapted from NGL.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.parseTrr = void 0;
var tslib_1 = require("tslib");
var mol_task_1 = require("../../../mol-task");
var result_1 = require("../result");
function parseInternal(data) {
return tslib_1.__awaiter(this, void 0, void 0, function () {
var dv, f, coordinates, boxes, times, offset, versionSize, boxSize, virSize, presSize, coordSize, velocitySize, forceSize, natoms, floatSize, natoms3, box, i, i, x, y, z, i, tmp, i, value, frameCoords, i;
return tslib_1.__generator(this, function (_a) {
dv = new DataView(data.buffer);
f = {
frames: [],
boxes: [],
times: [],
timeOffset: 0,
deltaTime: 0
};
coordinates = f.frames;
boxes = f.boxes;
times = f.times;
offset = 0;
while (true) {
// const magicnum = dv.getInt32(offset)
// const i1 = dv.getFloat32(offset + 4)
offset += 8;
versionSize = dv.getInt32(offset);
offset += 4;
offset += versionSize;
boxSize = dv.getInt32(offset + 8);
virSize = dv.getInt32(offset + 12);
presSize = dv.getInt32(offset + 16);
coordSize = dv.getInt32(offset + 28);
velocitySize = dv.getInt32(offset + 32);
forceSize = dv.getInt32(offset + 36);
natoms = dv.getInt32(offset + 40);
// const step = dv.getInt32(offset + 44)
// const nre = dv.getInt32(offset + 48)
offset += 52;
floatSize = boxSize / 9;
natoms3 = natoms * 3;
// let lambda
if (floatSize === 8) {
times.push(dv.getFloat64(offset));
// lambda = dv.getFloat64(offset + 8)
}
else {
times.push(dv.getFloat32(offset));
// lambda = dv.getFloat32(offset + 4)
}
offset += 2 * floatSize;
if (boxSize) {
box = new Float32Array(9);
if (floatSize === 8) {
for (i = 0; i < 9; ++i) {
box[i] = dv.getFloat64(offset) * 10;
offset += 8;
}
}
else {
for (i = 0; i < 9; ++i) {
box[i] = dv.getFloat32(offset) * 10;
offset += 4;
}
}
boxes.push(box);
}
// ignore, unused
offset += virSize;
// ignore, unused
offset += presSize;
if (coordSize) {
x = new Float32Array(natoms);
y = new Float32Array(natoms);
z = new Float32Array(natoms);
if (floatSize === 8) {
for (i = 0; i < natoms; ++i) {
x[i] = dv.getFloat64(offset) * 10;
y[i] = dv.getFloat64(offset + 8) * 10;
z[i] = dv.getFloat64(offset + 16) * 10;
offset += 24;
}
}
else {
tmp = new Uint32Array(data.buffer, offset, natoms3);
for (i = 0; i < natoms3; ++i) {
value = tmp[i];
tmp[i] = (((value & 0xFF) << 24) | ((value & 0xFF00) << 8) |
((value >> 8) & 0xFF00) | ((value >> 24) & 0xFF));
}
frameCoords = new Float32Array(data.buffer, offset, natoms3);
for (i = 0; i < natoms; ++i) {
x[i] = frameCoords[i * 3] * 10;
y[i] = frameCoords[i * 3 + 1] * 10;
z[i] = frameCoords[i * 3 + 2] * 10;
offset += 12;
}
}
coordinates.push({ count: natoms, x: x, y: y, z: z });
}
// ignore, unused
offset += velocitySize;
// ignore, unused
offset += forceSize;
if (offset >= data.byteLength)
break;
}
if (times.length >= 1) {
f.timeOffset = times[0];
}
if (times.length >= 2) {
f.deltaTime = times[1] - times[0];
}
return [2 /*return*/, f];
});
});
}
function parseTrr(data) {
var _this = this;
return mol_task_1.Task.create('Parse TRR', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var file, e_1;
return tslib_1.__generator(this, function (_a) {
switch (_a.label) {
case 0:
_a.trys.push([0, 2, , 3]);
ctx.update({ canAbort: true, message: 'Parsing trajectory...' });
return [4 /*yield*/, parseInternal(data)];
case 1:
file = _a.sent();
return [2 /*return*/, result_1.ReaderResult.success(file)];
case 2:
e_1 = _a.sent();
return [2 /*return*/, result_1.ReaderResult.error('' + e_1)];
case 3: return [2 /*return*/];
}
});
}); });
}
exports.parseTrr = parseTrr;