molstar
Version:
A comprehensive macromolecular library.
61 lines (60 loc) • 3.34 kB
JavaScript
;
/**
* Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.coordinatesFromNctraj = 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 coordinatesFromNctraj(file) {
var _this = this;
return mol_task_1.Task.create('Parse NCTRAJ', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
var deltaTime, offsetTime, frames, i, il, c, elementCount, x, y, z, j, jl, frame, lengths, x_1, y_1, z_1;
return 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.coordinates.length; i < il; ++i) {
c = file.coordinates[i];
elementCount = c.length / 3;
x = new Float32Array(elementCount);
y = new Float32Array(elementCount);
z = new Float32Array(elementCount);
for (j = 0, jl = c.length; j < jl; j += 3) {
x[j / 3] = c[j];
y[j / 3] = c[j + 1];
z[j / 3] = c[j + 2];
}
frame = {
elementCount: elementCount,
x: x,
y: y,
z: z,
xyzOrdering: { isIdentity: true },
time: (0, coordinates_1.Time)(offsetTime.value + deltaTime.value * i, deltaTime.unit)
};
// TODO: handle case where cell_lengths and cell_angles are set, i.e., angles not 90deg
if (file.cell_lengths) {
lengths = file.cell_lengths[i];
x_1 = linear_algebra_1.Vec3.scale((0, linear_algebra_1.Vec3)(), linear_algebra_1.Vec3.unitX, lengths[0]);
y_1 = linear_algebra_1.Vec3.scale((0, linear_algebra_1.Vec3)(), linear_algebra_1.Vec3.unitY, lengths[1]);
z_1 = linear_algebra_1.Vec3.scale((0, linear_algebra_1.Vec3)(), linear_algebra_1.Vec3.unitZ, lengths[2]);
frame.cell = cell_1.Cell.fromBasis(x_1, y_1, z_1);
}
frames.push(frame);
}
return [2 /*return*/, coordinates_1.Coordinates.create(frames, deltaTime, offsetTime)];
}
});
}); });
}
exports.coordinatesFromNctraj = coordinatesFromNctraj;