molstar
Version:
A comprehensive macromolecular library.
48 lines • 2.52 kB
JavaScript
;
/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.coordinatesFromXtc = void 0;
var tslib_1 = require("tslib");
var mol_task_1 = require("../../mol-task");
var coordinates_1 = require("../../mol-model/structure/coordinates");
var cell_1 = require("../../mol-math/geometry/spacegroup/cell");
var linear_algebra_1 = require("../../mol-math/linear-algebra");
function coordinatesFromXtc(file) {
var _this = this;
return mol_task_1.Task.create('Parse XTC', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
var deltaTime, offsetTime, frames, i, il, box, x, y, z;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0: return [4 /*yield*/, ctx.update('Converting to coordinates')];
case 1:
_a.sent();
deltaTime = (0, coordinates_1.Time)(file.deltaTime, 'step');
offsetTime = (0, coordinates_1.Time)(file.timeOffset, deltaTime.unit);
frames = [];
for (i = 0, il = file.frames.length; i < il; ++i) {
box = file.boxes[i];
x = linear_algebra_1.Vec3.fromArray((0, linear_algebra_1.Vec3)(), box, 0);
y = linear_algebra_1.Vec3.fromArray((0, linear_algebra_1.Vec3)(), box, 3);
z = linear_algebra_1.Vec3.fromArray((0, linear_algebra_1.Vec3)(), box, 6);
frames.push({
elementCount: file.frames[i].count,
cell: cell_1.Cell.fromBasis(x, y, z),
x: file.frames[i].x,
y: file.frames[i].y,
z: file.frames[i].z,
xyzOrdering: { isIdentity: true },
time: (0, coordinates_1.Time)(offsetTime.value + deltaTime.value * i, deltaTime.unit)
});
}
return [2 /*return*/, coordinates_1.Coordinates.create(frames, deltaTime, offsetTime)];
}
});
}); });
}
exports.coordinatesFromXtc = coordinatesFromXtc;
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